this document is classified in confidence and not for

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1 SITREP 039 Coronavirus disease 2019 (COVID-19) Issued: 1030 hours 1 September 2020 Information current at: 1000 hours This report provides a daily update on the COVID-19 health system response. New information is denoted by red text. Please use the single point of contact email [email protected] for help/support. Your email will be logged and promptly passed to the appropriate team. This document is classified IN CONFIDENCE and not for further distribution. Need to know COMMUNITY CASES NEW LAST 24 hrs 5 MIQ CASES NEW LAST 24 hrs 9 COMMUNITY CASES TOTAL RECOVERED 49 97 COMMUNITY CASES ACTIVE 99 TOTAL CASES SINCE 11 AUG 148 33 TOTAL CASES SINCE 9 JUN 130 TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 132 MIQ CASES TOTAL RECOVERED MIQ CASES ACTIVE LABORATORY TESTS 31 August 8599 LABORATORY TESTS 25 to 31 August 65,122 LABORATORY TESTS TOTAL 766,626

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1

SITREP 039

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 1 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

5

MIQ CASES

NEW LAST 24 hrs

9

COMMUNITY CASES

TOTAL RECOVERED

49

97

COMMUNITY CASES

ACTIVE

99 TOTAL CASES SINCE 11 AUG

148

33

TOTAL CASES SINCE 9 JUN

130

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 132

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

31 August

8599

LABORATORY TESTS

25 to 31 August

65,122

LABORATORY TESTS

TOTAL

766,626

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 01 September 2020

Case Status Active Recovered Deceased Total

Confirmed 132 (+2) 1252 (+12) 17 1401 (+14)

Probable 0 (-1) 346 (+1) 5 351

Total 132 (+1) 1598 (+13) 22 1752 (+14)*

*Net increase of 14 cases with 13 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 01 September 2020

New community cases since 0900 31 August 2020

1. Five new confirmed community cases have been reported. Of these all five have

epidemiological links, summarised as follows:

o One case is a household contact of the Botany case (reported on 28 August with no

epidemiological link to the cluster, genomically linked on 31 August).

o Three cases are in the second household linked to the Botany case.

o One case is a household contact of a known confirmed case linked to the public

exposure event.

Community cases linked to the Auckland Community Cluster August 2020

2. 146 of the 148 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 1 September. Of the two cases not linked to the cluster one

case, the Rydges employee, has been closed and an epidemiological and genomic link

to the community cluster is still under investigation for one case.

Community cases under investigation to determine a link to the community cluster

3. Case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. A partial

genome has been obtained from sequencing and this case has been provisionally

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 67 (+5) 35 (+1) 41 (+3) 4 147 (+5)

Probable 0 (-1) 0 0 0 0 (-1)

Total 67 (+4) 35 (+1) 41 (+3) 4 147 (+4)

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.

genomically linked to the community cluster. Further whole genome sequencing is in

progress.1

Community cases and household contacts at Jet Park

4. As at 0800 1 September there are 123 people isolating in Jet Park from the community.

79 are confirmed cases, the remaining 44 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.

MIQ cases

5. As at 0900 1 September there have been nine new cases detected at the border since

0900 31 August. In total there are 130 cases that have been detected at the border

since the establishment of MIFs/MIQs.

o Five cases are in Canterbury: all arrived from Delhi, India on 27 August (Flight

number: NZ1301), via Fiji (Flight number: GA7280).

o Three cases are in Auckland: two arrived from Delhi, India on 23 August (Flight

number: AI1320). One arrived on 26 August from Doha, Qatar and tested positive on

routine day 3 testing (Flight number: QR453).

o One case is in Wellington: arrived from Los Angeles, USA on 18 August (Flight

number: NZ1), tested positive on routine day 12 testing.

Cases in hospital

6. 10 cases are in hospital with COVID-19.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 1 September 2020

*Note: One case was discharged to Jet Park yesterday and a separate case was admitted yesterday. The total number of

patients is unchanged at three.

1 ARPHS Strategic Report 28 August 2020

DHB Hospital Number in a general

ward Number in ICU/HDU

Auckland Auckland City 2 0

Counties Manukau Middlemore 2 1

Waitematā North Shore 3* 0

Waikato Waikato 1 1

Total - 8 2

IN CONFIDENCE – NOT FOR DISTRIBUTION

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Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview

The cluster is currently continuing to grow within the parameters of the DHB’s modelling. The

impact of intensive case follow-up appears to be working. However, there are two cases with no

apparent links to the cluster, that raises the possibility of undetected further clusters that is a

priority for the investigation. There is one ‘mini-cluster’ related to Mt Roskill Evangelical Church and

it is likely that we will see more cases arise in this cluster.

Current outbreak investigation priorities2

o Contact tracing and containment around church sub cluster

o Seek to identify an epidemiological link for the case to the main cluster

o Clarify whether the case that is a returnee from June is a new infection, and clarify strain

o Contact trace and isolate close contacts exposed on Auckland bus journeys

o Seek to identify epidemiological link to the cluster for cases that have been genomically

linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS. This is due to ongoing

transmission occurring and concerns that not all contacts have been identified. Several

events are being scoped. The DHB is working closely with Church leaders to:

o Maintain relationships with and support for Church leaders.

o Understand the total number of people that need to be tested.

o Push testing coverage.

o Develop welfare support arrangements for those requiring quarantine.

9. There is a sports club associated with the Mt Roskill Evangelical Church.

The sports club has been

closed for the past two weeks, therefore none of the club members are being

considered close contacts. ARPHS sent comms to members regarding testing and to

date no positive cases have been reported.3

2 ARPHS Strategic Report 1 September 2020

3 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

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10. Four cases that have been genomically linked to the cluster are still being investigated

by ARPHS to identify their epidemiological link.

o source of infection is still under investigation. is no

longer being considered as the possible source because analysis of the test result

shows had a recent more infection. have

tested negative.4

o GP.

o The second Mount Albert Grammar student.

o Botany case: and lives in a household with

close links to a second household. Members of the second household are testing

positive.

4 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

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Waikato Investigation Updates

11. Waikato DHB is leading the contact tracing for the church services and event

associated with the Mount Roskill Evangelical Church sub-cluster.

12. A new case was reported in Tokoroa on the evening of 29 August5. The case is a contact

of an existing case from Tokoroa who is currently in hospital and associated with the

Auckland cluster. The new case works at a medical centre in Tokoroa and it is believed

they had contact with the existing case . The centre is

undergoing a terminal clean and has been closed pending completion of contact

tracing. Contact tracing is underway to contact all staff and patients of the medical

centre.

. Two testing sites were stood up yesterday for testing

staff and patients, these will be available for the rest of the week.

ESR and wider testing7 13. A further 23 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (3 cases), Church 2 (4 cases),

Finance Now (2 case), Finance Now HH (2 cases), Americold (1 case), Americold HH (4

cases), Household 1 (5 cases), Household 2 (1 case), NZ Courier post (1 case). These

cases are also epidemiologically linked to the cluster.

14.

5 Waikato PHU, email and phone conversation 29-30 August 2020

6 Deputy Director Public Health Email 0913 31 August 2020

7 ESR Update email, 0902 01 September 2020

Table 5: Waikato contact tracing and initial/day 12 testing by site as at 0700 01 September 20206

*These numbers will likely change throughout the day as the investigation continues.

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15. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

16. No direct links have been found between the community outbreak genome

sequencing, with the 35 full and 13 partial (checked for the community mutation, and

confirmed not to show it) genomes currently available from cases in managed isolation

facilities (MIFs).

17.

Contact tracing 18. Between 23 and 29 August 85% (455 of 534)8 of close contacts have been contacted

within 48 hours of being determined to be a contact. KPI for this metric is 80% of close

contacts within 48 hours.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 01 September 2020

29/08/2020 30/08/2020 31/08/2020 01/09/2020

Number of close contacts

identified1 2489 2587 2621 2743

Number of close contacts

successfully contacted (and are

self-isolating)

2425 2475 2505 2676

Number of close contacts

referred to "finding services"2 12 6 7 5

Number of close contacts

awaiting contact 52 106 109 62

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

8 Contact Tracing Data, COVID-19 NCCS Analytics and Reporting received 0906 01 September 2020

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IN CONFIDENCE – NOT FOR DISTRIBUTION

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COVID-19 Tracer App usage Figure 1: COVID-19 Tracer App9 cumulative registered users and daily scans/manual entries as at 1615

31 August 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

Testing

Swabs collected10 Table 7: Number of swabs collected nationally by stream as at 1800 31 August 2020

1. This data will change over time due to variation in the way DHBs report swab numbers (i.e. at different stages in the

testing process).

9 Response Analyst – Digital Channels, 1621 31 August 2020

10 Senior Advisor – COVID-19 Health Systems Response, 1803 31 August 2020

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COVID Tracer App usage Cumulative App registrations

Scans and manual entries

Swab Stream 31 August 25–31 August

Community 4560 67,110

MIF Staff 169 1666

MIF Guests 440 4181

Airport Staff 201 1444

Maritime Staff 120 420

Total 5490 74,821

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Laboratory testing numbers Table 8: Number of laboratory tests processed nationally as at 0900 31 August11 2020

Testing supply update12

19. There are approximately 270,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

Testing activity by region

Focus areas

20. There are 39 designated community testing centres in the wider Auckland region. Of

these, 20 testing sites are in Auckland city and 19 are community centres outside of the

Auckland city.

Healthline updates13 21. On 31 August there were 3,679 contacts in Healthline. Of those calls, 1,768 were to the

COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 715 contacts (22% higher than forecast).

22. The introduction of self-service text and digital channels on their IVR systems saw 89

people self-serve on 30 August. Healthline have put a live revised testing referral

process to support the testing strategy and will continue to quality assure this over the

weekend.

23. The main themes yesterday/today:

o Compared to other level changes there is quite a bit of mis-understanding by the

public (Alert Level 2, 2.5 vs 3), anti-South / West Auckland sentiment and towards

Aucklanders in general – examples from yesterday:

▪ Examples of people “reporting” west and south Aucklanders not staying at

Alert Level 3 and going into other parts of Auckland.

11 Daily Lab Report, 0936 01 September 2020

12 Health Supply Chain email, 0907 30 August 2020

13 National Telehealth Service Coronavirus Update, 0935 01 September 2020

Time period Number of laboratory tests

31 August 8599

Last 7 days (25 to 31 August) 65,122

Total 766,626

IN CONFIDENCE – NOT FOR DISTRIBUTION

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▪ Employers calling to see if they can hold meeting in their workplaces for more

than 10 people.

▪ People down country reporting Aucklander’s visiting them and attending

groups of more than 10.

▪ Schools and businesses calling to clarify the rules around the Alert Levels.

▪ Facemask requirements.

o Significant numbers of calls relating to communications around South and West

Aucklander’s needing to get tested. Healthline continued to advise service users with

the Healthline agreed interpretation of the testing strategy.

o Continued delay in access to care with our referral rates to Ambulance/ED/urgent

care, this needs reinforcing in communications.

o Symptomatic and asymptomatic Service User’s wanting to be tested.

o Questions relating to the new levels and what they mean.

o People having welfare needs associated with the lock down.

Logistics

Health Workforce14

24. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

25. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

26. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

14 Health Workforce Directorate, 0832 01 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

13

Hospital capacity15 Table 9: Number and occupancy of hospital beds by type as at 0800 01 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 353 240 (68.0%)

Ventilators 306 54 (17.6%)

Ward beds 7339 5882 (80.1%)

15 COVID-19 Hospital Summary, 0912 01 September 2020

14

Appendix 1: Case summary Table 10: All community cases reported between 0900 31 August and 0900 01 September

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Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification Indicator (as

per Table 9832) Refined Indicator description Target 24 August 25 August** 26 August 27 August 28 August** 29 August** 30 August**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 43% - 18% 50% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 27% - 11% 83% - - -

3 – (S003) Time from test sample taken to

close contact isolation / quarantine

80% within 72 hours 81% - 63% 100% 94% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours

0% *

(0/5) 0% *

(0/2) 0% *

(0/8) 40% 71% 50% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 100% 100% 30% 100% 56% 50% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 83% - 63% 100% 94% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated /

quarantined 80% within 24 hours 78% - 92% 100% 95% 100% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 83% - 63% 100% 95% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected

COVID-19 at the time of tracing <20% 0% - 8%

17% *

(1/6) 0% 0% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a

number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October

2020.

17

APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 31 August 2020

Table 1. Metro Auckland Summary Total of Testing for 31 August 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 2690 152 418 199 99 3558

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

Ethnicity Last 24 Hours %

Total since

12/8* %

Asian 861 18.8% 25482 16.9%

Maori 604 13.2% 22908 15.2%

Other 2033 44.5% 63163 42.0%

Pacific 916 20.0% 36178 24.1%

Unknown 157 3.4% 2659 1.8%

Total 4571 150390

Tests Last 24-hours

Ethnicity CTC Non-CTC Total %

Asian 748 113 861 18.8%

Maori 528 76 604 13.2%

Other 1702 331 2033 44.5%

Pacific 832 84 916 20.0%

Unknown 121 36 157 3.4%

Total 3931 640 4571

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

IN CONFIDENCE – NOT FOR DISTRIBUTION

18

Table 4. Estimated tests taken 12-31 August 2020, based on manual site reports at 5pm

Site 12/08-16/08 17/08-23/08 24/08 – 30/08 31/08*

MIQ Staff 2132 659 1488 152

Guests 2972 3767 3600 418

Border Airport 2129 933 1349 199

Port 1588 678 161 99

* 31/8 day still in progress

Table 5: Estimated tests taken at Metro Auckland CTCs, 12-31 August 2020, based on manual

site reports at 4pm

Site 12/08-16/08 (days

open)

17/08-23/08 (days

open)

24/08 – 30/08

(days open)

31/08*

Airport Oaks 1148 (4) 515 (7) 366 (7) 61

Auckland Netball

Centre

192 (1) 1065 (7) 884 (7) 148

Botany CTC 1151 (5) 948 (7) 905 (7) 174

Coast to Coast

Warkworth

334 (5) 109 (7) 70 (7) 12

Coast to Coast

Wellsford

203 (5) 114 (7) 116 (7) 23

Eventfinda Stadium 1800 (5) 527 (7) 517 (7) N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 159

Henderson 940 (4) 645 (7) 634 (7) 94

Mangere Town Centre 1748 (3) 1684 (7) 1599 (7) 76

Manurewa Marae N/A 124 (4) 268 (6) 70

Northcare A&M 253 (2) 463 (7) 527 (7) 187

Otara CTC 3221 (5) 1712 (7) 1429 (7) 223

Pukekohe CTC N/A 131 (4) 226 (6) 78

St Lukes 1368 (5) 1045 (7) 1414 (7) 178

Takanini Urgent Care 1886 (5) 1216 (7) 1153 (7) 204

Waiheke Medical

Centre

312 (5) 145 (7) 220 (7) 24

Whanau House 2502 (5) 1371 (7) 1442 (7) 232

Whanau Ora - Central 1957 (5) 964 (7) 1583 (7) 187

IN CONFIDENCE – NOT FOR DISTRIBUTION

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Whanau Ora - North 1442 (5) 669 (7) 637 (7) 190

Whanau Ora - South 2945 (5) 1250 (7) 718 (7) 175

Point England Pop Up N/A N/A 88 (3) N/A

Randwick Park Pop Up N/A N/A 303 (5) N/A

Ranui Pop Up N/A N/A 409 (5) N/A

Mt Smart Stadium Pop

Up

N/A N/A 219 (3) N/A

Massey Pop Up N/A N/A 787 (5) N/A

South Kaipara Pop Up N/A N/A 170 (4) N/A

Clendon Pop Up N/A N/A 368 (3) N/A

Mangere Pop Up N/A N/A 472 (2) N/A

Mangere East Pop Up N/A N/A 82 (2) N/A

Otara Pop Up N/A N/A 59 (2) N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A

Mt Roskill Pop Up (330

start)

N/A N/A 217 (2) 108

Sandringham Pop Up N/A N/A N/A 72

Ranui League Club Pop

Up

N/A N/A N/A No data

Waipuna Targeted Site 143 (2) 549 (7) 376 (7) 16

Blockhouse Bay

Targeted Site

N/A 277 (7) 921 (7) 71

Total 26,148 16,781 21,133 2,680 * 29/8 day still in progress N/A = not open as a CTC

IN CONFIDENCE – NOT FOR DISTRIBUTION

20

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 11: Number of people tested for COVID-19 from 12 August to 01 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 2784 5852 7715 16014 354 32719

Bay of Plenty 2360 288 468 5726 76 8918

Canterbury 1344 528 1369 11266 209 14716

Capital and Coast 1149 879 1022 7075 194 10319

Counties Manukau 5918 16629 7387 10216 436 40586

Hawkes Bay 1164 233 175 2978 56 4606

Hutt Valley 613 311 414 2330 41 3709

Lakes 1979 277 448 2572 101 5377

MidCentral 776 206 288 3044 64 4378

Nelson Marlborough 493 133 187 3561 63 4437

Northland 2570 186 209 3349 46 6360

South Canterbury 113 27 67 1211 24 1442

Southern 841 263 510 7188 95 8897

Tairāwhiti 729 49 43 656 20 1497

Taranaki 548 52 138 2072 41 2851

Waikato 3510 828 1102 7875 211 13526

Wairarapa 159 27 29 724 7 946

Waitematā 3604 3698 5750 19361 306 32719

West Coast 45 7 10 269 4 335

Whanganui 526 59 49 1155 20 1809

Unknown 1286 645 586 3467 1628 7612

Total 32511 31177 27966 112110 3996 207760

21

Table 12: Rate per 1000 people tested for COVID-19 from 12 August to 01 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 64 104.4 41.2 61.26 59.7

Bay of Plenty 39.5 64.8 23.9 36.39 37

Canterbury 25.6 37.2 22.5 25.25 25.7

Capital and Coast 31.5 39.6 20.4 33.25 32.1

Counties Manukau 66.5 138.5 48.9 48.82 71.3

Hawkes Bay 26.9 36.3 19.1 27.56 27.6

Hutt Valley 23.5 26.6 22.1 24.72 24.6

Lakes 51.4 108.4 46.1 42.88 48.6

MidCentral 21.3 37.1 18.6 24.6 24.2

Nelson Marlborough 30.7 53.8 25.2 28.3 29.2

Northland 42.2 49.5 25.3 30.72 35

South Canterbury 21.3 55.3 28.3 23.44 24.1

Southern 25.1 38.2 19.8 26.87 26.7

Tairāwhiti 29.4 43.8 36.8 29.67 30.4

Taranaki 23.5 37.3 22.2 23.05 23.6

Waikato 36.4 62.1 25 29.26 32

Wairarapa 19.9 32.5 23.3 20.29 20.7

Waitematā 57.6 82.9 40 50.63 51.7

West Coast 11.6 27.7 10.8 9.97 10.5

Whanganui 30.3 38.8 16.7 26.84 27.9

Total 41.8 97.5 36.5 36.2 41.9

1

SITREP 040

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 02 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

3

MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

57

97

COMMUNITY CASES

ACTIVE

94 TOTAL CASES SINCE 11 AUG

151

35

TOTAL CASES SINCE 9 JUN

132

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 129

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

01 September

10,934

LABORATORY TESTS

26 Aug to 01 Sep

67,497

LABORATORY TESTS

TOTAL

777,560

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 02 September 2020

Case Status Active Recovered Deceased Total

Confirmed 129 (-3) 1260 (+8) 17 1406 (+5)

Probable 0 346 5 351

Total 129 (-3) 1606 (+8) 22 1757 (+5)*

*Net increase of 5 cases with 8 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 02 September 2020

New community cases since 0900 1 September 2020

1. Three new confirmed community cases have been reported. Of these all three have

epidemiological links to the Mt Roskill Evangelical Church sub-cluster.

Community cases linked to the Auckland Community Cluster August 2020

2. 149 of the 151 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 02 September. One of the unlinked cases is the Rydges

employee (this investigation has been closed) and the other unlinked case is still under

investigation for an epidemiological and genomic link to the community cluster (see 3).

Community cases under investigation to determine a link to the community cluster

3. Case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. A partial

genome has been obtained from sequencing and this case has been provisionally

genomically linked to the community cluster. Further whole genome sequencing is in

progress.1

1 ARPHS Strategic Report 28 August 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 68 36 (+1) 43 (+2) 4 151 (+3)

Probable 0 0 0 0 0

Total 68 36 (+1) 43 (+2) 4 151 (+3)

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.

Community cases and household contacts at Jet Park

4. As at 0800 2 September there are 104 people isolating in Jet Park from the community.

75 are confirmed cases, the remaining 29 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.

MIQ cases

5. As at 0900 2 September there have been two new cases detected at the border since

0900 1 September. In total there are 132 cases that have been detected at the border

since the establishment of MIFs/MIQs.

o The two cases were detected in Rotorua via day 3 testing: one arrived from Dubai,

United Arab Emirates on 28 August (Flight number: EK448). The other one arrived

from Tashkent, Uzbekistan (via Dubai, UAE) on 28 August (Flight number: EK448).

Both cases have been transferred to Jet Park in Auckland for quarantine.

Cases in hospital

6. Seven cases are in hospital with COVID-19.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 2 September 2020

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

DHB Hospital Number in a general

ward Number in ICU/HDU

Auckland Auckland City 1 0

Counties Manukau Middlemore 1 1

Waitematā North Shore 2 0

Waikato Waikato 1 1

Total - 5 2

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4

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities2

o Contact tracing and containment around Mt Roskill church sub-cluster

o Seek to identify an epidemiological link for the case to the main cluster

o Clarify whether the case that is a returnee from June is a new infection, and clarify strain

o Contact trace and isolate close contacts exposed on Auckland bus journeys

o Seek to identify epidemiological link to the cluster for cases that have been genomically

linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS. This is due to ongoing

transmission occurring and concerns that not all contacts have been identified. Several

events are being scoped. The DHB is working closely with Church leaders to:

o Maintain relationships with and support for Church leaders.

o Understand the total number of people that need to be tested.

o Push testing coverage.

o Develop welfare support arrangements for those requiring quarantine.

9. The two family members were isolating at home from 22 August after the

case moved to hospital on 21 August. These family members moved to Jet Park

on 28 August. Contact tracing has not identified any further cases. Investigation to

identify the epidemiological link to the cluster is ongoing.

10. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 1 September). More information to come

when available.

11. There is a sports club associated with the Mt Roskill Evangelical Church. It is being

investigated as both an exposure event and a possible source of the Mt Roskill

Evangelical Church sub-cluster3.

The sports club has been closed for the past two weeks,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.4

12. There are new settings of interest being investigated for the Botany sub-cluster,

including casual work places. More information to come when available.

13. Possible Americold links to a previously reported event are being investigated.

More information to come when available.

2 ARPHS Strategic Report 31 August 2020

3 NRHCC Morning Report 2 September 2020

4 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

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14. Four cases that have been genomically linked to the cluster are still being investigated

by ARPHS to identify their epidemiological link.

o The source of infection is still under investigation. is no

longer being considered as the possible source because analysis of the test result

shows had a more recent infection. have

tested negative.5

o GP.

o The second Mount Albert Grammar student.

o Botany case: and lives in a household with

close links to a second household. Members of the second household are testing

positive.

5 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

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Waikato Investigation Updates

15. Waikato DHB is leading the contact tracing for the church services and event

associated with the Mount Roskill Evangelical Church sub-cluster.

16. A new case was reported in Tokoroa on the evening of 29 August6. The case is a contact

of an existing case from Tokoroa who is currently in hospital and associated with the

Auckland cluster. The new case works at a medical centre in Tokoroa and it is believed

they had contact with the existing case . The centre is

undergoing a terminal clean and has been closed pending completion of contact

tracing. Contact tracing was originally focused on contacting all staff and patients of

the medical centre back to 25 August, following standard procedures. Contact tracing is

now being extended prior to 25 August. This is a precautionary approach that is being

taken due to the case’s long incubation period and while the onset of symptoms was

27 August, the radiological findings suggest more advanced disease.

Two testing sites were stood up yesterday for testing staff and patients,

these will be available for the rest of the week.

ESR and wider testing8 17. A further 23 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (3 cases), Church 2 (4 cases),

Finance Now (2 case), Finance Now HH (2 cases), Americold (1 case), Americold HH (4

cases), Household 1 (5 cases), Household 2 (1 case), NZ Courier post (1 case). These

cases are also epidemiologically linked to the cluster.

18.

6 Waikato PHU, email and phone conversation 29-30 August 2020

7 Waikato DHB SITREP 0945 02 September 2020

8 ESR Update email, 0902 01 September 2020

Table 5: Waikato contact tracing and initial/day 12 testing by site as at 0700 02 September 20207

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9

19. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

20. No direct links have been found between the community outbreak genome

sequencing, with the 35 full and 13 partial (checked for the community mutation, and

confirmed not to show it) genomes currently available from cases in managed isolation

facilities (MIFs).

21.

Contact tracing 22. Between 24 August and 30 August 64% (637 of 993)9 of close contacts have been

contacted within 48 hours of being determined to be a contact. KPI for this metric is

80% of close contacts within 48 hours.

o Note: This is low mainly due to an exposure event and resulting sub-cluster during this period. Around 400 people were identified as close contacts through exposure to a case that was identified via a source attribution investigation. In this instance, the Case was not identified until more than 14 days after the exposure event. After 14 days from an exposure, the need to isolate close contacts has passed as this is the full incubation period, therefore close contacts were not isolated. Despite impacting metrics this delayed case identification and subsequent delayed close contact communication demonstrates that an effective trace back process occurred, leading to successful source identification.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 02 September 2020

30/08/2020 31/08/2020 01/09/2020 02/09/2020

Number of close contacts

identified1 2587 2621 2743 3192

Number of close contacts

successfully contacted (and are

self-isolating)

2475 2505 2676 2992

Number of close contacts

referred to "finding services"2 6 7 5 4

Number of close contacts

awaiting contact 106 109 62 196

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

9 Contact Tracing Data, COVID-19 NCCS Analytics and Reporting received 0937 02 September 2020

s 9(2)(g)(i)

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2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage Figure 1: COVID-19 Tracer App10 cumulative registered users and daily scans/manual entries as at

1615 01 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

23. Key Numbers:

o 2,022,800 - Total registered users

o 2,077,426 - QR code scans between 1200 31 August and 1200 01 September

10 Response Analyst – Digital Channels, 1621 01 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

/20

20

23

/05

/20

20

26

/05

/20

20

29

/05

/20

20

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6/2

02

04

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/20

20

7/0

6/2

02

01

0/0

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02

01

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02

01

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02

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02

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01

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02

07

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20

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20

13

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20

16

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20

19

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20

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20

25

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20

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20

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02

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20

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COVID Tracer App usage Cumulative App registrations

Scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Testing Table 8: Testing by functional groups, as at 0900 02 September 202011

Laboratory testing numbers Table 9: Number of laboratory tests processed nationally as at 0900 01 September12 2020

11 ÉCLAIR/MoH Public Health Intelligence, 1000 02 September 2020

12 Daily Lab Report, 0921 02 September 2020

Reason for test 01 September 26 August – 01 September

GPs and other primary health 3852 28,531

CBACs and pop-ups 2972 34,015

Border workers - air crew 19 214

Border workers - airport staff 107 1372

Border workers - maritime crew 2 44

Border workers - port staff 8 98

Border workers - MIF 71 903

Border workers - MIQ 60 164

Travellers - Staying at MIF 199 2102

Travellers - Staying at MIQ 0 165

Total 7290 67,608

Time period Number of laboratory tests

31 August 10,934

Last 7 days (26 Aug to 01

Sep)

67,497

Total 777,560

IN CONFIDENCE – NOT FOR DISTRIBUTION

12

Testing supply update13

24. There are approximately 270,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

Testing activity by region

Focus areas

25. There are 39 designated community testing centres in the wider Auckland region. Of

these, 20 testing sites are in Auckland city and 19 are community centres outside of the

Auckland city.

Healthline updates14 26. There are incorrect media reports by Radio New Zealand that Healthline had issued

instructions to its staff telling them to instruct South and West Aucklander’s to get

tested. There is no email as reported, nor were our staff or scripts ever changed to

reflect this. Our clinical advice to staff was inline with the Ministry’s intent and agreed

with the Ministry late last week. Once media started reporting the incorrect information,

we advised our staff that this information was not correct and adherence to our scripts

was paramount as always. Our comms team is working with MOH comms to have this

potentially retracted.

27. On 01 September there were 3,334 contacts in Healthline. Of those calls, 1,618 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 648 contacts (in line with forecast).

28. The introduction of self-service text and digital channels on their IVR systems saw 89

people self-serve on 30 August. Healthline have put a live revised testing referral

process to support the testing strategy and will continue to quality assure this over the

weekend.

29. The main themes yesterday/today:

o On 01 September Healthline continued to have people call regarding confusion on

South and West Aucklander’s needing to get tested. Healthline continued to advise

callers inline with the Healthline agreed interpretation of the testing strategy and

how they support this.

o Healthline reported that certain communities are feeling particularly vulnerable with

the most recent change in Alert Levels. Their concern is particularly around returning

to work. The pressure they are feeling is regarding two areas:

13 Health Supply Chain email, 0907 30 August 2020

14 National Telehealth Service Coronavirus Update, 0932 02 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

13

▪ Unlike previously, communications have not singled out certain communities

and how their risk is different/increased.

▪ Due to the duration of COVID, the heightened pressure from employers to

have them back in the workplace regardless of the risk posed to their

community (COVID-19)

o Symptomatic and asymptomatic Service User’s wanting to be tested.

o People having welfare needs associated with the lock down.

Logistics

Health Workforce15

30. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

31. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

32. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

Hospital capacity16 Table 10: Number and occupancy of hospital beds by type as at 0800 02 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 342 230 (67.3%)

Ventilators 305 57 (18.7%)

Ward beds 7328 5928 (80.9%)

15 Health Workforce Directorate, 0832 01 September 2020

16 COVID-19 Hospital Summary, 0913 02 September 2020

14

Appendix 1: Case summary Table 11: All community cases reported between 0900 01 September and 0900 02 September

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Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification Indicator (as

per Table 9832) Refined Indicator description Target 25 August** 26 August*** 27 August 28 August 29 August** 30 August** 31 August**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - 5% 50% 76% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - 3% 83% 67% - - -

3 – (S003) Time from test sample taken to

close contact isolation / quarantine

80% within 72 hours - 44% 100% 95% 86% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours

0% *

(0/2) 0% *

(0/8) 40% 71% 33% 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 100% 30% 100% 56% 50% 100% 36%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 44% 100% 94% 86% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated /

quarantined 80% within 24 hours - 55% 100% 95% 100% 100% 81%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 63% 100% 95% 86% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected

COVID-19 at the time of tracing <20% - 4% 17% 0% 0% 0% 2%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• *** The metrics for Indicators S001, S002, S003, P002 on the 25 August are low mainly due to an exposure event and resulting sub-cluster during this period. Around 400 people were identified as close contacts through exposure to a case that was identified via a

source attribution investigation. In this instance, the Case was not identified until more than 14 days after the exposure event. After 14 days from an exposure, the need to isolate close contacts has passed as this is the full incubation period, therefore close contacts

were not isolated. Despite impacting metrics this delayed case identification and subsequent delayed close contact communication demonstrates that an effective trace back process occurred, leading to successful source identification.

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 01 September 2020

Table 1. Metro Auckland Summary Total of Testing for 01 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 2202 10 399 205 18 2834

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 4. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-16/08 17/08-23/08 24/08 – 30/08 31/08* 01/09*

MIQ Staff 2132 659 1488 152 10

Guests 2972 3767 3600 418 399

Border Airport 2129 933 1349 199 205

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 529 342 871 16.0% 26447 16.9%

Maori 546 306 852 15.7% 23756 15.2%

Other 1239 960 2199 40.4% 65473 42.0%

Pacific 914 468 1382 25.4% 37626 24.1%

Unknown 38 97 135 2.5% 2735 1.8%

Total 3266 2173 5439 156037

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Port 1588 678 161 99 18

(started

at 1pm)

* 01/09 day still in progress

Table 5: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08

(days

open)

17/08-23/08

(days open)

24/08 – 30/08

(days open)

31/08 01/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 61 39

Auckland Netball Centre 192 (1) 1065 (7) 884 (7) 148 107

Botany CTC 1151 (5) 948 (7) 905 (7) 180 120

Coast to Coast Warkworth 334 (5) 109 (7) 70 (7) 12 9

Coast to Coast Wellsford 203 (5) 114 (7) 116 (7) 23 16

Eventfinda Stadium 1800 (5) 527 (7) 517 (7) N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 159 145

Henderson 940 (4) 645 (7) 634 (7) 94 80

Mangere Town Centre 1748 (3) 1684 (7) 1599 (7) 76 190

Manurewa Marae N/A 124 (4) 268 (6) 70 40

Northcare A&M 253 (2) 463 (7) 527 (7) 63 240

Otara CTC 3221 (5) 1712 (7) 1429 (7) 249 170

Pukekohe CTC N/A 131 (4) 226 (6) 78 65

St Lukes 1368 (5) 1045 (7) 1414 (7) 178 131

Takanini Urgent Care 1886 (5) 1216 (7) 1153 (7) 204 124

Waiheke Medical Centre 312 (5) 145 (7) 220 (7) 24 23

Whanau House 2502 (5) 1371 (7) 1442 (7) 232 172

Whanau Ora - Central 1957 (5) 964 (7) 1583 (7) 187 137

Whanau Ora - North 1442 (5) 669 (7) 637 (7) 207 212

Whanau Ora - South 2945 (5) 1250 (7) 718 (7) 175 91

Point England Pop Up N/A N/A 88 (3) N/A

Randwick Park Pop Up N/A N/A 303 (5) N/A

Ranui Pop Up N/A N/A 409 (5) N/A

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Mt Smart Stadium Pop Up N/A N/A 219 (3) N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A

South Kaipara Pop Up N/A N/A 170 (4) N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A

Mangere East Pop Up N/A N/A 109 (2) N/A No data

Otara Pop Up N/A N/A 59 (2) N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A

Mt Roskill Pop Up (330 start) N/A N/A 217 (2) 108 N/A

Sandringham Pop Up N/A N/A N/A 72 69

Ranui League Club Pop Up N/A N/A N/A 34 No data

Glen Eden Pop Up N/A N/A N/A N/A No data

Southmall Pop Up N/A N/A N/A N/A No data

Waipuna Targeted Site 143 (2) 549 (7) 376 (7) 16 22

Blockhouse Bay Targeted Site N/A 277 (7) 921 (7) 71 No data

Total 26,148 16,781 21,215 2,722 2,202 * 01/09 day still in progress N/A = not open as a CTC

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20

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 12: Number of people tested for COVID-19 from 12 August to 02 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 2818 5914 7801 16199 356 33088

Bay of Plenty 2392 292 476 5835 76 9071

Canterbury 1364 533 1384 11470 212 14963

Capital and Coast 1182 907 1052 7288 202 10631

Counties Manukau 5968 16733 7432 10305 436 40874

Hawkes Bay 1189 243 177 3024 57 4690

Hutt Valley 629 328 428 2401 41 3827

Lakes 2046 281 467 2703 101 5598

MidCentral 781 207 290 3050 64 4392

Nelson Marlborough 497 133 188 3616 63 4497

Northland 2603 189 211 3406 46 6455

South Canterbury 119 27 67 1289 24 1526

Southern 859 266 528 7387 97 9137

Tairāwhiti 730 49 43 658 20 1500

Taranaki 563 54 140 2116 41 2914

Waikato 3596 849 1120 8095 215 13875

Wairarapa 160 27 29 728 7 951

Waitematā 3653 3746 5827 19509 307 33042

West Coast 45 7 12 269 4 337

Whanganui 526 59 50 1155 20 1810

Unknown 1301 661 608 3547 1669 7786

Total 33021 31505 28330 114051 4058 210965

21

Table 12: Rate per 1000 people tested for COVID-19 from 12 August to 02 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 64.8 105.5 41.7 61.97 60.4

Bay of Plenty 40 65.7 24.3 37.09 37.6

Canterbury 26 37.6 22.8 25.71 26.1

Capital and Coast 32.4 40.9 21 34.25 33.1

Counties Manukau 67 139.3 49.2 49.25 71.8

Hawkes Bay 27.5 37.9 19.3 27.99 28.1

Hutt Valley 24.1 28.1 22.8 25.47 25.4

Lakes 53.2 110 48 45.07 50.6

MidCentral 21.5 37.3 18.7 24.64 24.2

Nelson Marlborough 31 53.8 25.3 28.73 29.6

Northland 42.8 50.3 25.5 31.25 35.5

South Canterbury 22.4 55.3 28.3 24.95 25.5

Southern 25.6 38.6 20.5 27.61 27.4

Tairāwhiti 29.5 43.8 36.8 29.76 30.5

Taranaki 24.1 38.8 22.5 23.54 24.1

Waikato 37.3 63.7 25.4 30.07 32.8

Wairarapa 20.1 32.5 23.3 20.41 20.8

Waitematā 58.4 84 40.5 51.02 52.2

West Coast 11.6 27.7 13 9.97 10.5

Whanganui 30.3 38.8 17.1 26.84 27.9

Total 42.5 98.5 37 36.8 42.5

1

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SITREP 041

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 03 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

1

MIQ CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

73

97

COMMUNITY CASES

ACTIVE

79 TOTAL CASES SINCE 11 AUG

152

36

TOTAL CASES SINCE 9 JUN

133

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 115

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

02 September

10,521

LABORATORY TESTS

27 Aug to 02 Sep

68,761

LABORATORY TESTS

TOTAL

788,081

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 03 September 2020

Case Status Active Recovered Deceased Total

Confirmed 115 (-14) 1276 (+16) 17 1408 (+2)

Probable 0 346 5 351

Total 115 (-14) 1622(+16) 22 1759 (+2)*

*Net increase of 2 cases with 16 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 03 September 20201

*Please note a decrease in two cases at Waikato DHB due to previous movement of two cases already reported from Waikato

DHB to Counties Manukau DHB. The totals in the table only reflect the one new case being reported today due to these changes

occurring previously.

New community cases since 0900 02 September 2020

1. One new confirmed community case has been reported. The case has an

epidemiological link with cases associated with the Americold household sub-cluster.

Community cases linked to the Auckland Community Cluster August 2020

2. 150 of the 152 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 03 September. One of the unlinked cases is the Rydges

employee (this investigation has been closed) and the other unlinked case is still under

investigation for an epidemiological and genomic link to the community cluster (see 3).

Community cases under investigation to determine a link to the community cluster

3. Case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. A partial

1 EpiSurv

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 71 (+1) 36 43 2 152 (+1)

Probable 0 0 0 0 0

Total 71 (+1) 36 43 2* 152 (+1)

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3

.

genome has been obtained from sequencing and this case has been provisionally

genomically linked to the community cluster. Further whole genome sequencing is in

progress.2

Community cases and household contacts at Jet Park

4. As at 0800 3 September there are 92 people isolating in Jet Park from the community.

67 are confirmed cases, the remaining 25 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases

5. As at 0900 3 September there has been one new case detected at the border since

0900 2 September. In total there are 133 cases that have been detected at the border

since the establishment of MIFs/MIQs.

o The case was detected in Christchurch via day 3 testing. They arrived in New Zealand

on 29 August from Philippines via Hong Kong and have been in managed isolation at

upon arrival.4

Cases in hospital

6. As at 0800 3 September there are seven cases in hospital with COVID-19.5

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 3 September 2020

*Please note within the last 24 hours a patient from Waitematā, North Shorth Hospital was discharged to Jet Park and one new

patient was admitted.

2 ARPHS Strategic Report 28 August 2020

3 NRHCC Morning Report 3 September 2020

4 EpiSurv

5 NRHCC Morning Report 3 September 2020 and Waikato DHB Morning Report 3 September 2020

DHB Hospital Number in a general

ward Number in ICU/HDU

Auckland Auckland City 1 0

Counties Manukau Middlemore 1 1

Waitematā North Shore 2* 0

Waikato Waikato 1 1

Total - 5 2

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Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities7

o Contact tracing and containment around Mt Roskill church sub-cluster

o Seek to identify an epidemiological link for the case to the main cluster

o Clarify whether the case that is a returnee from June is a new infection, and clarify strain

o Contact trace and isolate close contacts exposed on Auckland bus journeys

o Seek to identify epidemiological link to the cluster for cases that have been genomically

linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS due to ongoing transmission

occurring and concerns that not all contacts have been identified. Several events

including church services and a wedding are being scoped. This is a joint effort with

ARPHS completing contact tracing for the events and Waikato focusing on source

attribution.8 The DHBs are working closely with Church leaders to:

o Maintain relationships with and support for Church leaders.

o Understand the total number of people that need to be tested.

o Push testing coverage.

o Develop welfare support arrangements for those requiring quarantine.

Sub-clusters and settings of interest

9. The two family members of the were isolating at home from 22 August after the

case moved to hospital on 21 August. These family members moved to Jet Park

6 ARPHS Strategic Report 31 August 2020

7 ARPHS Strategic Report 31 August 2020

8 ARPHS, Waikato DHB and MoH teleconference 3pm 3 September 2020

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on 28 August. Contact tracing has not identified any further cases. Investigation to

identify the epidemiological link to the cluster is ongoing.

10. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 1 September). More information to come

when available.

11. There are new settings of interest being investigated for the Botany sub-cluster,

including casual work places. More information to come when available.

12. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.9 It is being investigated as both a

possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster10.

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.11 Surveillance testing is underway.12

13. Further investigation of the event mentioned in the 2 September SitRep as a

setting of interest has been explored. Possible links between the event and

Americold associated cases were explored as a possible source of transmission of the

cases infection. The investigation found the onset date and infectious period

dates of the cases do not align. As a result, APRHS have has ruled out this possibility of

transmission source and link of the case to the Americold associated cases.

Further investigation for an epidemiological link for the case is underway.

Case investigation

14. Four cases that have been genomically linked to the cluster are still being investigated

by ARPHS to identify their epidemiological link.

o The source of infection is still under investigation. is no

longer being considered as the possible source because analysis of the test result

shows had a more recent infection. have

tested negative.13

o GP.

o The second Mount Albert Grammar student.

o Botany case: and lives in a household with

close links to a second household. Members of the second household are testing

positive.

9 NRHCC Morning Report 3 September 2020

10 NRHCC Morning Report 2 September 2020

11 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

12 NRHCC Morning Report 3 September 2020

13 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

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15. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

staff. The centre is completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe that is being taken due

to the case’s long incubation period radiological findings suggest more advanced

disease despite 27 August symptom onset date.

. No contacts

have been identified at the . Two testing sites were stood up 30 August for

testing staff and patients, these will be available for the rest of the week.

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IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing14 16. A total of 104 cases (69%) from the main cluster have been sequenced, 93 (62% of total

confirmed cases) yielded a high-quality genome sequence. Three cases yielded partial

genomes but had sufficient data to indicate that these cases are part of the outbreak

cluster. The remaining eight cases did not have sufficient genetic material to be

sequenced.

17.

18. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

19. No direct links have been found between the community outbreak genome

sequencing, with the 49 full genomes currently available from cases in managed

isolation facilities (MIFs).

20.

Contact tracing 21. Between 25 August and 31 August 70% (722 of 1029)15 of close contacts have been

contacted within 48 hours of being determined to be a contact. KPI for this metric is

80% of close contacts within 48 hours.

o Note: This is low mainly due to an exposure event and resulting sub-cluster during this period. Around 400 people were identified as close contacts through exposure to a case that was identified via a source attribution investigation. In this instance, the Case was not identified until more than 14 days after the exposure event. After 14 days from an exposure, the need to isolate close contacts has passed as this is the full incubation period, therefore close contacts were not isolated. Despite impacting metrics this delayed case identification and subsequent delayed close contact communication demonstrates that an effective trace back process occurred, leading to successful source identification.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

14 ESR Whole Genome Sequencing Report 02 September 2020

15 Contact Tracing Data, COVID-19 NCCS Analytics and Reporting received 0929 03 September 2020

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Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 03 September 2020

31/08/2020 01/09/2020 02/09/2020 03/09/2020

Number of close contacts

identified1 2621 2743 3192 3162

Number of close contacts

successfully contacted (and are

self-isolating)

2505 2676 2992 2984

Number of close contacts

referred to "finding services"2 7 5 4 4

Number of close contacts

awaiting contact 109 62 196 174

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage Figure 1: COVID-19 Tracer App16 cumulative registered users and daily scans/manual entries as at

1615 02 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

16 Response Analyst – Digital Channels, 1625 02 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

/20

20

23

/05

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20

26

/05

/20

20

29

/05

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20

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04

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01

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02

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02

01

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02

07

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20

10

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13

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20

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20

19

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20

22

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25

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31

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aily

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and

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pp

reg

istr

atio

ns

COVID Tracer App usage Cumulative App registrations

Scans and manual entries

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11

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

22. Key Numbers:

o 2,050,200 - Total registered users

o 2,123,391 - QR code scans between 1200 01 and 1200 02 September

Testing Table 8: Testing by functional groups, as at 0900 03 September 202017

Laboratory testing numbers Table 9: Number of laboratory tests processed nationally as at 0900 02 September18 2020

17 ÉCLAIR/MoH Public Health Intelligence, 1000 03 September 2020

18 Daily Lab Report, 0928 03 September 2020

Reason for test 02 September 27 August – 02 September

GPs and other primary health 5683 29715

CBACs and pop-ups 3624 33742

Border workers - air crew 40 225

Border workers - airport staff 271 1590

Border workers - maritime crew 2 47

Border workers - port staff 194 285

Border workers - MIF 212 927

Border workers - MIQ 31 186

Travellers - Staying at MIF 392 2152

Travellers - Staying at MIQ 72 155

Total 10521 69024

Time period Number of laboratory tests

02 September 10,521

Last 7 days (27 Aug to 02

Sep)

68,761

Total 788,081

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12

Testing supply update19

23. There are approximately 270,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

Testing activity by region

Focus areas

24. There are 39 designated community testing centres in the wider Auckland region. Of

these, 20 testing sites are in Auckland city and 19 are community centres outside of the

Auckland city.

Healthline updates20 25. After following up with Radio New Zealand, the online items are being updated to

clarify the situation relating to Healthline’s position on instructing South and West

Aucklander’s to get tested. Work is underway to implement the equity improvements

for Pacific peoples that have been identified in the last week.

26. On 02 September there were 2,864 contacts in Healthline. Of those calls, 1,292 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 624 contacts (in line with forecast).

27. The main themes yesterday/today:

o On 02 September Healthline reported that certain communities are feeling

particularly vulnerable with the most recent change in Alert Levels. Their concern is

particularly around returning to work. The pressure they are feeling is regarding two

areas:

▪ Unlike previously, communications have not singled out certain communities

and how their risk is different/increased.

▪ Due to the duration of COVID, the heightened pressure from employers to

have them back in the workplace regardless of the risk posed to their

community (COVID-19).

o Symptomatic and asymptomatic Service User’s wanting to be tested.

o People having welfare needs associated with the lock down.

19 Health Supply Chain email, 0907 30 August 2020

20 National Telehealth Service Coronavirus Update, 0938 03 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

13

Logistics

Health Workforce21

28. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

29. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

30. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

Hospital capacity22 Table 10: Number and occupancy of hospital beds by type as at 0800 03 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 342 220 (64.3%)

Ventilators 305 52 (17.0%)

Ward beds 7271 5841 (80.3%)

21 Health Workforce Directorate, 0832 01 September 2020

22 COVID-19 Hospital Summary, 0918 03 September 2020

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Appendix 1: Case summary Table 11: All community cases reported between 0900 02 September and 0900 03 September

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15

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Appendix 2: International case

investigations

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Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification Indicator (as

per Table 9832) Refined Indicator description Target 26 August*** 27 August 28 August 29 August 30 August** 31 August** 01

September**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 5% 50% 76% 51% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 3% 83% 67% 79% - - -

3 – (S003) Time from test sample taken to

close contact isolation / quarantine

80% within 72 hours 53% 100% 95% 84% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours

0%*

(0/8) 40% 71% 33% 100% 67% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 30% 100% 56% 50% 100% 36% 80%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 53% 100% 94% 84% 100% 93% -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% 100% 86%

8 – (P003) Time from close contact identification to isolated /

quarantined 80% within 24 hours 64% 100% 95% 100% 100% 93% 70%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 63% 100% 95% 84% 100% 93% -

C – (S005) Proportion of close contacts with confirmed or suspected

COVID-19 at the time of tracing <20% 4% 17% 0% 0% 0% 5% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• *** The metrics for Indicators S001, S002, S003, P002 on the 26 August are low mainly due to an exposure event and resulting sub-cluster during this period. Around 400 people were identified as close contacts through exposure to a case that was identified via a source attribution investigation. In this instance, the

Case was not identified until more than 14 days after the exposure event. After 14 days from an exposure, the need to isolate close contacts has passed as this is the full incubation period, therefore close contacts were not isolated. Despite impacting metrics this delayed case identification and subsequent delayed

close contact communication demonstrates that an effective trace back process occurred, leading to successful source identification.

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 02 September 2020

Table 1. Metro Auckland Summary Total of Testing for 01 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1733 163 468 252 52 2668

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-16/08 17/08-23/08 24/08 – 30/08 31/08 01/09 02/09*

MIQ Staff 2132 659 1488 152 100 163

Guests 2972 3767 3600 418 399 468

Border Airport 2129 933 1349 199 205 252

Port 1588 678 161 99 19 52

* 02/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 465 333 798 17.1% 27,469 17.0%

Maori 468 251 719 15.4% 24,656 15.2%

Other 1004 867 1871 40.2% 68,000 42.0%

Pacific 716 378 1094 23.5% 38,985 24.1%

Unknown 76 100 176 3.8% 2865 1.8%

Total 2729 1929 4658 161,975

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Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08

(days

open)

17/08-

23/08

(days

open)

24/08 –

30/08 (days

open)

31/08 01/09 02/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 61 39 24

Auckland Netball Centre 192 (1) 1065 (7) 884 (7) 148 107 107

Botany CTC 1151 (5) 948 (7) 905 (7) 180 125 85

Coast to Coast Warkworth 334 (5) 109 (7) 70 (7) 12 9 4

Coast to Coast Wellsford 203 (5) 114 (7) 116 (7) 23 16 17

Eventfinda Stadium 1800 (5) 527 (7) 517 (7) N/A N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 159 150 107

Henderson 940 (4) 645 (7) 634 (7) 94 80 58

Mangere Town Centre 1748 (3) 1684 (7) 1599 (7) 76 190 160

Manurewa Marae N/A 124 (4) 268 (6) 70 40 N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 63 260 124

Otara CTC 3221 (5) 1712 (7) 1429 (7) 249 187 116

Pukekohe CTC N/A 131 (4) 226 (6) 78 65 39

St Lukes 1368 (5) 1045 (7) 1414 (7) 178 131 118

Takanini Urgent Care 1886 (5) 1216 (7) 1153 (7) 204 124 89

Waiheke Medical Centre 312 (5) 145 (7) 220 (7) 24 23 12

Whanau House 2502 (5) 1371 (7) 1442 (7) 232 172 104

Whanau Ora - Central 1957 (5) 964 (7) 1583 (7) 187 141 112

Whanau Ora - North 1442 (5) 669 (7) 637 (7) 207 230 160

Whanau Ora - South 2945 (5) 1250 (7) 718 (7) 175 110 94

Point England Pop Up N/A N/A 88 (3) N/A N/A N/A

Randwick Park Pop Up N/A N/A 303 (5) N/A N/A N/A

Ranui Pop Up N/A N/A 409 (5) N/A N/A N/A

Mt Smart Stadium Pop Up N/A N/A 219 (3) N/A N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A N/A

South Kaipara Pop Up N/A N/A 170 (4) N/A N/A N/A

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19

Clendon Pop Up N/A N/A 368 (3) N/A N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A N/A

Mangere East Pop Up N/A N/A 109 (2) N/A No

data

N/A

Otara Pop Up N/A N/A 59 (2) N/A N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A N/A

Mt Roskill Pop Up (330 start) N/A N/A 217 (2) 108 N/A N/A

Sandringham Pop Up N/A N/A N/A 87 74 19

Ranui League Club Pop Up N/A N/A N/A 32 101 No

Data

Glen Eden Pop Up N/A N/A N/A N/A 29 24

Southmall Pop Up N/A N/A N/A N/A 108 105

Waipuna Targeted Site 143 (2) 549 (7) 376 (7) 16 25 58

Blockhouse Bay Targeted Site N/A 277 (7) 921 (7) 71 16 No

Data

Total 26,148 16,781 21,215 2735 2552 1733 * 02/09 day still in progress N/A = not open as a CTC

cmaguire
Sticky Note
Unmarked set by cmaguire

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20

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 12: Number of people tested for COVID-19 from 12 August to 03 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 2846 5914 7415 16210 255 32640

Bay of Plenty 2081 236 441 5245 52 8055

Canterbury 1337 521 1271 11038 152 14319

Capital and Coast 1170 893 1026 7295 153 10537

Counties Manukau 6017 16689 7042 10192 359 40299

Hawkes Bay 1134 230 173 2946 38 4521

Hutt Valley 637 332 412 2407 31 3819

Lakes 2008 267 411 2679 74 5439

MidCentral 841 224 296 3366 59 4786

Nelson Marlborough 490 131 194 3539 45 4399

Northland 2603 181 208 3417 31 6440

South Canterbury 120 31 66 1315 13 1545

Southern 848 269 524 7474 67 9182

Tairāwhiti 727 44 47 677 13 1508

Taranaki 575 57 132 2137 31 2932

Waikato 3634 848 1071 8133 168 13854

Wairarapa 173 29 27 791 5 1025

Waitematā 3738 3847 5810 19796 227 33418

West Coast 41 7 12 270 6 336

Whanganui 562 63 51 1232 14 1922

Unknown 1201 593 531 3323 1065 6713

Total 32783 31406 27160 113483 2858 207690

21

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Table 12: Rate per 1000 people tested for COVID-19 from 12 August to 03 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 65.4 105.5 39.6 62 59.5

Bay of Plenty 34.8 53.1 22.5 33.3 33.4

Canterbury 25.5 36.7 20.9 24.7 25

Capital and Coast 32 40.3 20.4 34.3 32.8

Counties Manukau 67.6 139 46.6 48.7 70.8

Hawkes Bay 26.2 35.8 18.9 27.3 27.1

Hutt Valley 24.4 28.4 22 25.5 25.3

Lakes 52.2 104.5 42.2 44.7 49.1

MidCentral 23.1 40.4 19.1 27.2 26.4

Nelson Marlborough 30.5 53 26.1 28.1 29

Northland 42.8 48.2 25.1 31.3 35.4

South Canterbury 22.6 63.5 27.9 25.5 25.8

Southern 25.3 39.1 20.3 27.9 27.5

Tairāwhiti 29.3 39.4 40.3 30.6 30.7

Taranaki 24.6 40.9 21.2 23.8 24.3

Waikato 37.7 63.6 24.3 30.2 32.7

Wairarapa 21.7 34.9 21.7 22.2 22.4

Waitematā 59.7 86.3 40.4 51.8 52.8

West Coast 10.6 27.7 13 10 10.5

Whanganui 32.4 41.4 17.4 28.6 29.6

Total 42.2 98.2 35.4 36.7 41.9

1

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SITREP 042

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 04 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

3

MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

80

98

COMMUNITY CASES

ACTIVE

75 TOTAL CASES SINCE 11 AUG

155

37

TOTAL CASES SINCE 9 JUN

135

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 112

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

03 September

9,909

LABORATORY TESTS

28 Aug to 03 Sep

67,660

LABORATORY TESTS

TOTAL

797,990

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 04 September 2020

Case Status Active Recovered Deceased Total

Confirmed 112 (-3) 1284 (+8) 17 1413 (+5)

Probable 0 346 5 351

Total 112 (-3) 1630 (+8) 22 1764 (+5)*

*Net increase of 5 cases with 8 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 04 September 20201

New community cases since 0900 03 September 2020

1. Three new confirmed community case has been reported.

o Two cases are from one household and are epidemiologically linked with cases

associated with the Mt Roskill Evangelical Church sub-cluster.

o One case has very recently been reported in EpiSurv and no information currently

exists about relationships to other cases.

Community cases linked to the Auckland Community Cluster August 2020

2. 152 of the 155 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 04 September.

o One of the unlinked cases is the Rydges employee (this investigation has been

closed).

o One case is still under investigation for an epidemiological link to the community

cluster and there is insufficient data to confirm a genomic link to the community

cluster (see 3).

o A new case reported 04 September currently has no information available about

relationships to other cases. The case will be scoped today.

1 EpiSurv

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 73 (+2) 37 (+1) 43 2 155 (+3)

Probable 0 0 0 0 0

Total 73 (+2) 37 (+1) 43 2 155 (+3)

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3

Community cases under investigation to determine a link to the community cluster

3. Case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.2

Community cases and household contacts at Jet Park

4. As at 0800 4 September there are 82 people isolating in Jet Park from the community.

59 are confirmed cases, the remaining 23 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases

5. As at 0900 4 September there has been two new cases detected at the border since

0900 3 September. In total there are 135 cases that have been detected at the border

since the establishment of MIFs/MIQs.

o Both cases were detected in Auckland, and are part of a family group that arrived

from India on 23 August. The family was transferred from managed isolation to Jet

Park Quarantine on 28 August after one family member tested positive at Day 3

testing. Subsequently three other family members have tested positive.4

Cases in hospital

6. As at 0800 4 September there are six cases in hospital with COVID-19.5

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 4 September 2020

2 ESR WGS report 3 September 2020

3 NRHCC Morning Report 4 September 2020

4 EpiSurv

5 NRHCC Morning Report 4 September 2020 and Waikato DHB Morning Report 4 September 2020

DHB Hospital Number in a general

ward Number in ICU/HDU

Auckland Auckland City 1 0

Counties Manukau Middlemore 0 1

Waitematā North Shore 2 0

Waikato Waikato 1 1

Total - 4 2

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities7

o Contact tracing and containment around Mt Roskill church sub-cluster

o Seek to identify an epidemiological link for the case to the main cluster

o Clarify whether the case that is a returnee from June is a new infection, and clarify strain

o Contact trace and isolate close contacts exposed on Auckland bus journeys

o Seek to identify epidemiological link to the cluster for cases that have been genomically

linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS due to ongoing transmission

occurring and concerns that not all contacts have been identified. Several events

including church services and a are being scoped. This is a joint effort with

ARPHS completing contact tracing for the events and Waikato focusing on source

attribution.8 The DHBs are working closely with Church leaders to:

o Maintain relationships with and support for Church leaders.

o Understand the total number of people that need to be tested.

o Push testing coverage.

o Develop welfare support arrangements for those requiring quarantine.

Sub-clusters and settings of interest

6 ARPHS Strategic Report 31 August 2020

7 ARPHS Strategic Report 31 August 2020

8 ARPHS, Waikato DHB and MoH teleconference 3pm 3 September 2020

s 9(2)(a)

s 9(2)(a)

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5

9. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 1 September).

10. Settings of interest are being investigated for the Botany sub-cluster, including casual

work places. More information to come when available.

11. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.9 It is being investigated as both a

possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster.10

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.11 Surveillance testing is underway.12

Case investigation

12. Four cases that have been genomically linked to the cluster are still being investigated

by ARPHS to identify their epidemiological link.

o The source of infection is still under investigation.

o GP.

o The second Mount Albert Grammar student.

o Botany case: and lives in a household with

close links to a second household. Members of the second household are testing

positive.

13. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.

14. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

staff. The centre is completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe that is being taken due

to the case’s long incubation period radiological findings suggest more advanced

disease despite 27 August symptom onset date.

. Two testing sites were stood up

30 August for testing staff and patients, these will be available for the rest of the week.

9 NRHCC Morning Report 3 September 2020

10 NRHCC Morning Report 2 September 2020

11 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

12 NRHCC Morning Report 3 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

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1.

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ESR and wider testing13 15. A total of 104 cases (69%) from the main cluster have been sequenced, 93 (62% of total

confirmed cases) yielded a high-quality genome sequence. Three cases yielded partial

genomes but had sufficient data to indicate that these cases are part of the outbreak

cluster. The remaining eight cases did not have sufficient genetic material to be

sequenced.

16.

17. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

18. No direct links have been found between the community outbreak genome

sequencing, with the 49 full genomes currently available from cases in managed

isolation facilities (MIFs).

19.

Contact tracing14 20. Between 26 August and 01 September 71% (747 of 1057) of close contacts have been

contacted within 48 hours of being determined to be a contact. KPI for this metric is

80% of close contacts within 48 hours.

o Note: This is low mainly due to an exposure event and resulting sub-cluster during this period. Around 400 people were identified as close contacts through exposure to a case that was identified via a source attribution investigation. In this instance, the Case was not identified until more than 14 days after the exposure event. After 14 days from an exposure, the need to isolate close contacts has passed as this is the full incubation period, therefore close contacts were not isolated. Despite impacting metrics this delayed case identification and subsequent delayed close contact communication demonstrates that an effective trace back process occurred, leading to successful source identification.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

13 ESR Whole Genome Sequencing Report 02 September 2020

14 COVID-19 NCCS Analytics and Reporting 0904 04 September 2020

s 9(2)(g)(i)

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Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 04 September 2020

01/09/2020 02/09/2020 03/09/2020 04/09/2020

Number of close contacts

identified1 2743 3192 3162 3191

Number of close contacts

successfully contacted (and are

self-isolating)

2676 2992 2984 3136

Number of close contacts

referred to "finding services"2 5 4 4 4

Number of close contacts

awaiting contact 62 196 174 51

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage15 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

03 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

15 Response Analyst – Digital Channels, 1625 03 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

/20

20

23

/05

/20

20

26

/05

/20

20

29

/05

/20

20

1/0

6/2

02

04

/06

/20

20

7/0

6/2

02

01

0/0

6/2

02

01

3/0

6/2

02

01

6/0

6/2

02

01

9/0

6/2

02

02

2/0

6/2

02

02

5/0

6/2

02

02

8/0

6/2

02

01

/07

/20

20

4/0

7/2

02

07

/07

/20

20

10

/07

/20

20

13

/07

/20

20

16

/07

/20

20

19

/07

/20

20

22

/07

/20

20

25

/07

/20

20

28

/07

/20

20

31

/07

/20

20

3/0

8/2

02

06

/08

/20

20

9/0

8/2

02

01

2/0

8/2

02

01

5/0

8/2

02

01

8/0

8/2

02

02

1/0

8/2

02

02

4/0

8/2

02

02

7/0

8/2

02

03

0/0

8/2

02

02

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/20

20 D

aily

sca

ns

and

man

ual

en

trie

s

Cu

mu

lati

ve A

pp

reg

istr

atio

ns

COVID Tracer App usage Cumulative App registrations

Scans and manual entries

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10

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

21. Key Numbers:

o 2,073,900 - Total registered users

o 2,253,122 - QR code scans between 1200 02 and 1200 03 September

Testing16 Table 6: Testing by functional groups, as at 0900 03 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers17 Table 7: Number of laboratory tests processed nationally as at 0900 03 September 2020

16 ÉCLAIR/MoH Public Health Intelligence, 1000 03 September 2020

17 Daily Lab Report, 0930 04 September 2020

Reason for test 03 September 28 August – 03 September

GPs and other primary health 4728 26,841

CBACs and pop-ups 4238 35,501

Border workers - air crew 41 223

Border workers - airport staff 289 1705

Border workers - maritime crew 0 39

Border workers – Port of Tauranga staff 130 269

Border workers – Remaining Port staff 19 221

Border workers - MIF 210 928

Border workers - MIQ 26 202

Travellers - Staying at MIF 228 2082

Travellers - Staying at MIQ 0 131

Total 9909 68142*

Time period Number of laboratory tests

03 September 9909

Last 7 days (28 Aug to 03 Sep) 67,660

Total 797,990

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11

Testing supply update18

22. There are approximately 270,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

Testing activity by region

Focus areas

23. As at 1700 03 September there are 24 Community testing Centres in the Metro

Auckland area. Two of these are closed CTC's for close contacts only.19

Healthline updates20 24. Overnight Healthline had a water main burst in one of their Auckland sites. The floor

has been closed and staff relocated to other sites. This is NOT impacting service

delivery.

25. After following up with Radio New Zealand, the online items are being updated to

clarify the situation relating to Healthline’s position on instructing South and West

Aucklander’s to get tested. Work is underway to implement the equity improvements

for Pacific peoples that have been identified in the last week.

26. On 03 September there were 2,769 contacts in Healthline. Of those calls, 1,132 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 639 contacts (in line with forecast).

27. The main themes yesterday/today:

o On 02 September Healthline reported that certain communities are feeling

particularly vulnerable with the most recent change in Alert Levels. Their concern is

particularly around returning to work. The pressure they are feeling is regarding two

areas:

▪ Unlike previously, communications have not singled out certain communities

and how their risk is different/increased.

▪ Due to the duration of COVID, the heightened pressure from employers to

have them back in the workplace regardless of the risk posed to their

community (COVID-19).

o Symptomatic and asymptomatic Service User’s wanting to be tested.

o People having welfare needs associated with the lock down.

18 Health Supply Chain email, 0907 30 August 2020

19 Community Testing Centres report, 1809 03 September 2020

20 National Telehealth Service Coronavirus Update, 0944 04 September 2020

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12

Logistics

Health Workforce21

28. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

29. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

30. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

Hospital capacity22 Table 8: Number and occupancy of hospital beds by type as at 0800 04 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 342 218 (63.7%)

Ventilators 305 56 (18.4%)

Ward beds 7273 5829 (80.1%)

21 Health Workforce Directorate, 0832 01 September 2020

22 COVID-19 Hospital Summary, 0855 04 September 2020

13

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Appendix 1: Case summaryError! Bookmark not defined. Table 9: All community cases reported between 0900 03 September and 0900 04 September

s 9(2)(a)

14

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Appendix 2: International case

investigations

s 9(2)(a)

15

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Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification14 Indicator (as

per Table 9832) Refined Indicator description Target 27 August 28 August 29 August 30 August 31 August** 1 September**

2 September**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 50% 76% 51% 100% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 83% 67% 79% 100% - - -

3 – (S003) Time from test sample taken to

close contact isolation / quarantine

80% within 72 hours 100% 95% 84% 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 40% 71% 33% 50% 57%

0% *

(0/3) -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 100% 56% 50% 100% 36% 80% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 100% 94% 84% 100% 94% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated /

quarantined 80% within 24 hours 100% 95% 100% 100% 94% 71% 55%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 100% 95% 84% 100% 94% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected

COVID-19 at the time of tracing <20% 17% 0% 0% 0% 5% 0% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• *** The metrics for Indicators S001, S002, S003, P002 on the 26 August are low mainly due to an exposure event and resulting sub-cluster during this period. Around 400 people were identified as close contacts through exposure to a case that was identified via a source attribution investigation. In this instance, the

Case was not identified until more than 14 days after the exposure event. After 14 days from an exposure, the need to isolate close contacts has passed as this is the full incubation period, therefore close contacts were not isolated. Despite impacting metrics this delayed case identification and subsequent delayed

close contact communication demonstrates that an effective trace back process occurred, leading to successful source identification.

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

16

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APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 03 September 2020

Table 1. Metro Auckland Summary Total of Testing for 03 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1623 120 492 167 74 2476

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 01/09 02/09 03/09*

MIQ Staff 2132 659 1488 152 100 265 120

Guests 2972 3767 3600 418 399 468 492

Border Airport 2129 933 1349 199 205 252 167

Port 1588 678 161 99 19 52 74

* 03/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 430 402 832 22.3% 28,804 17.2%

Maori 319 202 521 14.0% 24,865 14.8%

Other 727 725 1452 38.9% 70,863 42.3%

Pacific 499 323 822 22.0% 39,983 23.8%

Unknown 30 71 101 2.7% 3163 1.9%

Total 2005 1723 3728 167,678

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17

Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08

(days

open)

17/08-

23/08

(days

open)

24/08 –

30/08

(days

open)

31/08 01/09 02/09 03/09*

Airport Oaks 1148

(4)

515 (7) 366 (7) 61 39 24 45

Auckland Netball Centre 192 (1) 1065 (7) 884 (7) 148 107 107 86

Botany CTC 1151

(5)

948 (7) 905 (7) 180 125 85 91

Coast to Coast Warkworth 334 (5) 109 (7) 70 (7) 12 9 4 0

Coast to Coast Wellsford 203 (5) 114 (7) 116 (7) 23 16 17 11

Eventfinda Stadium 1800

(5)

527 (7) 517 (7) N/A N/A N/A N/A

Health New Lynn 2603

(5)

1258 (7) 1703 (7) 159 150 126 111

Henderson 940 (4) 645 (7) 634 (7) 94 80 58 76

Mangere Town Centre 1748

(3)

1684 (7) 1599 (7) 76 190 160 152

Manurewa Marae N/A 124 (4) 268 (6) 70 40 N/A N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 63 260 152 107

Otara CTC 3221

(5)

1712 (7) 1429 (7) 249 187 116 77

Pukekohe CTC N/A 131 (4) 226 (6) 78 65 39 41

St Lukes 1368

(5)

1045 (7) 1414 (7) 178 131 118 101

Takanini Urgent Care 1886

(5)

1216 (7) 1153 (7) 204 124 89 80

Waiheke Medical Centre 312 (5) 145 (7) 220 (7) 24 23 12 12

Whanau House 2502

(5)

1371 (7) 1442 (7) 232 172 104 103

Whanau Ora - Central 1957

(5)

964 (7) 1583 (7) 187 141 125 125

Whanau Ora - North 1442

(5)

669 (7) 637 (7) 207 230 171 108

IN CONFIDENCE – NOT FOR DISTRIBUTION

18

Whanau Ora - South 2945

(5)

1250 (7) 718 (7) 175 110 98 84

Point England Pop Up N/A N/A 88 (3) N/A N/A N/A N/A

Randwick Park Pop Up N/A N/A 303 (5) N/A N/A N/A N/A

Ranui Pop Up N/A N/A 409 (5) N/A N/A N/A N/A

Mt Smart Stadium Pop Up N/A N/A 219 (3) N/A N/A N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A N/A N/A

South Kaipara Pop Up N/A N/A 170 (4) N/A N/A N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A N/A N/A

Mangere East Pop Up N/A N/A 109 (2) N/A No

data

N/A No

Data

Otara Pop Up N/A N/A 59 (2) N/A N/A N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A N/A N/A

Mt Roskill Pop Up (330 start) N/A N/A 217 (2) 108 N/A N/A N/A

Sandringham Pop Up N/A N/A N/A 87 74 19 N/A

Ranui League Club Pop Up N/A N/A N/A 32 101 No

Data

N/A

Glen Eden Pop Up N/A N/A N/A N/A 29 24 43

Southmall Pop Up N/A N/A N/A N/A 108 105 78

Orakei Pop Up N/A N/A N/A N/A N/A N/A No

Data

Papatoetoe Pop Up N/A N/A N/A N/A N/A N/A 30

Waipuna Targeted Site 143 (2) 549 (7) 376 (7) 16 25 58 45

Blockhouse Bay Targeted Site N/A 277 (7) 921 (7) 71 16 No

Data

17

Total 26,148 16,781 21,215 2735 2552 1733 1623 * 03/09 day still in progress N/A = not open as a CTC

IN CONFIDENCE – NOT FOR DISTRIBUTION

19

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 04 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 2921 6073 7666 16681 264 33605

Bay of Plenty 2157 245 459 5437 53 8351

Canterbury 1358 530 1303 11280 160 14631

Capital and Coast 1218 925 1064 7571 158 10936

Counties Manukau 6222 17083 7280 10512 366 41463

Hawkes Bay 1177 233 176 3047 41 4674

Hutt Valley 658 350 435 2522 33 3998

Lakes 2063 268 416 2749 75 5571

MidCentral 866 229 299 3444 64 4902

Nelson Marlborough 505 136 199 3645 47 4532

Northland 2659 185 217 3493 31 6585

South Canterbury 124 31 66 1405 12 1638

Southern 890 281 549 7824 66 9610

Tairāwhiti 749 44 49 688 15 1545

Taranaki 583 57 133 2189 33 2995

Waikato 3736 873 1124 8429 166 14328

Wairarapa 179 31 27 830 5 1072

Waitematā 3839 3931 6026 20338 237 34371

West Coast 41 7 12 272 5 337

Whanganui 571 66 52 1248 14 1951

Unknown 1231 606 556 3422 1115 6930

Total 33747 32184 28108 117027 2960 214026

20

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 04 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 67.2 108.3 41 63.8 61.3

Bay of Plenty 36.1 55.1 23.4 34.6 34.6

Canterbury 25.9 37.4 21.4 25.3 25.5

Capital and Coast 33.3 41.7 21.2 35.6 34

Counties Manukau 69.9 142.3 48.2 50.2 72.8

Hawkes Bay 27.2 36.3 19.2 28.2 28

Hutt Valley 25.2 30 23.2 26.8 26.5

Lakes 53.6 104.9 42.8 45.8 50.3

MidCentral 23.8 41.3 19.3 27.8 27.1

Nelson Marlborough 31.5 55 26.8 29 29.9

Northland 43.7 49.2 26.2 32 36.2

South Canterbury 23.3 63.5 27.9 27.2 27.4

Southern 26.5 40.8 21.3 29.2 28.8

Tairāwhiti 30.2 39.4 42 31.1 31.4

Taranaki 25 40.9 21.4 24.3 24.8

Waikato 38.8 65.5 25.5 31.3 33.9

Wairarapa 22.4 37.3 21.7 23.3 23.4

Waitematā 61.3 88.2 41.9 53.2 54.3

West Coast 10.6 27.7 13 10.1 10.5

Whanganui 32.9 43.4 17.8 29 30.1

Total 43.4 100.6 36.7 37.8 43.2

1

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SITREP 043

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 05 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

2

MIQ CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

81

98

COMMUNITY CASES

ACTIVE

74 TOTAL CASES SINCE 11 AUG

157

38

TOTAL CASES SINCE 9 JUN

136

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 112

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

04 September

9,470

LABORATORY TESTS

29 Aug to 04 Sep

67,139

LABORATORY TESTS

TOTAL

807,460

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 05 September 2020

Case Status Active Recovered Deceased Total

Confirmed 112 1285 (+1) 19 (+2) 1416 (+3)

Probable 0 346 5 351

Total 112 1631 (+1) 24 (+2) 1767 (+3)*

*Net increase of 3 cases, with 1 case classified as recovered and 2 deaths reported.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 05 September 20201

New community cases since 0900 04 September 2020

1. Two new community cases have been reported, as at 0900 05 September.

o One case is a close contact of a confirmed case and is linked to the Americold

household sub-cluster. The case has been in isolation at Jet Park from 18 August.

o One case is a close contact of a confirmed case that is linked to the Mt Roskill

Evangelical Church sub-cluster.

Community cases linked to the Auckland Community Cluster August 2020

2. 155 of the 157 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 05 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

1 EpiSurv

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 74 (+1) 38 (+1) 43 2 157 (+2)

Probable 0 0 0 0 0

Total 74 (+1) 38 (+1) 43 2 157 (+2)

IN CONFIDENCE – NOT FOR DISTRIBUTION

3

o

Community cases under investigation to determine a link to the Auckland community

cluster

3. Case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster. 2 Their epidemiological link to the community cluster is still

under investigation.

Community cases and household contacts at Jet Park

4. As at 0800 05 September there are 77 people isolating in Jet Park from the community.

60 are confirmed cases, the remaining 17 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases since 0900 04 September 2020

5. One new case4 detected at the border, as at 0900 05 September. In total 136 cases have

been detected at the border since the establishment of MIFs/MIQs.

o The case arrived from India on 23 August and was identified as a close contact of an

existing confirmed case.

Cases in hospital

6. As at 0800 05 September there are two cases in hospital with COVID-19.5

o Two deaths have been reported; one case6 on 04 September was in ICU at

Middlemore Hospital and one case3 on 05 September at Auckland Hospital.

o Two cases were discharged; one case6 on 04 September from Waikato Hospital and

one case on 04 September from North Shore Hospital.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 05 September 2020

2 ESR WGS report 3 September 2020

3 NRHCC Morning Report 5 September 2020

4 EpiSurv

5 NRHCC Morning Report 5 September 2020 and Waikato DHB Morning Report 5 September 2020

6 ARPHS, Waikato DHB and MoH teleconference 3pm 4 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Counties Manukau Middlemore 0 0

Waitematā North Shore 1 0

Waikato Waikato 0 1

Total - 1 1

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview7

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities8

o Contact tracing and containment around Mt Roskill church sub-cluster.

o Seek to identify an epidemiological link for the case to the main cluster.

o Clarify whether the case that is a returnee from June is a new infection and clarify strain.

o Contact trace and isolate close contacts exposed on Auckland bus journeys.

o Seek to identify epidemiological link to the cluster for cases that have been genomically

linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS due to ongoing transmission

occurring and concerns that not all contacts have been identified. Several events

including church services and a wedding are being scoped. This is a joint effort with

ARPHS completing contact tracing for the events and Waikato focusing on source

attribution.9 The DHBs are working closely with Church leaders to:

o Maintain relationships with and support for Church leaders.

o Understand the total number of people that need to be tested.

o Push testing coverage.

o Develop welfare support arrangements for those requiring quarantine.

Sub-clusters and settings of interest

7 ARPHS Strategic Report 31 August 2020

8 ARPHS Strategic Report 31 August 2020

9 ARPHS, Waikato DHB and MoH teleconference 3pm 3 September 2020

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

9. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 1 September).

10. Settings of interest for the Botany sub-cluster are being investigated, including casual

work places. More information to come when available.

11. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.10 It is being investigated as both

a possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster.11

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.12 Surveillance testing is ongoing.13

Case investigation

12. Four cases that have been genomically linked to the cluster are still being investigated

by ARPHS to identify their epidemiological link.

o The source of infection is still under investigation.

o GP.

o The second Mount Albert Grammar student.

o Botany case: and lives in a household with

close links to a second household. Members of the second household are testing

positive.

13. The community case reported in SITREP 043 04 September, that had no information

available on their relationship to other cases, has now been confirmed to have an

epidemiological link to other confirmed cases and is linked to the Mt Roskill Evangelical

Church sub-cluster.14

14. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.

15. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

10 NRHCC Morning Report 3 September 2020

11 NRHCC Morning Report 2 September 2020

12 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

13 NRHCC Morning Report 3 September 2020

14 EpiSurv

s 9(2)(a)

s 9(2)(a)

s 9(2)(a) s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

6

staff. The centre is completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe that is being taken due

to the case’s long incubation period radiological findings suggest more advanced

disease despite 27 August symptom onset date.

On 30 August two testing sites

were stood up for testing staff and patients, these will be available for the rest of the

week.

s 9(2)(a)

7

IN CONFIDENCE – NOT FOR DISTRIBUTION

s 9(2)(a)

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

8

s 9(2)(a)

9

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing15 16. A total of 104 cases (69%) from the main cluster have been sequenced, 93 (62% of total

confirmed cases) yielded a high-quality genome sequence. Three cases yielded partial

genomes but had sufficient data to indicate that these cases are part of the outbreak

cluster. The remaining eight cases did not have sufficient genetic material to be

sequenced.

17.

18. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

19. No direct links have been found between the community outbreak genome

sequencing, with the 49 full genomes currently available from cases in managed

isolation facilities (MIFs).

20.

Contact tracing16 21. Between 27 August and 02 September 93% (439 of 472) of close contacts have been

contacted within 48 hours of being determined to be a contact. KPI for this metric is

80% of close contacts within 48 hours.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 05 September 2020

02/09/2020 03/09/2020 04/09/2020 05/09/2020

Number of close contacts

identified1 3192 3162 3191 3222

Number of close contacts

successfully contacted (and are

self-isolating)

2992 2984 3136 3177

15 ESR Whole Genome Sequencing Report 02 September 2020

16 COVID-19 NCCS Analytics and Reporting 0918 05 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

IN CONFIDENCE – NOT FOR DISTRIBUTION

10

Number of close contacts

referred to "finding services"2 4 4 4 4

Number of close contacts

awaiting contact 196 174 51 41

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

04 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

22. Key Numbers:

o 2,093,900 - Total registered users

o 2,347,579 - QR code scans between 1200 03 and 1200 04 September

17 Response Analyst – Digital Channels, 1628 04 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

/20

20

23

/05

/20

20

26

/05

/20

20

29

/05

/20

20

1/0

6/2

02

04

/06

/20

20

7/0

6/2

02

01

0/0

6/2

02

01

3/0

6/2

02

01

6/0

6/2

02

01

9/0

6/2

02

02

2/0

6/2

02

02

5/0

6/2

02

02

8/0

6/2

02

01

/07

/20

20

4/0

7/2

02

07

/07

/20

20

10

/07

/20

20

13

/07

/20

20

16

/07

/20

20

19

/07

/20

20

22

/07

/20

20

25

/07

/20

20

28

/07

/20

20

31

/07

/20

20

3/0

8/2

02

06

/08

/20

20

9/0

8/2

02

01

2/0

8/2

02

01

5/0

8/2

02

01

8/0

8/2

02

02

1/0

8/2

02

02

4/0

8/2

02

02

7/0

8/2

02

03

0/0

8/2

02

02

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/20

20 D

aily

sca

ns

and

man

ual

en

trie

s

Cu

mu

lati

ve A

pp

reg

istr

atio

ns

COVID Tracer App usage Cumulative App registrations

Scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Testing18 Table 6: Testing by functional groups, as at 0900 03 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 7: Number of laboratory tests processed nationally as at 0900 04 September 2020

Testing supply update20

23. There are approximately 270,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 03 September 2020

19 Daily Lab Report, 0859 05 September 2020

20 Health Supply Chain email, 0907 30 August 2020

Reason for test 03 September 28 August – 03 September

GPs and other primary health 4728 26,841

CBACs and pop-ups 4238 35,501

Border workers - air crew 41 223

Border workers - airport staff 289 1705

Border workers - maritime crew 0 39

Border workers – Port of Tauranga staff 130 269

Border workers – Remaining Port staff 19 221

Border workers - MIF 210 928

Border workers - MIQ 26 202

Travellers - Staying at MIF 228 2082

Travellers - Staying at MIQ 0 131

Total 9909 68142*

Time period Number of laboratory tests

04 September 9470

Last 7 days (29 Aug to 04 Sep) 67,139

Total 807,460

IN CONFIDENCE – NOT FOR DISTRIBUTION

12

Testing activity by region

Focus areas

24. As at 1700 03 September there are 24 Community testing Centres in the Metro

Auckland area. Two of these are closed CTC's for close contacts only.21

Healthline updates22 25. On 04 September there were 2,525 contacts in Healthline. Of those calls, 970 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 639 contacts (in line with forecast).

26. The main themes yesterday/today:

o Clarification of level announcements made during 04 September.

o Community concern following the announcement of the death late 04 September.

o Symptomatic and asymptomatic Service User’s wanting to be tested.

o People having welfare needs associated with the lock down.

Logistics

Health Workforce23

27. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

28. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

29. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

21 Community Testing Centres report, 1809 03 September 2020

22 National Telehealth Service Coronavirus Update, 0920 05 September 2020

23 Health Workforce Directorate, 0832 01 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

13

Hospital capacity24 Table 8: Number and occupancy of hospital beds by type as at 0800 05 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 342 212 (62.0%)

Ventilators 305 46 (15.1%)

Ward beds 7267 5443 (74.9%)

24 COVID-19 Hospital Summary, 0910 05 September 2020

14

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 1: Case summary

Table 9: All community cases reported between 0900 04 September and 0900 05 September

s 9(2)(a)

15

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 2: International case

investigations

s 9(2)(a)

16

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification16 Indicator (as

per Table 9832) Refined Indicator description Target 28 August 29 August 30 August 31 August 1 September**

2 September**

3 September**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 68% 50% 100% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 60% 79% 100% - - - -

3 – (S003) Time from test sample taken to

close contact isolation / quarantine

80% within 72 hours 93% 85% 100% 100% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 71% 33% 50% 63% 0%

(0/3) - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 56% 50% 100% 36% 80% 100% -

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 93% 85% 97% 99% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% 100% -

8 – (P003) Time from close contact identification to isolated /

quarantined 80% within 24 hours 95% 100% 97% 99% 71% 55% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 95% 85% 100% 99% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected

COVID-19 at the time of tracing <20% 0% 0% 0% 4% 0% 0% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons,

including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 04 September 2020

Table 1. Metro Auckland Summary Total of Testing for 04 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1227 148 505 156 104 2140

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 01/09 02/09 03/09 04/09*

MIQ Staff 2132 659 1488 152 100 265 120 148

Guests 2972 3767 3600 418 399 468 492 505

Border Airport 2129 933 1349 199 205 252 167 156

Port 1588 678 161 99 19 52 74 104

* 04/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 520 447 967 23.4% 30,090 17.4%

Maori 307 245 552 13.4% 25,473 14.7%

Other 754 782 1536 37.2% 73,222 42.3%

Pacific 551 373 924 22.4% 41,121 23.7%

Unknown 40 112 152 3.7% 3337 1.9%

Total 2172 1959 4131 173,243

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18

Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08

(days

open)

17/08-

23/08

(days

open)

24/08 –

30/08

(days

open)

31/08 01/0

9

02/0

9

03/09 04/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 61 39 24 45 28

Auckland Netball

Centre

192 (1) 1065 (7) 884 (7) 148 107 115 96 56

Botany CTC 1151 (5) 948 (7) 905 (7) 180 125 85 96 86

Coast to Coast

Warkworth

334 (5) 109 (7) 70 (7) 12 9 4 0 4

Coast to Coast

Wellsford

203 (5) 114 (7) 116 (7) 23 16 17 12 3

Eventfinda

Stadium

1800 (5) 527 (7) 517 (7) N/A N/A N/A N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 159 150 126 115 75

Henderson 940 (4) 645 (7) 634 (7) 94 80 58 76 43

Mangere Town

Centre

1748 (3) 1684 (7) 1599 (7) 76 190 160 152 98

Manurewa Marae N/A 124 (4) 268 (6) 70 40 N/A N/A N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 63 260 152 107

Otara CTC 3221 (5) 1712 (7) 1429 (7) 249 187 116 95 102

Pukekohe CTC N/A 131 (4) 226 (6) 78 65 39 41 41

St Lukes 1368 (5) 1045 (7) 1414 (7) 178 131 118 101 91

Takanini Urgent

Care

1886 (5) 1216 (7) 1153 (7) 204 124 89 80 71

Waiheke Medical

Centre

312 (5) 145 (7) 220 (7) 24 23 12 12 12

Whanau House 2502 (5) 1371 (7) 1442 (7) 232 172 104 103 106

Whanau Ora -

Central

1957 (5) 964 (7) 1583 (7) 187 141 125 139 95

Whanau Ora -

North

1442 (5) 669 (7) 637 (7) 207 230 171 111 93

Whanau Ora -

South

2945 (5) 1250 (7) 718 (7) 175 110 98 90 84

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19

Point England

Pop Up

N/A N/A 88 (3) N/A N/A N/A N/A N/A

Randwick Park

Pop Up

N/A N/A 303 (5) N/A N/A N/A N/A N/A

Ranui Pop Up N/A N/A 409 (5) N/A N/A N/A N/A N/A

Mt Smart

Stadium Pop Up

N/A N/A 219 (3) N/A N/A N/A N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A N/A N/A N/A

South Kaipara

Pop Up

N/A N/A 170 (4) N/A N/A N/A N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A N/A N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A N/A N/A N/A

Mangere East

Pop Up

N/A N/A 109 (2) N/A No

data

N/A No

Data

N/A

Otara Pop Up N/A N/A 59 (2) N/A N/A N/A N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A N/A N/A N/A

Mt Roskill Pop

Up (330 start)

N/A N/A 217 (2) 108 N/A N/A N/A N/A

Sandringham

Pop Up

N/A N/A N/A 87 74 28 N/A N/A

Ranui League

Club Pop Up

N/A N/A N/A 32 101 39 N/A N/A

Glen Eden Pop

Up

N/A N/A N/A N/A 29 24 43 34

Southmall Pop

Up

N/A N/A N/A N/A 108 105 78 N/A

Orakei Pop Up N/A N/A N/A N/A N/A N/A 33 No

data

Papatoetoe Pop

Up

N/A N/A N/A N/A N/A N/A 35 28

Te Atatu Pop Up N/A N/A N/A N/A N/A 39 18 8

Mangere East

Marae Pop Up

N/A N/A N/A N/A N/A N/A N/A No

data

Waipuna

Targeted Site

143 (2) 549 (7) 376 (7) 16 25 58 45 34

Blockhouse Bay

Targeted Site

N/A 277 (7) 921 (7) 71 16 22 17 35

Total 26,148 16,781 21,215 2735 2552 1925 1740 1227 * 04/09 day still in progress N/A = not open as a CTC

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20

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 04 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 2921 6073 7666 16681 264 33605

Bay of Plenty 2157 245 459 5437 53 8351

Canterbury 1358 530 1303 11280 160 14631

Capital and Coast 1218 925 1064 7571 158 10936

Counties Manukau 6222 17083 7280 10512 366 41463

Hawkes Bay 1177 233 176 3047 41 4674

Hutt Valley 658 350 435 2522 33 3998

Lakes 2063 268 416 2749 75 5571

MidCentral 866 229 299 3444 64 4902

Nelson Marlborough 505 136 199 3645 47 4532

Northland 2659 185 217 3493 31 6585

South Canterbury 124 31 66 1405 12 1638

Southern 890 281 549 7824 66 9610

Tairāwhiti 749 44 49 688 15 1545

Taranaki 583 57 133 2189 33 2995

Waikato 3736 873 1124 8429 166 14328

Wairarapa 179 31 27 830 5 1072

Waitematā 3839 3931 6026 20338 237 34371

West Coast 41 7 12 272 5 337

Whanganui 571 66 52 1248 14 1951

Unknown 1231 606 556 3422 1115 6930

Total 33747 32184 28108 117027 2960 214026

21

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 04 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 67.2 108.3 41 63.8 61.3

Bay of Plenty 36.1 55.1 23.4 34.6 34.6

Canterbury 25.9 37.4 21.4 25.3 25.5

Capital and Coast 33.3 41.7 21.2 35.6 34

Counties Manukau 69.9 142.3 48.2 50.2 72.8

Hawkes Bay 27.2 36.3 19.2 28.2 28

Hutt Valley 25.2 30 23.2 26.8 26.5

Lakes 53.6 104.9 42.8 45.8 50.3

MidCentral 23.8 41.3 19.3 27.8 27.1

Nelson Marlborough 31.5 55 26.8 29 29.9

Northland 43.7 49.2 26.2 32 36.2

South Canterbury 23.3 63.5 27.9 27.2 27.4

Southern 26.5 40.8 21.3 29.2 28.8

Tairāwhiti 30.2 39.4 42 31.1 31.4

Taranaki 25 40.9 21.4 24.3 24.8

Waikato 38.8 65.5 25.5 31.3 33.9

Wairarapa 22.4 37.3 21.7 23.3 23.4

Waitematā 61.3 88.2 41.9 53.2 54.3

West Coast 10.6 27.7 13 10.1 10.5

Whanganui 32.9 43.4 17.8 29 30.1

Total 43.4 100.6 36.7 37.8 43.2

1

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SITREP 044

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 06 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

4

MIQ CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

82

98

COMMUNITY CASES

ACTIVE

77 TOTAL CASES SINCE 11 AUG

161

39

TOTAL CASES SINCE 9 JUN

137

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 116

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

05 September

7,178

LABORATORY TESTS

30 Aug to 05 Sep

63,830

LABORATORY TESTS

TOTAL

814,638

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 06 September 2020

Case Status Active Recovered Deceased Total

Confirmed 116 (+4)* 1286 (+1) 19 1421 (+5)

Probable 0 346 5 351

Total 116 (+4)* 1632 (+1) 24 1772 (+5)

*Net increase of 5 cases, with 1 case classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 06 September 20201

New community cases since 0900 05 September 2020

1. Four new community cases have been reported, as at 0900 06 September.

o All four cases are close contacts confirmed cases linked to the Mt Roskill Evangelical

Church sub-cluster. Three of the cases are from one household.

Community cases linked to the Auckland Community Cluster August 2020

2. 159 of the 161 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 06 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

1 EpiSurv

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 74 42 (+4) 43 2 161 (+4)

Probable 0 0 0 0 0

Total 74 42 (+4) 43 2 161 (+4)

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3

o

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.2 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 06 September there are 75 people isolating in Jet Park from the community.

58 are confirmed cases, the remaining 17 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases since 0900 05 September 2020

5. One new case4 detected at the border, as at 0900 06 September. In total 137 cases have

been detected at the border since the establishment of MIFs/MIQs.

o The case arrived from India on 23 August and is a close contact of an existing

confirmed case. The case tested positive on day 11.

Cases in hospital

6. As at 0800 06 September there are four cases in hospital with COVID-19.5

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 05 September 2020

2 ESR WGS report 3 September 2020

3 NRHCC Morning Report 6 September 2020

4 EpiSurv

5 NRHCC Morning Report 6 September 2020 and Waikato DHB phone call 6 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Counties Manukau Middlemore 1 0

Waitematā North Shore 2 0

Waikato Waikato 0 1

Total - 3 1

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities7

o Contact tracing and containment around Mt Roskill Evangelical Church sub-cluster.

o Seek to identify an epidemiological link to the main cluster for the case.

o Clarify whether the case that is a returnee from June is a new infection and clarify strain.

o Contact trace and isolate close contacts exposed on Auckland bus journeys.

o Seek to identify an epidemiological link to the main cluster for cases that have been

genomically linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS due to ongoing transmission

occurring and concerns that not all contacts have been identified. Several events

including church services and a are being scoped. This is a joint effort with

ARPHS completing contact tracing for the events and Waikato focusing on source

attribution.8 The DHBs are working closely with Church leaders to:

o Maintain relationships with and support for Church leaders.

o Understand the total number of people that need to be tested.

o Push testing coverage.

o Develop welfare support arrangements for those requiring quarantine.

Sub-clusters and settings of interest

6 ARPHS Strategic Report 31 August 2020

7 ARPHS Strategic Report 31 August 2020

8 ARPHS, Waikato DHB and MoH teleconference 3pm 3 September 2020

s 9(2)(a)

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

9. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 1 September).

10. Settings of interest for the Botany sub-cluster are being investigated, including casual

work places. More information to come when available.

11. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.9 It is being investigated as both a

possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster.10

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.11 Surveillance testing is ongoing.12

Case investigation

12. Four cases that have been genomically linked to the main cluster are still being

investigated by ARPHS to identify their epidemiological link to the main cluster.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

13. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.

14. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

. The centre has had a final deep clean and has reopened with reduced

staff. The centre is completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe due to the case’s long

incubation period and radiological findings suggesting more advanced disease despite

the 27 August symptom onset date.

On 30 August two testing sites were stood

up for testing staff and patients, these will be available for the rest of the week.

9 NRHCC Morning Report 3 September 2020

10 NRHCC Morning Report 2 September 2020

11 ARPHS, Waikato DHB and MoH teleconference 3pm 31 August 2020

12 NRHCC Morning Report 3 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

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s 9(2)(a)

s 9(2)(a)

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7

s 9(2)(a)

8

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ESR and wider testing13 15. A total of 104 cases (69%) from the main cluster have been sequenced, 93 (62% of total

confirmed cases) yielded a high-quality genome sequence. Three cases yielded partial

genomes but had sufficient data to indicate that these cases are part of the outbreak

cluster. The remaining eight cases did not have sufficient genetic material to be

sequenced.

16.

17. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

18. No direct links have been found between the community outbreak genome

sequencing, with the 49 full genomes currently available from cases in managed

isolation facilities (MIFs).

19.

Contact tracing14 20. Between 27 August and 02 September 93% (439 of 472) of close contacts have been

contacted within 48 hours of being determined to be a contact. KPI for this metric is

80% of close contacts within 48 hours.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

o Notes: The close contact numbers for today have fallen slightly due to the reclassification of some older cases from community to border cases.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 05 September 2020

03/09/2020 04/09/2020 05/09/2020 06/09/2020

Number of close contacts

identified1 3162 3191 3222 3217

13 ESR Whole Genome Sequencing Report 02 September 2020

14 COVID-19 NCCS Analytics and Reporting 1008 06 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

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9

Number of close contacts

successfully contacted (and are

self-isolating)

2984 3136 3177 3187

Number of close contacts

referred to "finding services"2 4 4 4 4

Number of close contacts

awaiting contact 174 51 41 26

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage15 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1015

05 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

21. Key Numbers:

o 2,106,700 - Total registered users

o 1,823,959 - QR code scans between 1200 04 and 1000 05 September

15 Response Analyst – Digital Channels, 1628 04 September 2020

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10

Testing16 Table 6: Testing by functional groups, as at 0900 04 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers17 Table 7: Number of laboratory tests processed nationally as at 0900 05 September 2020

Testing supply update18

22. There are approximately 270,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

16 ÉCLAIR/MoH Public Health Intelligence, 1000 05 September 2020

17 Daily Lab Report, 0826 06 September 2020

18 Health Supply Chain email, 0907 30 August 2020

Reason for test 04 September 29 August – 04 September

GPs and other primary health 1291 23634

CBACs and pop-ups 1287 31,439

Border workers - air crew 5 196

Border workers - airport staff 117 1564

Border workers - maritime crew 1 40

Border workers – Port of Tauranga staff 72 340

Border workers – Remaining Port staff 87 232

Border workers - MIF 30 789

Border workers - MIQ 34 177

Travellers - Staying at MIF 71 2000

Travellers - Staying at MIQ 2 128

Total 2997 60,539*

Time period Number of laboratory tests

05 September 7178

Last 7 days (30 Aug to 05 Sep) 63,830

Total 814,638

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11

Testing activity by region

Focus areas

23. As at 1700 03 September there are 24 Community testing Centres in the Metro

Auckland area. Two of these are closed CTC's for close contacts only.19

Healthline updates20 24. On 05 September there were 2,890 contacts in Healthline. Of those calls, 1,106 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 605 contacts (in line with forecast).

25. The main themes yesterday/today:

o Community concern and general anxiety following the announcement of the deaths

over 04 – 05 September.

o Clarification of level announcements made during 04 September.

o Symptomatic and asymptomatic Service User’s wanting to be tested.

o People having welfare needs associated with the lock down.

Logistics

Health Workforce21

26. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

27. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

28. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

19 Community Testing Centres report, 1809 03 September 2020

20 National Telehealth Service Coronavirus Update, 0847 06 September 2020

21 Health Workforce Directorate, 0832 01 September 2020

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12

Hospital capacity22 Table 8: Number and occupancy of hospital beds by type as at 0800 06 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 247 146 (59.1%)

Ventilators 201 40 (19.9%)

Ward beds 5161 3773 (73.1%)

22 COVID-19 Hospital Summary, 0905 06 September 2020

13

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Appendix 1: Case summary

Table 9: All community cases reported between 0900 05 September and 0900 06 September

s 9(2)(a)

14

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 2: International case

investigations

s 9(2)(a)

15

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification14 Indicator (as

per Table 9832) Refined Indicator description Target 29 August 30 August 31 August 1 Sept** 2 Sept** 3 Sept 4 Sept#

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 50% 100% - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 79% 100% - - - - -

3 – (S003) Time from test sample taken to

close contact isolation / quarantine

80% within 72 hours 85% 100% 100% - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 33% 50% 63% 0%

(0/3) - - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 50% 100% 36% 80% 100% - -

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 85% 97% 99% 100% - - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% - -

8 – (P003) Time from close contact identification to isolated /

quarantined 80% within 24 hours 100% 97% 99% 71% 55% - -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 85% 100% 99% 100% - - -

C – (S005) Proportion of close contacts with confirmed or suspected

COVID-19 at the time of tracing <20% 0% 0% 4% 0% 0% 0% -

• # Figures not available due to database outage. Work is currently underway to resolve.

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

16

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APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 04 September 2020

Table 1. Metro Auckland Summary Total of Testing for 04 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1227 148 505 156 104 2140

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 01/09 02/09 03/09 04/09*

MIQ Staff 2132 659 1488 152 100 265 120 148

Guests 2972 3767 3600 418 399 468 492 505

Border Airport 2129 933 1349 199 205 252 167 156

Port 1588 678 161 99 19 52 74 104

* 04/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 520 447 967 23.4% 30,090 17.4%

Maori 307 245 552 13.4% 25,473 14.7%

Other 754 782 1536 37.2% 73,222 42.3%

Pacific 551 373 924 22.4% 41,121 23.7%

Unknown 40 112 152 3.7% 3337 1.9%

Total 2172 1959 4131 173,243

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17

Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08

(days

open)

17/08-

23/08

(days

open)

24/08 –

30/08

(days

open)

31/08 01/0

9

02/0

9

03/09 04/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 61 39 24 45 28

Auckland Netball

Centre

192 (1) 1065 (7) 884 (7) 148 107 115 96 56

Botany CTC 1151 (5) 948 (7) 905 (7) 180 125 85 96 86

Coast to Coast

Warkworth

334 (5) 109 (7) 70 (7) 12 9 4 0 4

Coast to Coast

Wellsford

203 (5) 114 (7) 116 (7) 23 16 17 12 3

Eventfinda

Stadium

1800 (5) 527 (7) 517 (7) N/A N/A N/A N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 159 150 126 115 75

Henderson 940 (4) 645 (7) 634 (7) 94 80 58 76 43

Mangere Town

Centre

1748 (3) 1684 (7) 1599 (7) 76 190 160 152 98

Manurewa Marae N/A 124 (4) 268 (6) 70 40 N/A N/A N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 63 260 152 107

Otara CTC 3221 (5) 1712 (7) 1429 (7) 249 187 116 95 102

Pukekohe CTC N/A 131 (4) 226 (6) 78 65 39 41 41

St Lukes 1368 (5) 1045 (7) 1414 (7) 178 131 118 101 91

Takanini Urgent

Care

1886 (5) 1216 (7) 1153 (7) 204 124 89 80 71

Waiheke Medical

Centre

312 (5) 145 (7) 220 (7) 24 23 12 12 12

Whanau House 2502 (5) 1371 (7) 1442 (7) 232 172 104 103 106

Whanau Ora -

Central

1957 (5) 964 (7) 1583 (7) 187 141 125 139 95

Whanau Ora -

North

1442 (5) 669 (7) 637 (7) 207 230 171 111 93

Whanau Ora -

South

2945 (5) 1250 (7) 718 (7) 175 110 98 90 84

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18

Point England

Pop Up

N/A N/A 88 (3) N/A N/A N/A N/A N/A

Randwick Park

Pop Up

N/A N/A 303 (5) N/A N/A N/A N/A N/A

Ranui Pop Up N/A N/A 409 (5) N/A N/A N/A N/A N/A

Mt Smart

Stadium Pop Up

N/A N/A 219 (3) N/A N/A N/A N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A N/A N/A N/A

South Kaipara

Pop Up

N/A N/A 170 (4) N/A N/A N/A N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A N/A N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A N/A N/A N/A

Mangere East

Pop Up

N/A N/A 109 (2) N/A No

data

N/A No

Data

N/A

Otara Pop Up N/A N/A 59 (2) N/A N/A N/A N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A N/A N/A N/A

Mt Roskill Pop

Up (330 start)

N/A N/A 217 (2) 108 N/A N/A N/A N/A

Sandringham

Pop Up

N/A N/A N/A 87 74 28 N/A N/A

Ranui League

Club Pop Up

N/A N/A N/A 32 101 39 N/A N/A

Glen Eden Pop

Up

N/A N/A N/A N/A 29 24 43 34

Southmall Pop

Up

N/A N/A N/A N/A 108 105 78 N/A

Orakei Pop Up N/A N/A N/A N/A N/A N/A 33 No

data

Papatoetoe Pop

Up

N/A N/A N/A N/A N/A N/A 35 28

Te Atatu Pop Up N/A N/A N/A N/A N/A 39 18 8

Mangere East

Marae Pop Up

N/A N/A N/A N/A N/A N/A N/A No

data

Waipuna

Targeted Site

143 (2) 549 (7) 376 (7) 16 25 58 45 34

Blockhouse Bay

Targeted Site

N/A 277 (7) 921 (7) 71 16 22 17 35

Total 26,148 16,781 21,215 2735 2552 1925 1740 1227 * 04/09 day still in progress N/A = not open as a CTC

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19

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 06 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 2955 6112 7736 16821 267 33891

Bay of Plenty 2184 246 471 5521 53 8475

Canterbury 1367 532 1326 11419 160 14804

Capital and Coast 1219 927 1065 7582 158 10951

Counties Manukau 6261 17198 7341 10596 369 41765

Hawkes Bay 1179 233 176 3047 41 4676

Hutt Valley 659 350 437 2529 33 4008

Lakes 2065 268 416 2749 75 5573

MidCentral 866 229 299 3447 65 4906

Nelson Marlborough 505 136 199 3649 47 4536

Northland 2665 185 219 3517 31 6617

South Canterbury 124 31 66 1405 12 1638

Southern 890 282 549 7826 66 9613

Tairāwhiti 749 44 49 688 15 1545

Taranaki 590 57 134 2221 33 3035

Waikato 3742 873 1124 8436 167 14342

Wairarapa 181 31 27 833 5 1077

Waitematā 3863 3967 6083 20503 238 34654

West Coast 41 8 12 277 5 343

Whanganui 572 66 52 1250 14 1954

Unknown 1237 608 577 3453 1122 6997

Total 33914 32383 28358 117770 2976 215401

20

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 06 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 67.9 109 41.3 64.3 61.8

Bay of Plenty 36.5 55.3 24 35.1 35.1

Canterbury 26.1 37.5 21.8 25.6 25.8

Capital and Coast 33.4 41.8 21.2 35.6 34

Counties Manukau 70.3 143.2 48.6 50.6 73.3

Hawkes Bay 27.3 36.3 19.2 28.2 28

Hutt Valley 25.3 30 23.3 26.8 26.6

Lakes 53.7 104.9 42.8 45.8 50.3

MidCentral 23.8 41.3 19.3 27.9 27.1

Nelson Marlborough 31.5 55 26.8 29 29.9

Northland 43.8 49.2 26.5 32.3 36.4

South Canterbury 23.3 63.5 27.9 27.2 27.4

Southern 26.5 41 21.3 29.3 28.8

Tairāwhiti 30.2 39.4 42 31.1 31.4

Taranaki 25.3 40.9 21.5 24.7 25.1

Waikato 38.8 65.5 25.5 31.3 33.9

Wairarapa 22.7 37.3 21.7 23.3 23.6

Waitematā 61.7 89 42.3 53.6 54.7

West Coast 10.6 31.7 13 10.3 10.7

Whanganui 32.9 43.4 17.8 29 30.1

Total 43.6 101.3 37 38 43.4

1

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SITREP 045

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 07 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

2

MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

84

98

COMMUNITY CASES

ACTIVE

77 TOTAL CASES SINCE 11 AUG

163

41

TOTAL CASES SINCE 9 JUN

139

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 118

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

06 September

3,991

LABORATORY TESTS

31 Aug to 06 Sep

60,602

LABORATORY TESTS

TOTAL

818,629

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 07 September 2020

Case Status Active Recovered Deceased Total

Confirmed 118 (+2)* 1288 (+2) 19 1425 (+4)

Probable 0 346 5 351

Total 118 (+2)* 1634 (+2) 24 1776 (+4)

*Net increase of 4 cases, with 2 case classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 07 September 20201

*Please note that the decrease in 1 case for Waikato DHB is due to a case transferring to Counties Manukau (Jet Park). The 2 cases

reported on 07 September are associated with Waitematā DHB.

New community cases since 0900 06 September 2020

1. Two new community cases have been reported, as at 0900 07 September.

o A case is a close contact of an existing confirmed case and is linked to the Samoan

Methodist Church sub-cluster.

o The other case is a household contact of a confirmed case and is linked to the Mt

Roskill Evangelical Church sub-cluster.

Community cases linked to the Auckland Community Cluster August 2020

2. 161 of the 163 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 07 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

1 EpiSurv

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 75 (+1) 44 (+2) 43 1 (-1) 163 (+2)

Probable 0 0 0 0 0

Total 75 (+1) 44 (+2) 43 1 (-1) 163 (+2)

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3

o

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.2 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 07 September there are 70 people isolating in Jet Park from the community.

52 are confirmed cases, the remaining 18 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases since 0900 06 September 2020

5. Two new cases4 detected at the border, as at 0900 07 September. In total 139 cases

have been detected at the border since the establishment of MIFs/MIQs.

o Both cases arrived from India on 23 August and are close contacts of an existing

confirmed case. One case tested positive on day 8 and the other on day 11.

Cases in hospital

6. As at 0800 07 September there are four cases in hospital with COVID-19.5

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 07 September 2020

2 ESR WGS report 3 September 2020

3 NRHCC Morning Report 6 September 2020

4 EpiSurv

5 NRHCC Morning Report 7 September 2020 and COVID-19 Hospital Summary, 0900 07 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Counties Manukau Middlemore 1 0

Waitematā North Shore 2 0

Waikato Waikato 0 1

Total - 3 1

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities7

o Contact tracing and containment around Mt Roskill Evangelical Church sub-cluster.

o Seek to identify an epidemiological link to the main cluster for the case.

o Clarify whether the case that is a returnee from June is a new infection and clarify strain.

o Contact trace and isolate close contacts exposed on Auckland bus journeys.

o Seek to identify an epidemiological link to the main cluster for cases that have been

genomically linked but not epidemiologically linked.

8. Mt Roskill Evangelical Church is a priority for ARPHS due to ongoing transmission

occurring and concerns that not all contacts have been identified. Several events

including church services and a wedding are being scoped. This is a joint effort with

ARPHS completing contact tracing for the events and Waikato focusing on source

attribution.8

Sub-clusters and settings of interest

9. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 1 September).9

10. Settings of interest for the Botany sub-cluster are being investigated, including casual

work places. More information to come when available.9

6 ARPHS Strategic Report 31 August 2020

7 ARPHS Strategic Report 31 August 2020

8 ARPHS, Waikato DHB and MoH teleconference 1500 3 September 2020

9 NRHCC Morning Report 7 September 2020

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

11. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.10 It is being investigated as both

a possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster.11

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.12 Surveillance testing is ongoing.10

Case investigation

12. Four cases that have been genomically linked to the main cluster are still being

investigated by ARPHS to identify their epidemiological link to the main cluster.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

13. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.9

The case in Tokoroa reported on 29 August is a contact of an existing case from Tokoroa who is

linked to the Auckland cluster. The case works at a medical centre in Tokoroa and it is believed

they had contact with the existing case The centre has had a

final deep clean and has reopened with reduced staff and are completing most consultations

virtually. Contact tracing is being completed back to 20 August. This is a precautionary

timeframe due to the case’s long incubation period and radiological findings suggesting more

advanced disease despite the 27 August symptom onset date. To date, all contacts tested have

received negative results (See table 4).13

10 NRHCC Morning Report 3 September 2020

11 NRHCC Morning Report 2 September 2020

12 ARPHS, Waikato DHB and MoH teleconference 1500 31 August 2020

13 Waikato DHB Morning Report 7 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

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1.

s 9(2)(a)

s 9(2)(a)s 9(2)(a)

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7

s 9(2)(a)

8

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing14 14. A total of 104 cases (69%) from the main cluster have been sequenced, 93 (62% of total

confirmed cases) yielded a high-quality genome sequence. Three cases yielded partial

genomes but had sufficient data to indicate that these cases are part of the outbreak

cluster. The remaining eight cases did not have sufficient genetic material to be

sequenced.

15.

16. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

17. No direct links have been found between the community outbreak genome

sequencing, with the 49 full genomes currently available from cases in managed

isolation facilities (MIFs).

18.

Contact tracing15 19. New data was unavailable at time of publication, this will be updated for the 08

September SitRep. Between 27 August and 02 September 93% (439 of 472) of close

contacts have been contacted within 48 hours of being determined to be a contact. KPI

for this metric is 80% of close contacts within 48 hours.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

o Notes: The close contact numbers for today have fallen slightly due to the reclassification of some older cases from community to border cases.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 07 September 2020

04/09/2020 05/09/2020 06/09/2020 07/09/2020

Number of close contacts

identified1 3191 3222 3217 3224

14 ESR Whole Genome Sequencing Report 02 September 2020

15 COVID-19 NCCS Analytics and Reporting 1008 06 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

IN CONFIDENCE – NOT FOR DISTRIBUTION

9

Number of close contacts

successfully contacted (and are

self-isolating)

3136 3177 3187 3199

Number of close contacts

referred to "finding services"2 4 4 4 0

Number of close contacts

awaiting contact 51 41 26 25

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage16 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1100

06 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20. Key Numbers:

o 2,125,300 - Total registered users

o 2,453,787 - QR code scans between 1200 04 and 1000 05 September

16 Response Analyst – Digital Channels, 1628 04 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

/20

20

23

/05

/20

20

26

/05

/20

20

29

/05

/20

20

1/0

6/2

02

04

/06

/20

20

7/0

6/2

02

01

0/0

6/2

02

01

3/0

6/2

02

01

6/0

6/2

02

01

9/0

6/2

02

02

2/0

6/2

02

02

5/0

6/2

02

02

8/0

6/2

02

01

/07

/20

20

4/0

7/2

02

07

/07

/20

20

10

/07

/20

20

13

/07

/20

20

16

/07

/20

20

19

/07

/20

20

22

/07

/20

20

25

/07

/20

20

28

/07

/20

20

31

/07

/20

20

3/0

8/2

02

06

/08

/20

20

9/0

8/2

02

01

2/0

8/2

02

01

5/0

8/2

02

01

8/0

8/2

02

02

1/0

8/2

02

02

4/0

8/2

02

02

7/0

8/2

02

03

0/0

8/2

02

02

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20

5/0

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02

0 Dai

ly s

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pp

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atio

ns

COVID Tracer App usage Cumulative App registrations

Scans and manual entries

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10

Testing17 Table 6: Testing by functional groups, as at 0900 07 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers18 Table 7: Number of laboratory tests processed nationally as at 0900 07 September 2020

Testing supply update19

21. There are approximately 280,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

17 ÉCLAIR/MoH Public Health Intelligence, 1000 07 September 2020

18 Daily Lab Report, 0830 07 September 2020

19 Daily Lab Report, 0830 07 September 2020

Reason for test 06 September 31 August – 06 September

GPs and other primary health 1666 23,726

CBACs and pop-ups 1926 31,206

Border workers - air crew 5 227

Border workers - airport staff 86 1500

Border workers - maritime crew 1 41

Border workers – Port of Tauranga staff 77 459

Border workers – Remaining Port staff 69 363

Border workers - MIF 51 1043

Border workers - MIQ 23 209

Travellers - Staying at MIF 84 1994

Travellers - Staying at MIQ 3 198

Total 3991 60,966*

Time period Number of laboratory tests

06 September 3,991

Last 7 days (31 Aug to 06 Sep) 60,602

Total 818,629

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11

Testing activity by region

Focus areas

22. As at 0900 07 September there are 19 Community testing Centres in the Metro

Auckland area. Two of these are closed CTC's for close contacts only.20

Healthline updates21 23. On 06 September there were 2,875 contacts in Healthline. Of those calls, 1,130 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 596 contacts (in line with forecast).

24. The main themes yesterday/today:

o Community concern and general anxiety following the announcement of the deaths

over 04 – 05 September.

o Symptomatic Service User’s wanting to be tested.

Logistics

Health Workforce22

25. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

26. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

27. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

20 Community Testing Centres report, 0858 07 September 2020

21 National Telehealth Service Coronavirus Update, 0919 07 September 2020

22 Health Workforce Directorate, 0832 01 September 2020

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12

Hospital capacity23 Table 8: Number and occupancy of hospital beds by type as at 0800 07 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 389 146 (37.5%)

Ventilators 272 40 (14.7%)

Ward beds 6620 5079 (76.7%)

23 COVID-19 Hospital Summary, 0905 07 September 2020

13

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Appendix 1: Case summary

Table 9: All community cases reported between 0900 06 September and 0900 07 September

s 9(2)(a)

14

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Appendix 2: International case

investigations

s 9(2)(a)

15

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Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification15

The COVID-19 Provisional Disease Indicators table was unavailable due to technical issues and will be reported in the 08 September SitRep.

16

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APPENDIX: 4 The next NRHCC Testing report will be issued at 1700 07 September 2020 and will be reported in

the 08 September SitRep.

Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 07 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3,101 6,383 8,170 17,660 308 35,622

Bay of Plenty 2,281 259 489 5,735 55 8,819

Canterbury 1,436 566 1,445 12,021 170 15,638

Capital and Coast 1,289 972 1,129 7,973 167 11,530

Counties Manukau 6,514 18,028 7,842 11,198 391 43,973

Hawkes Bay 1,213 244 184 3,137 45 4,823

Hutt Valley 690 377 461 2,675 35 4,238

Lakes 2,152 278 430 2,911 81 5,852

MidCentral 874 231 306 3,491 67 4,969

Nelson Marlborough 537 140 233 3,817 50 4,777

Northland 2,780 190 233 3,679 37 6,919

South Canterbury 130 31 72 1,552 12 1,797

Southern 941 293 597 8,424 70 10,325

Tairāwhiti 750 47 49 691 17 1,554

Taranaki 618 58 138 2,338 37 3,189

Waikato 3,900 916 1,202 8,890 179 15,087

Wairarapa 201 34 31 906 7 1,179

Waitematā 4,017 4,203 6,517 21,549 266 36,552

West Coast 44 8 13 296 6 367

Whanganui 572 67 53 1,256 14 1,962

Unknown 1,298 627 605 3,610 1,286 7,426

Total 35,338 33,952 30,199 123,810 3,300 226,599

17

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 07 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 71.3 113.8 43.7 67.6 65.0

Bay of Plenty 38.1 58.3 25.0 36.5 36.6

Canterbury 27.4 39.9 23.8 26.9 27.3

Capital and Coast 35.3 43.8 22.5 37.5 35.8

Counties Manukau 73.2 150.1 51.9 53.5 77.2

Hawkes Bay 28.0 38.0 20.1 29.0 28.9

Hutt Valley 26.5 32.3 24.6 28.4 28.1

Lakes 55.9 108.8 44.2 48.5 52.8

MidCentral 24.0 41.6 19.7 28.2 27.4

Nelson Marlborough 33.5 56.6 31.4 30.3 31.5

Northland 45.7 50.5 28.2 33.8 38.0

South Canterbury 24.5 63.5 30.4 30.0 30.0

Southern 28.0 42.5 23.1 31.5 30.9

Tairāwhiti 30.3 42.1 42.0 31.3 31.6

Taranaki 26.5 41.6 22.2 26.0 26.4

Waikato 40.5 68.7 27.2 33.0 35.7

Wairarapa 25.2 40.9 24.9 25.4 25.8

Waitematā 64.2 94.3 45.3 56.4 57.7

West Coast 11.3 31.7 14.1 11.0 11.5

Whanganui 32.9 44.0 18.1 29.2 30.3

Total 45.4 106.2 39.4 40.0 45.7

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SITREP 046

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 08 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

4

MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

85

98

COMMUNITY CASES

ACTIVE

80 TOTAL CASES SINCE 11 AUG

167

43

TOTAL CASES SINCE 9 JUN

141

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 123

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

07 September

4,525

LABORATORY TESTS

01 to 07 Sep

56,528

LABORATORY TESTS

TOTAL

823,154

CASES DECEASED

2

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Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 08 September 2020

Case Status Active Recovered Deceased Total

Confirmed 123* (+5) 1289 (+1) 19 1431 (+6)

Probable 0 346 5 351

Total 123* (+5) 1635 (+1) 24 1782 (+6)

*Net increase of 6 cases, with 1 case classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 08 September 20201

New community cases since 0900 07 September 2020

1. Four new community cases have been reported, as at 0900 08 September.

o All four cases have epidemiological links to existing cases and are associated with

the Mt Roskill Evangelical Church sub-cluster. See details in Para 7.

Community cases linked to the Auckland Community Cluster August 2020

1. 165 of the 167 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 08 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

2. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

1 EpiSurv

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 75 48 (+4) 43 1 167 (+4)

Probable 0 0 0 0 0

Total 75 48 (+4) 43 1 167 (+4)

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o

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.2 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

3. As at 0800 08 September there are 69 people isolating in Jet Park from the community.

52 are confirmed cases, the remaining 17 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases since 0900 07 September 2020

4. Two new cases4 detected at the border, as at 0900 08 September. In total 141 cases

have been detected at the border since the establishment of MIFs/MIQs.

o Both cases arrived in New Zealand on 3 September from the Philippines and have

been in managed isolation since arrival. Tested positive as part of day 3 surveillance

testing.

Cases in hospital

5. As at 0800 08 September there are four cases in hospital with COVID-19.5

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 08 September 2020

• One case in North Shore Hospital that was on a general ward 07 September has been transferred

to ICU as a precautionary measure.

2 ESR WGS report 03 September 2020

3 NRHCC Morning Report 08 September 2020

4 EpiSurv

5 NRHCC Morning Report 08 September 2020 and COVID-19 Hospital Summary, 0900 08 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Counties Manukau Middlemore 1 0

Waitematā North Shore 1 1

Waikato Waikato 0 1

Total - 2 2

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Health system response

Overall approach

6. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

There is now a clear increase in cases as a result of the new Mt Roskill Evangelical Church sub-

cluster. Some of these cases have recent symptoms. While the impact of intensive case follow-up

appears to be working overall, the number of cases associated with the Mt Roskill Evangelical

Church sub-cluster has continued to increase and it is likely that more cases will arise.

Current outbreak investigation priorities7

o Contact tracing and containment around Mt Roskill Evangelical Church sub-cluster.

o Seek to identify an epidemiological link to the main cluster for the case.

o Clarify whether the case that is a returnee from June is a new infection and clarify strain.

o Contact trace and isolate close contacts exposed on Auckland bus journeys.

o Seek to identify an epidemiological link to the main cluster for cases that have been

genomically linked but not epidemiologically linked.

Sub-clusters and settings of interest

7. As at 2000 07 September, a new potential sub-cluster and exposure event was

identified within Mt Roskill, with an epidemiological link to Mt Roskill evangelical

church.

A death (not COVID related) occurred Between 24th August and 2nd September,

there were multiple gatherings associated with the bereavement. Funeral at a

funeral home, approximately 50 attendees. Good records kept, including sign in. An extended

family member of the deceased became a confirmed case on 07 September. Contact tracing from

this case identified the funeral and mourning events as exposure settings.

There are three confirmed cases linked to this initial case. All are extended family and include four

separate households. One case was confirmed on 06 September and has been isolating since then.

The other three cases have been isolating since 07 September. All four new cases presented

themselves for testing.

6 ARPHS Strategic Report 31 August 2020

7 ARPHS Strategic Report 31 August 2020

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One of the new cases is in a Managed Quarantine and Isolation (MIQ) facility. Two additional cases,

plus household members, are moving to MIQ today (08 September).

All have been stood down and will be tested today (08 September).

There are four close contacts from these cases.

ARPHS actions8:

o Scoping new cases.

o Gathering lists of attendees at the bereavement gatherings which occurred

between 24 August and 02 September. ARPHS are working with Māori and Pacific

liaison, and through Mt Roskill Evangelical Church, to identify attendees. All close

contacts will be tested and isolated.

o There are comprehensive records from the funeral on . All attendees will

be tested, and work is underway to move these contacts into isolation.

o Quarantine and testing of household contacts of the new cases. Testing is underway for

household contacts, including repeat testing as needed for people previously tested

from the Mt Roskill church.

o They are being tested today (08

September), and are in isolation.

8. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 01 September).9

9. Settings of interest for the Botany sub-cluster are being investigated, including casual

work places. More information to come when available.9

10. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.10 It is being investigated as both

a possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster.11

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.12 Surveillance testing is ongoing.10

8 ARPHS Phone Call, 0930 08 September 2020

9 NRHCC Morning Report 07 September 2020

10 NRHCC Morning Report 03 September 2020

11 NRHCC Morning Report 02 September 2020

12 ARPHS, Waikato DHB and MoH teleconference 1500 31 August 2020

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Case investigation

11. Four cases that have been genomically linked to the main cluster are still being

investigated by ARPHS to identify their epidemiological link to the main cluster.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

12. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.9

13. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

staff and are completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe due to the case’s long

incubation period and radiological findings suggesting more advanced disease despite

the 27 August symptom onset date. To date, all contacts tested have received negative

results (See table 4).13

13 Waikato DHB Morning Report 07 September 2020

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ESR and wider testing14 14. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) (3 cases).15

15.

16. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

17. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

18.

Contact tracing16 19. Between 30 August and 05 September 98% (61/62) of Community close contacts and

95% (100/105) MIQ close contacts have been contacted within 48 hours of being

determined to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Notes: This metric reports all cases during the specified period, including those in Managed Isolation and Quarantine, and does not include casual contacts.

o Notes: The close contact numbers for today have fallen slightly due to the reclassification of some older cases from community to border cases.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 08 September 2020

05/09/2020 06/09/2020 07/09/2020 08/09/2020

Number of close contacts

identified1 3222 3217 3224 3274

14 ESR Whole Genome Sequencing Report 02 September 2020

15 ESR email update 0900 08 September 2020

16 COVID-19 NCCS Analytics and Reporting 0938 08 September 2020

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Number of close contacts

successfully contacted (and are

self-isolating)

3177 3187 3199 3228

Number of close contacts

referred to "finding services"2 4 4 0 0

Number of close contacts

awaiting contact 41 26 25 46

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

07 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20. Key Numbers:

o 2,145,500 - Total registered users

o 2,192,953 - QR code scans between 1200 05 and 1200 06 September

17 Response Analyst – Digital Channels, 1620 07 September 2020

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Testing18 Table 6: Testing by functional groups, as at 0900 08 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 7: Number of laboratory tests processed nationally as at 0900 08 September 2020

Testing supply update20

21. There are approximately 280,000 complete tests in NZ. Resupply continues to largely

match usage, and additional swab deliveries are expected to arrive this week.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 07 September 2020

19 Daily Lab Report, 0855 08 September 2020

20 Daily Lab Report, 0855 08 September 2020

Reason for test 07 September 01 – 07 September

GPs and other primary health 179 21,146

CBACs and pop-ups 361 25,957

Border workers - air crew 3 177

Border workers - airport staff 53 1307

Border workers - maritime crew 0 7

Border workers – Port of Tauranga staff 0 456

Border workers – Remaining Port staff 4 336

Border workers - MIF 5 994

Border workers - MIQ 3 209

Travellers - Staying at MIF 92 1607

Travellers - Staying at MIQ 3 192

Total 703 52,388*

Time period Number of laboratory tests

07 September 4,525

Last 7 days (01 Sep to 07 Sep) 56,528

Total 823,154

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Testing activity by region

Focus areas

22. As at 1700 07 September there are 16 Community testing Centres in the Metro

Auckland area. Two of these are closed CTC's for close contacts only.21

Healthline updates22 23. On 07 September there were 3,176 contacts in Healthline. Of those calls, 1,349 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 596 contacts (in line with forecast).

24. Work continues to implement the revised testing strategy and how it relates to our

public facing advice – particularly the role we may play in supporting DHB’s around

local asymptomatic testing plans.

25. The main themes yesterday/today:

o Community concern and general anxiety following the announcement of the deaths

over 04 – 05 September.

o Symptomatic Service User’s wanting to be tested.

Logistics

Health Workforce23

26. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

27. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

28. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

21 Community Testing Centres report, 1659 07 September 2020

22 National Telehealth Service Coronavirus Update, 1014 08 September 2020

23 Health Workforce Directorate, 0832 01 September 2020

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Hospital capacity24 Table 8: Number and occupancy of hospital beds by type as at 0800 08 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 354 206 (58.2%)

Ventilators 307 44 (14.3%)

Ward beds 7316 5786 (79.1%)

24 COVID-19 Hospital Summary, 0905 07 September 2020

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Appendix 1: Case summary

Table 9: All community cases reported between 0900 07 September and 0900 08 September

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Appendix 2: International case

investigations

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Appendix 3: COVID-19 Provisional Disease Indicators, by date

of case notification16 Data for cases in the community

Indicator (as per Table 9832) Refined Indicator description Target 31-Aug 1-Sep 2-Sep 3 Sept ** 4 Sept ** 5 Sept ** 6 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

92% 0% *

(0/8) 100% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

92% 0% *

(0/8) 86% - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 100% 100% 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

67% 0% *

(0/1)

0% *

(0/2) - 33% 100% -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

67% 100% 100% 0% *

(0/1) 25%

0% *

(0/1) 20%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 100% 100% 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% 22% 100% 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 100% 100% 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 8% 0% 0% 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Data for cases in Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 31-Aug 1-Sep 2 Sept ** 3-Sep 4 Sept ** 5 Sept ** 6 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

0% * (0/15)

0% * (0/2)

- 100% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

100% 100% - 0% * (0/3)

- - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 100% 71% 100% 40% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

50% 0% * (0/2)

- 0% * (0/1)

- - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

25% 0% * (0/1)

100% 100% 100% - 0%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 100% 71% 100% 40% - -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% - 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% 100% 71% 100% 40% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 100% 71% 100% 40% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 4% 0% 0% 67% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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APPENDIX: 4

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 07 September 2020

Table 1. Metro Auckland Summary Total of Testing for 07 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1631 86 483 153 19 2372

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-16/08 17/08-23/08 24/08 – 30/08 31/08 – 06/09 07/09*

MIQ Staff 2132 659 1488 912 86

Guests 2972 3767 3600 3406 468

Border Airport 2129 933 1349 1158 153

Port 1588 678 161 392 19

* 07/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 200 229 429 19.7% 32,406 17.6%

Maori 158 78 236 10.9% 26,582 14.5%

Other 391 399 790 36.3% 77,649 42.2%

Pacific 435 96 531 24.4% 43,357 23.6%

Unknown 15 174 189 8.7% 3846 2.1%

Total 1199 976 2175 183,840

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Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-16/08

(days open)

17/08-

23/08

(days

open)

24/08 –

30/08

(days

open)

31/08 –

06/09

07/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 265 (7) 39

Auckland Netball Centre 192 (1) 1065 (7) 884 (7) 640 (7) 134

Botany CTC 1151 (5) 948 (7) 905 (7) 749 (7) 135

Coast to Coast

Warkworth

334 (5) 109 (7) 70 (7) 35 (7) 17

Coast to Coast

Wellsford

203 (5) 114 (7) 116 (7) 81 (7) 15

Eventfinda Stadium 1800 (5) 527 (7) 517 (7) N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 732 (7) 129

Henderson 940 (4) 645 (7) 634 (7) 351 (5) N/A

Mangere Town Centre 1748 (3) 1684 (7) 1599 (7) 860 (7) 144

Manurewa Marae N/A 124 (4) 268 (6) 110 (2) N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 741 (7) 57

Otara CTC 3221 (5) 1712 (7) 1429 (7) 930 (7) 108

Pukekohe CTC N/A 131 (4) 226 (6) 298 (6) N/A

St Lukes 1368 (5) 1045 (7) 1414 (7) 797 (7) 99

Takanini Urgent Care 1886 (5) 1216 (7) 1153 (7) 684 (7) 13

Waiheke Medical Centre 312 (5) 145 (7) 220 (7) 98 (7) 92

Whanau House 2502 (5) 1371 (7) 1442 (7) 928 (7) 261

Whanau Ora - Central 1957 (5) 964 (7) 1583 (7) 937 (7) 80

Whanau Ora - North 1442 (5) 669 (7) 637 (7) 982 (7) 105

Whanau Ora - South 2945 (5) 1250 (7) 718 (7) 677 (7) 108

Point England Pop Up N/A N/A 88 (3) N/A N/A

Randwick Park Pop Up N/A N/A 303 (5) N/A N/A

Ranui Pop Up N/A N/A 409 (5) N/A N/A

Mt Smart Stadium Pop

Up

N/A N/A 219 (3) N/A N/A

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Massey Pop Up N/A N/A 787 (5) N/A N/A

South Kaipara Pop Up N/A N/A 170 (4) N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A

Mangere East Pop Up N/A N/A 109 (2) N/A N/A

Otara Pop Up N/A N/A 59 (2) N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A

Mt Roskill Pop Up (330

start)

N/A N/A 217 (2) 164 (3) N/A

Sandringham Pop Up N/A N/A N/A 189 (3) N/A

Ranui League Club Pop

Up

N/A N/A N/A 172 (3) N/A

Glen Eden Pop Up N/A N/A N/A 127 (4) N/A

Southmall Pop Up N/A N/A N/A 291 (3) N/A

Orakei Pop Up N/A N/A N/A 118 (3) N/A

Papatoetoe Pop Up N/A N/A N/A 74 (3) N/A

Te Atatu Pop Up N/A N/A N/A 65 (3) N/A

Mangere East Marae

Pop Up

N/A N/A N/A No Data N/A

Mangere Leagues Club N/A N/A N/A No Data N/A

Tamaki College Pop Up N/A N/A N/A 109 (2) N/A

Papatoetoe EFKS Pop

Up

N/A N/A N/A 74 (1) N/A

Botany Town Centre

Pop Up

N/A N/A N/A 121 (2) N/A

Sylvia Park Pop Up N/A N/A N/A 21 (2) N/A

East Tamaki Pop Up N/A N/A N/A 161 (1) N/A

Rowandale Pop Up N/A N/A N/A 41 (1) N/A

Henderson EFKS Pop Up N/A N/A N/A N/A 43

Waipuna Targeted Site 143 (2) 549 (7) 376 (7) 219 (7) 42

Blockhouse Bay

Targeted Site

N/A 277 (7) 921 (7) 161 (5) N/A

Henderson Targeted

Site

N/A N/A N/A N/A 6

Total 26,148 16,781 21,215 13,002 1631 * 07/09 day still in progress N/A = not open as a CTC

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Appendix 5: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 07 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3128 6436 8262 17845 314 35985

Bay of Plenty 2298 261 501 5792 55 8907

Canterbury 1446 572 1478 12131 174 15801

Capital and Coast 1303 978 1142 8085 173 11681

Counties Manukau 6556 18241 7938 11301 395 44431

Hawkes Bay 1244 255 186 3218 48 4951

Hutt Valley 692 380 469 2716 36 4293

Lakes 2156 278 431 2923 81 5869

MidCentral 923 240 320 3666 72 5221

Nelson Marlborough 542 140 240 3876 50 4848

Northland 2791 193 234 3693 38 6949

South Canterbury 131 31 72 1555 13 1802

Southern 944 298 603 8500 73 10418

Tairāwhiti 783 51 54 711 17 1616

Taranaki 626 59 141 2364 39 3229

Waikato 3922 935 1234 8973 188 15252

Wairarapa 202 34 31 915 7 1189

Waitematā 4042 4228 6584 21675 270 36799

West Coast 44 8 13 297 6 368

Whanganui 597 68 57 1334 14 2070

Unknown 1306 639 616 3675 1344 7580

Total 35676 34325 30606 125246 3407 229260

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 07 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 71.9 114.8 44.1 68.3 65.6

Bay of Plenty 38.4 58.7 25.6 36.8 36.9

Canterbury 27.6 40.3 24.3 27.2 27.5

Capital and Coast 35.7 44.1 22.8 38 36.3

Counties Manukau 73.6 151.9 52.5 54 78

Hawkes Bay 28.8 39.7 20.3 29.8 29.7

Hutt Valley 26.6 32.5 25 28.8 28.5

Lakes 56 108.8 44.3 48.7 53

MidCentral 25.4 43.3 20.6 29.6 28.8

Nelson Marlborough 33.8 56.6 32.3 30.8 31.9

Northland 45.9 51.3 28.3 33.9 38.2

South Canterbury 24.7 63.5 30.4 30.1 30.1

Southern 28.1 43.3 23.4 31.8 31.2

Tairāwhiti 31.6 45.6 46.3 32.2 32.9

Taranaki 26.8 42.4 22.6 26.3 26.7

Waikato 40.7 70.1 28 33.3 36.1

Wairarapa 25.3 40.9 24.9 25.6 26

Waitematā 64.6 94.8 45.8 56.7 58.1

West Coast 11.3 31.7 14.1 11 11.5

Whanganui 34.4 44.7 19.5 31 31.9

Total 45.9 107.3 39.9 40.5 46.2

1

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SITREP 047

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 09 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

6

MIQ CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

89

98

COMMUNITY CASES

ACTIVE

82 TOTAL CASES SINCE 11 AUG

173

43

TOTAL CASES SINCE 9 JUN

141

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 125

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

08 September

8,363

LABORATORY TESTS

02 to 08 Sep

53,957

LABORATORY TESTS

TOTAL

831,517

CASES DECEASED

2

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Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 09 September 2020

Case Status Active Recovered Deceased Total

Confirmed 125* (+2) 1293 (+4) 19 1437 (+6)

Probable 0 346 5 351

Total 125* (+2) 1639 (+4) 24 1788 (+6)

*Net increase of 6 cases, with 4 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 09 September 20201

New community cases since 0900 08 September 2020

1. Six new community cases have been reported, as at 0900 09 September.

o All six cases have epidemiological links to existing cases and are associated with the

Mt Roskill Evangelical Church sub-cluster. (See 8). Of these, four cases are associated

with bereavement events. The other two cases require further investigation to

determine if they are associated with bereavement events or with the wider Mt

Roskill Evangelical Church sub-cluster.

Community cases linked to the Auckland Community Cluster August 2020

2. 171 of the 173 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 09 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

1 EpiSurv Database, 0900 09 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 75 51 (+3) 45 (+2) 1 172 (+5)

Probable 1 (+1) 0 0 0 1 (+1)

Total 76 (+1) 51 (+3) 45 (+2) 1 173 (+6)

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o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.2 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 09 September there are 74 people isolating in Jet Park from the community.

58 are confirmed cases, the remaining 16 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases since 0900 08 September 2020

5. There are no new cases4 detected at the border, as at 0900 09 September. In total 141

cases have been detected at the border since the establishment of MIFs/MIQs.

Cases in hospital

6. As at 0800 09 September there are four cases in hospital with COVID-19.5

o One patient on general ward in Counties Manukau was discharged to Jet Park

yesterday.

o .

o One new case admitted to North Shore Hospital (reported today).

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 09 September 2020

2 ESR WGS report 03 September 2020

3 NRHCC Morning Report 08 September 2020

4 EpiSurv

5 NRHCC Morning Report 08 September 2020 and COVID-19 Hospital Summary, 0900 08 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Counties Manukau Middlemore 0 0

Waitematā North Shore 2 1

Waikato Waikato 0 1

Total - 2 2

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Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

8. There is now a clear increase in cases as a result of the new Mt Roskill Evangelical

Church sub-cluster. Some of these cases have recent symptoms. While the impact of

intensive case follow-up appears to be working overall, the number of cases associated

with the Mt Roskill Evangelical Church sub-cluster has continued to increase and it is

likely that more cases will arise.

Current outbreak investigation priorities7

o Contact tracing and containment around Mt Roskill Evangelical Church sub-cluster

o Clarify whether the case that is a returnee from June is a new infection and clarify strain.

o Seek to identify an epidemiological link to the main cluster for cases that have been

genomically linked but not epidemiologically linked.

Sub-clusters and settings of interest

9. On 7 September, a new potential sub-cluster and exposure event was identified within

Mt Roskill, with an epidemiological link to Mt Roskill Evangelical Church.8 There are

clear links between the Church and the new sub-cluster.9 ARPHS have being working to

develop rapport, trust and cooperation with the Mt Roskill Evangelical Church leaders,

which is critical for further scoping and investigation. The following events described

below were not disclosed to ARPHS until 7 September, when ARPHS were doing

contact tracing work around a newly identified case identified who attended the

bereavement events.10

A death (not COVID related) Between 24 August and 2

September, there were multiple gatherings associated with the bereavement. A funeral

occurred on at a funeral home with approximately 50 attendees. Good

records of attendees were kept by the funeral home, including sign in. An extended

6 ARPHS Strategic Report 31 August 2020

7 ARPHS Strategic Report 31 August 2020

8 ARPHS, Waikato DHB and MoH teleconference 0830 08 September 2020

9 NRHCC Morning Report 09 September 2020

10 ARPHS, Waikato DHB and MoH teleconference 1500 08 September 2020

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family member of the deceased was confirmed as a case on 7 September. Contact

tracing from this case identified the funeral and mourning events as exposure settings.

Some of the attendees of the bereavement events are linked to the Mt Roskill

Evangelical Church sub-cluster.

All funeral attendees are considered close contacts and will self-isolate and be tested.

All other contacts at Mt Roskill Evangelical Church (who did not attend the funeral) are

considered to be casual contacts unless symptomatic - unless they have symptoms they

are not required to self-isolate.10 ARPHS are working with the church today (9

September) to determine a strategy for testing casual contacts at the church.9

There were three confirmed cases linked to the case identified on 7 September. They

are members of an extended family and include four separate households. One case

was confirmed on 06 September and has been isolating since then. One case became

on 5th September and began isolating then. The other two cases have

been isolating since 07 September. All four cases presented themselves for testing. Of

the four cases,

One of the initial cases is in a Managed Quarantine and Isolation (MIQ) facility. Two

additional cases, plus household members moved to MIQ 8 September.

There are four close contacts from these cases. All

close contacts have been stood down and were tested 8 September.

A new setting of interest is St Dominic’s College in Henderson, Auckland. A confirmed

case attended the school.9

The school has been informed and communications

have been sent. The case is linked to new sub-cluster associated with the bereavement

events.

ARPHS actions:

o Maintain and strengthen relationships with Church leaders and liaise with Church

members about their need for financial and welfare support if asked to isolate.10

o Scoping new cases.

o Gathering lists of attendees at the daily bereavement gatherings which occurred

between 24 August and 02 September. ARPHS are working with Māori and Pacific

liaison, and through Mt Roskill Evangelical Church, to identify attendees. All close

contacts will be tested and isolated.8

o There are comprehensive records from the funeral on . All attendees will

be tested, and work is underway to move these contacts into isolation.8

o Quarantine and testing of household contacts of the new cases. Testing is underway

for household contacts, including repeat testing as needed for people previously

tested from the Mt Roskill church.8

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o All contacts have been stood down. They are being tested 08 September

and are in isolation.8

o Developing and implementing a testing strategy which includes communication with

church leaders around the reason for testing and who should be tested.10

10. Contact tracing investigation and testing is ongoing for the Botany sub-cluster. This

sub-cluster includes the Botany case reported 28 August and four other cases reported

recently (one on 31 August and three on 01 September).11

11. Settings of interest for the Botany sub-cluster are being investigated, including casual

work places. More information to come when available.11

12. There is a sports club associated with the Mt Roskill Evangelical Church. To date there

are no known exposures confirmed at the sports club.12 It is being investigated as both

a possible exposure event and a possible source of the Mt Roskill Evangelical Church

sub-cluster.13 .

ARPHS advised on 31 August the sports club had been closed for the two weeks prior,

therefore none of the club members are being considered close contacts. ARPHS sent

comms to members regarding testing and to date no positive cases have been

reported.14 Surveillance testing is ongoing.12

Case investigation

13. Four cases that have been genomically linked to the main cluster are still being

investigated by ARPHS to identify their epidemiological link to the main cluster.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

14. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.11

15. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster.

and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

staff and are completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe due to the case’s long

incubation period and radiological findings suggesting more advanced disease despite

11 NRHCC Morning Report 07 September 2020

12 NRHCC Morning Report 03 September 2020

13 NRHCC Morning Report 02 September 2020

14 ARPHS, Waikato DHB and MoH teleconference 1500 31 August 2020

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the 27 August symptom onset date. To date, all contacts tested have received negative

results. Day 12 testing so far have also all returned negative results (See table 4).

8

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1.

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15 NRHCC Email, 0900 09 September 2020

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ESR and wider testing16 16. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).17

17.

18. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

19. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

20.

Contact tracing18 21. Between 31 August and 06 September 100% (45/45) of Community close contacts and

94% (85/90) MIQ close contacts have been contacted within 48 hours of being

determined to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Notes: This metric does not include casual contacts.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 09 September 2020

06/09/2020 07/09/2020 08/09/2020 09/09/2020

Number of close contacts

identified1 3217 3224 3274 3346

16 ESR Whole Genome Sequencing Report 02 September 2020

17 ESR email update 0900 08 September 2020

18 COVID-19 NCCS Analytics and Reporting 0856 09 September 2020

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Number of close contacts

successfully contacted (and are

self-isolating)

3187 3199 3228 3305

Number of close contacts

referred to "finding services"2 4 0 0 0

Number of close contacts

awaiting contact 26 25 46 41

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage19 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

08 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

22. Key Numbers:

o 2,156,400 - Total registered users

o 1,997,361 - QR code scans between 1200 06 and 1200 07 September

19 Response Analyst – Digital Channels, 1617 08 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

20

/05

23

/05

26

/05

29

/05

01

/06

04

/06

07

/06

10

/06

13

/06

16

/06

19

/06

22

/06

25

/06

28

/06

01

/07

04

/07

07

/07

10

/07

13

/07

16

/07

19

/07

22

/07

25

/07

28

/07

31

/07

03

/08

06

/08

09

/08

12

/08

15

/08

18

/08

21

/08

24

/08

27

/08

30

/08

02

/09

05

/09

08

/09

COVID TRACER APP USAGE

Cumulative App registrations Scans and manual entries

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Testing20 Table 6: Testing by functional groups, as at 0900 09 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers21 Table 7: Number of laboratory tests processed nationally as at 0900 08 September 2020

Testing supply update22

23. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

20 ÉCLAIR/MoH Public Health Intelligence, 1015 09 September 2020

21 Daily Lab Report, 0928 09 September 2020

22 Testing supply email, 1001 09 September 2020

Reason for test 08 September 02 – 08 September

GPs and other primary health 2342 20,255

CBACs and pop-ups 2918 25,344

Border workers - air crew 22 205

Border workers - airport staff 94 1267

Border workers - maritime crew 0 4

Border workers – Port of Tauranga staff 3 497

Border workers – Remaining Port staff 9 358

Border workers - MIF 56 1027

Border workers - MIQ 41 203

Travellers - Staying at MIF 363 1966

Travellers - Staying at MIQ 0 194

Total 5848 51,320*

Time period Number of laboratory tests

08 September 8,363

Last 7 days (02 Sep to 08 Sep) 53,957

Total 831,517

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13

Testing activity by region

Focus areas

24. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.23

Healthline updates24 25. On 07 September there were 3,176 contacts in Healthline. Of those calls, 1,349 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 596 contacts (in line with forecast).

26. Work continues to implement the revised testing strategy and how it relates to our

public facing advice – particularly the role we may play in supporting DHB’s around

local asymptomatic testing plans.

27. The main themes yesterday/today:

o Community concern and general anxiety following the announcement of the deaths

over 04 – 05 September.

o Symptomatic Service User’s wanting to be tested.

Logistics

Health Workforce25

28. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

29. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

30. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

23 Community Testing Centres report, 1800 08 September 2020

24 National Telehealth Service Coronavirus Update, 1014 08 September 2020

25 Health Workforce Directorate, 0832 01 September 2020

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Hospital capacity26 Table 8: Number and occupancy of hospital beds by type as at 0800 09 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 354 214 (60.5%)

Ventilators 307 58 (18.9%)

Ward beds 7317 5862 (80.1%)

26 COVID-19 Hospital Summary, 0906 08 September 2020

15

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Appendix 1: Case summary

Table 9: All community cases reported between 0900 08 September and 0900 09 September

s 9(2)(a)

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification18 Data for cases in the community

Indicator (as per Table 9832) Refined Indicator description Target 1-Sep 2-Sep 3 Sept ** 4-Sep 5 Sept ** 6 Sept ** 7 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

0% *

(0/8) 100% - 100% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

0% *

(0/8) 86% - 100% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 100% 100% 100% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

0% *

(0/1)

0% *

(0/2) - 33% 100% 50% -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% 100% 0% *

(0/1) 25%

0% *

(0/1) 20% 75%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 100% 100% 100% - 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

22% 100% 100% 100% - 100% 71%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 100% 100% 100% - 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 0% 0% 0% 0% - 0% 15%

Note: • * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Data for cases in Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 1-Sep 2-Sep** 3 Sept 4-Sep** 5 Sept ** 6 Sept ** 7 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

0% * (0/2)

- 100% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

100% - 0% * (0/3)

- - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 71% 100% 40% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

0% * (0/2)

- 0% * (0/1)

- - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

0% * (0/1)

100% 100% 100% - 0% * (0/2)

100%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 71% 100% 40% - 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% 71% 100% 40% - 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 71% 100% 40% - 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% 0% 67% 0% - 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

18

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APPENDIX: 3

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 08 September 2020

Table 1. Metro Auckland Summary Total of Testing for 08 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1016 75 608 68 10 1777

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-16/08 17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 08/09*

MIQ Staff 2132 659 1488 912 88 75

Guests 2972 3767 3600 3406 483 608

Border Airport 2129 933 1349 1158 153 68

Port 1588 678 161 392 19 10

* 08/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 245 317 562 15.9% 33,057 17.6%

Maori 228 295 523 14.8% 27,135 14.4%

Other 581 840 1421 40.2% 79,484 42.3%

Pacific 459 432 891 25.2% 44,325 23.6%

Unknown 13 129 142 4.0% 4005 2.1%

Total 1526 2013 3539 188,006

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19

Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08 (days

open)

17/08-

23/08

(days

open)

24/08 –

30/08

(days

open)

31/08 –

06/09

07/09 08/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 265 (7) 39 27

Auckland Netball

Centre

192 (1) 1065 (7) 884 (7) 640 (7) 134 N/A

Botany CTC 1151 (5) 948 (7) 905 (7) 749 (7) 145 113

Coast to Coast

Warkworth

334 (5) 109 (7) 70 (7) 35 (7) 17 N/A

Coast to Coast

Wellsford

203 (5) 114 (7) 116 (7) 81 (7) 15 N/A

Eventfinda Stadium 1800 (5) 527 (7) 517 (7) N/A N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 732 (7) 129 58

Henderson 940 (4) 645 (7) 634 (7) 351 (5) N/A N/A

Mangere Town

Centre

1748 (3) 1684 (7) 1599 (7) 860 (7) 144 76

Manurewa Marae N/A 124 (4) 268 (6) 110 (2) N/A N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 741 (7) 57 N/A

Otara CTC 3221 (5) 1712 (7) 1429 (7) 930 (7) 126 100

Pukekohe CTC N/A 131 (4) 226 (6) 298 (6) N/A N/A

St Lukes 1368 (5) 1045 (7) 1414 (7) 797 (7) 99 95

Takanini Urgent Care 1886 (5) 1216 (7) 1153 (7) 684 (7) 92 73

Waiheke Medical

Centre

312 (5) 145 (7) 220 (7) 98 (7) 13 N/A

Whanau House 2502 (5) 1371 (7) 1442 (7) 928 (7) 261 117

Whanau Ora - Central 1957 (5) 964 (7) 1583 (7) 937 (7) 142 104

Whanau Ora - North 1442 (5) 669 (7) 637 (7) 982 (7) 139 101

Whanau Ora - South 2945 (5) 1250 (7) 718 (7) 677 (7) 103 60

Point England Pop

Up

N/A N/A 88 (3) N/A N/A N/A

Randwick Park Pop

Up

N/A N/A 303 (5) N/A N/A N/A

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Ranui Pop Up N/A N/A 409 (5) N/A N/A N/A

Mt Smart Stadium

Pop Up

N/A N/A 219 (3) N/A N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A N/A

South Kaipara Pop

Up

N/A N/A 170 (4) N/A N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A No data

Mangere Pop Up N/A N/A 472 (2) N/A N/A N/A

Mangere East Pop Up N/A N/A 109 (2) N/A N/A N/A

Otara Pop Up N/A N/A 59 (2) N/A N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A N/A

Mt Roskill Pop Up

(330 start)

N/A N/A 217 (2) 164 (3) N/A N/A

Sandringham Pop Up N/A N/A N/A 189 (3) N/A N/A

Ranui League Club

Pop Up

N/A N/A N/A 172 (3) N/A N/A

Glen Eden Pop Up N/A N/A N/A 127 (4) N/A N/A

Southmall Pop Up N/A N/A N/A 291 (3) N/A N/A

Orakei Pop Up N/A N/A N/A 118 (3) N/A N/A

Papatoetoe Pop Up N/A N/A N/A 74 (3) N/A N/A

Te Atatu Pop Up N/A N/A N/A 65 (3) N/A N/A

Mangere East Marae

Pop Up

N/A N/A N/A No Data N/A N/A

Mangere Leagues

Club

N/A N/A N/A No Data N/A N/A

Tamaki College Pop

Up

N/A N/A N/A 109 (2) N/A N/A

Papatoetoe EFKS Pop

Up

N/A N/A N/A 74 (1) N/A N/A

Botany Town Centre

Pop Up

N/A N/A N/A 121 (2) N/A N/A

Sylvia Park Pop Up N/A N/A N/A 21 (2) N/A N/A

East Tamaki Pop Up N/A N/A N/A 161 (1) N/A N/A

Rowandale Pop Up N/A N/A N/A 41 (1) N/A N/A

Henderson EFKS Pop

Up

N/A N/A N/A N/A 43 40

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Mangere Central

Community Hall Pop

Up

N/A N/A N/A N/A N/A 12

Waipuna Targeted

Site

143 (2) 549 (7) 376 (7) 219 (7) 44 34

Blockhouse Bay

Targeted Site

N/A 277 (7) 921 (7) 161 (5) N/A N/A

Henderson Targeted

Site

N/A N/A N/A N/A 6 6

Total 26,148 16,781 21,215 13,002 1631 1016 * 08/09 day still in progress N/A = not open as a CTC

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22

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 09 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3168 6522 8358 18139 319 36506

Bay of Plenty 2351 262 508 5892 55 9068

Canterbury 1480 582 1504 12406 180 16152

Capital and Coast 1321 992 1157 8216 175 11861

Counties Manukau 6658 18481 8072 11516 397 45124

Hawkes Bay 1250 257 189 3237 48 4981

Hutt Valley 697 395 477 2769 37 4375

Lakes 2187 283 436 2981 82 5969

MidCentral 924 240 321 3675 74 5234

Nelson Marlborough 543 141 240 3884 50 4858

Northland 2808 193 235 3728 38 7002

South Canterbury 132 32 72 1568 14 1818

Southern 974 308 611 8734 73 10700

Tairāwhiti 783 51 54 714 17 1619

Taranaki 637 59 142 2392 41 3271

Waikato 4000 947 1273 9177 194 15591

Wairarapa 205 35 32 926 7 1205

Waitematā 4102 4301 6676 22007 274 37360

West Coast 44 8 13 298 6 369

Whanganui 598 68 58 1336 14 2074

Unknown 1315 639 613 3734 1404 7705

Total 36177 34796 31041 127330 3499 232843

23

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 09 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 72.8 116.3 44.7 69.4 66.6

Bay of Plenty 39.3 58.9 25.9 37.4 37.6

Canterbury 28.2 41 24.7 27.8 28.2

Capital and Coast 36.2 44.7 23 38.6 36.9

Counties Manukau 74.8 153.9 53.4 55 79.2

Hawkes Bay 28.9 40 20.6 30 29.8

Hutt Valley 26.7 33.8 25.4 29.4 29

Lakes 56.8 110.8 44.8 49.7 53.9

MidCentral 25.4 43.3 20.7 29.7 28.9

Nelson Marlborough 33.8 57.1 32.3 30.9 32

Northland 46.1 51.3 28.4 34.2 38.5

South Canterbury 24.9 65.5 30.4 30.4 30.4

Southern 29 44.7 23.7 32.6 32.1

Tairāwhiti 31.6 45.6 46.3 32.3 32.9

Taranaki 27.3 42.4 22.8 26.6 27.1

Waikato 41.5 71 28.8 34.1 36.9

Wairarapa 25.7 42.1 25.7 26 26.3

Waitematā 65.5 96.4 46.4 57.6 59

West Coast 11.3 31.7 14.1 11 11.5

Whanganui 34.4 44.7 19.8 31 32

Total 46.5 108.8 40.5 41.1 46.9

1

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SITREP 048

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 10 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

2

MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

92

104

COMMUNITY CASES

ACTIVE

81 TOTAL CASES SINCE 11 AUG

175

39

TOTAL CASES SINCE 9 JUN

143

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 120

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

09 September

7,950

LABORATORY TESTS

03 to 09 Sep

51,386

LABORATORY TESTS

TOTAL

839,467

CASES DECEASED

2

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 10 September 2020

Case Status Active Recovered Deceased Total

Confirmed 120* (-5) 1302 (+9) 19 1441 (+4)

Probable 0 346 5 351

Total 120* (-5) 1648 (+9) 24 1792 (+4)

*Net increase of 4 cases, with 9 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 10 September 20201

New community cases since 0900 09 September 2020

1. Two new community cases have been reported, as at 0900 10 September.

o Both cases have epidemiological links to existing cases and are associated with the

Mt Roskill Evangelical Church sub-cluster. (See 8). Both cases are associated with the

bereavement events.

Community cases linked to the Auckland Community Cluster August 2020

2. 173 of the 175 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 10 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

1 EpiSurv Database, 0900 10 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 76 (+1) 52 (+1) 45 1 174 (+2)

Probable 1 0 0 0 1

Total 77 (+1) 52 (+1) 45 1 175 (+2)

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3

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.2 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 10 September there are 72 people isolating in Jet Park from the community.

56 are confirmed cases, the remaining 16 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.3

MIQ cases since 0900 09 September 2020

5. There have been two new cases4 detected at the border, as at 0900 10 September. In

total 143 cases have been detected at the border since the establishment of

MIFs/MIQs.

o One case returned from India via Fiji on 27 August 2020.

o One case still awaiting further information.

Cases in hospital

6. As at 0800 10 September there are three cases in hospital with COVID-19.5

o One patient on ward at North Shore Hospital.

o

o One patient in Waikato Hospital in ICU.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 10 September 2020

2 ESR WGS report 03 September 2020

3 NRHCC Morning Report, 0900 10 September 2020

4 EpiSurv database, 0900 10 September 2020

5 NRHCC Morning Report 08 September 2020 and COVID-19 Hospital Summary, 0900 08 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Counties Manukau Middlemore 0 0

Waitematā North Shore 1 1

Waikato Waikato 0 1

Total - 1 2

s 9(2)(a)

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Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Overview6

o The recent rate of increase in new cases observed during the last report has stabilised.

There are currently two sub-clusters in which most new community cases are linked to

(Mount Roskill Evangelical Church and Botany sub-cluster). There are currently 43

confirmed cases in the Mount Roskill Evangelical Church sub-cluster and 5 confirmed

cases in the Botany sub-cluster.

Current outbreak investigation priorities7

o Contact tracing and containment around Mount Roskill Evangelical Church sub-cluster

and more recent bereavement events.

o Contact tracing and containment around Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

Sub-clusters and settings of interest

8. On 07 September, a new sub-cluster and exposure event was identified within Mt

Roskill, with an epidemiological link to Mt Roskill Evangelical Church.8 A death (not

COVID-19 related) Between 24 August and 02 September, there

were multiple gatherings associated with the bereavement, the investigation is

ongoing. There is good engagement with the church leadership who are assisting with

the investigation.9

48 people attended the funeral on . All 48 close contacts from the funeral

have been identified, with 43 tested. Eight have tested positive, 27 have tested negative

and eight are pending.

6 ARPHS Strategic Report 09 September 2020

7 ARPHS Strategic Report 31 August 2020

8 ARPHS, Waikato DHB and MoH teleconference 0830 08 September 2020

9 NRHCC Morning report, 0900 10 September 2020

s 9(2)(a)

s 9(2)(a)

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A new setting of interest is St Dominic’s College in Henderson, Auckland. A confirmed

case attended the school.10

The school has been informed and communications

have been sent. The case is linked to new sub-cluster associated with the bereavement

events. A list of all contacts has been gathered by the school. Testing of all school

students and staff is being completed.

ARPHS actions:10

o Maintain positive relationships with Church leaders and liaise with Church members

about their need for financial and welfare support if asked to isolate.

o Scoping new cases.

o Quarantine and testing of household contacts of the new cases. Testing is underway

for household contacts, including repeat testing as needed for people previously

tested from the Mt Roskill church.

o All contacts have been stood down. They are being tested 08 September

and are in isolation.

o Developing and implementing a testing strategy which includes communication with

church leaders around the reason for testing and who should be tested.

9. Contact tracing investigation and testing is ongoing for the Botany sub-cluster.

10. Investigation of settings of interest for the Botany sub-cluster, including casual work

places. More information to come when available.

Case investigation

11. Four cases that have been genomically linked to the main cluster are still being

investigated by ARPHS to identify their epidemiological link to the main cluster.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

12. Investigation into source attribution of the Botany cases infection is continuing. A

possible epidemiological link is being explored between the Botany case and previously

reported cases within another household. The symptom onset dates of the possible

epidemiological linked household are prior to the Botany cases’ symptom onset dates.

Further investigation is underway.10

13. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

staff and are completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe due to the case’s long

10 ARPHS, Waikato DHB and MoH teleconference 0830 08 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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incubation period and radiological findings suggesting more advanced disease despite

the 27 August symptom onset date. To date, all contacts tested have received negative

results. Day 12 testing so far have also all returned negative results (See table 4)

1

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s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

2

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ESR and wider testing11 14. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).12

15.

16. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

17. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

18.

11 ESR Whole Genome Sequencing Report 02 September 2020

12 ESR email update 0900 08 September 2020

s 9(2)(a) s 9(2)(a)

s 9(2)(g)(i)

s 9(2)(g)(i)

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Contact tracing13 19. Between 01 and 07 September 100% (136/136) of Community close contacts and 87%

(33/38) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Notes: This metric does not include casual contacts.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 10 September 2020

07/09/2020 08/09/2020 09/09/2020 10/09/2020

Number of close contacts

identified1 3224 3274 3346 3372

Number of close contacts

successfully contacted (and are

self-isolating)

3199 3228 3305 3354

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 25 46 41 18

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

13 COVID-19 NCCS Analytics and Reporting 0956 10 September 2020

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4

COVID-19 Tracer App usage14 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

09 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20. Key Numbers:

o 2,166,800 - Total registered users

o 2,036,940 - QR code scans between 1200 07 and 1200 08 September

Testing15 Table 6: Testing by functional groups, as at 0900 10 September 2020

14 Response Analyst – Digital Channels, 1617 08 September 2020

15 ÉCLAIR/MoH Public Health Intelligence, 1015 09 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

20

/05

23

/05

26

/05

29

/05

01

/06

04

/06

07

/06

10

/06

13

/06

16

/06

19

/06

22

/06

25

/06

28

/06

01

/07

04

/07

07

/07

10

/07

13

/07

16

/07

19

/07

22

/07

25

/07

28

/07

31

/07

03

/08

06

/08

09

/08

12

/08

15

/08

18

/08

21

/08

24

/08

27

/08

30

/08

02

/09

05

/09

08

/09

COVID TRACER APP USAGE

Cumulative App registrations Scans and manual entries

Reason for test 09 September 03 – 09 September

GPs and other primary health 3768 20842

CBACs and pop-ups 3191 24779

Border workers - air crew 54 237

Border workers - airport staff 140 1259

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*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers16 Table 7: Number of laboratory tests processed nationally as at 0900 10 September 2020

Testing supply update17

21. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

Testing activity by region

Focus areas

22. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.18

Healthline updates19 23. On 09 September there were 2529 contacts in Healthline. Of those calls, 1421 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 719 contacts (slightly above forecast).

16 Daily Lab Report, 0928 09 September 2020

17 Testing supply email, 1001 09 September 2020

18 Community Testing Centres report, 1800 08 September 2020

19 National Telehealth Service Coronavirus Update, 0929 10 September 2020

Border workers - maritime crew 0 39

Border workers – Port of Tauranga staff 0 364

Border workers – Remaining Port staff 30 329

Border workers - MIF 132 1290

Border workers - MIQ 47 301

Travellers - Staying at MIF 587 2174

Travellers - Staying at MIQ 1 123

Total 7950 51737*

Time period Number of laboratory tests

09 September 7,950

Last 7 days (03 Sep to 09 Sep) 51,386

Total 839,467

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24. Work continues to implement the revised testing strategy and how it relates to our

public facing advice – particularly the role we may play in supporting DHB’s around

local asymptomatic testing plans.

25. The main themes yesterday/today:

o Most of the callers are calling because they are symptomatic and want to get a test,

o Calls relating to the latest exposure events,

o Confusion around Alert Level rules (i.e. crowd sizes in Auckland, around the rest of

the country etc) it is recommended to reemphasise this given recent media

confusion.

Logistics

Health Workforce20

26. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

27. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

28. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

Hospital capacity21 Table 8: Number and occupancy of hospital beds by type as at 0800 10 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 347 218 (62.8%)

Ventilators 302 54 (17.9%)

Ward beds 7109 5711 (80.3%)

20 Health Workforce Directorate, 0832 01 September 2020

21 COVID-19 Hospital Summary, 0909 10 September 2020

7

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Appendix 1: Case summary

Table 9: All community cases reported between 0900 09 September and 0900 10 September

s 9(2)(a)

8

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification13 Data for cases in the community

Indicator (as per Table 9832) Refined Indicator description Target 2-Sep 3-Sep 4-Sep 5 Sept ** 6 Sept ** 7 Sept ** 8 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

100% 100% 100% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

86% 100% 100% - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 100% 100% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

0% *

(0/2) 100% 33% 100% 50% 50% -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% 0% *

(0/1) 25%

0% *

(0/1) 20% 75% 80%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 100% 100% - 100% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% 100% 100% - 100% 97% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 100% 100% - 100% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% 0% 0% - 0% 5% 0%

Note: • * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

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9

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

Data for cases in Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 2-Sep ** 3-Sep 4-Sep ** 5 Sept ** 6 Sept ** 7 Sept ** 8 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

- 100% - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

- 0% - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

71% 100% 40% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

- 0% * (0/1)

- - - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% 100% 100% - 0% * (0/2)

100% -

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

71% 100% 40% - 100% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 0% * (0/1)

100% 100% -

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

71% 100% 40% - 100% 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

71% 100% 40% - 100% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% 67% 0% - 0% 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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APPENDIX: 3

NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 09 September 2020

Table 1. Metro Auckland Summary Total of Testing for 09 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1939 173 345 154 39 2650

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and

reported later than this; tests only included if coded and received and acknowledged by lab, result

not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 08/09 09/09*

MIQ Staff 2132 659 1488 912 88 75 173

Guests 2972 3767 3600 3406 483 609 345

Border Airport 2129 933 1349 1158 153 68 154

Port 1588 678 161 392 19 15 39

* 09/09 day still in progress

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 81 448 529 17.2% 33,847 17.6%

Maori 111 361 472 15.4% 27,757 14.4%

Other 270 939 1209 39.3% 81,439 42.3%

Pacific 108 538 646 21.0% 45,187 23.5%

Unknown 19 198 217 7.1% 4231 2.2%

Total 589 2484 3073 192,461

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11

Table 4: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on

manual site reports at 4pm

Site 12/08-

16/08

(days

open)

17/08-

23/08

(days

open)

24/08 –

30/08

(days

open)

31/08 –

06/09

07/09 08/09 09/09*

Airport Oaks 1148 (4) 515 (7) 366 (7) 265 (7) 39 27 39

Auckland Netball

Centre

192 (1) 1065 (7) 884 (7) 640 (7) 134 N/A N/A

Botany CTC 1151 (5) 948 (7) 905 (7) 749 (7) 145 113 107

Coast to Coast

Warkworth

334 (5) 109 (7) 70 (7) 35 (7) 17 N/A N/A

Coast to Coast

Wellsford

203 (5) 114 (7) 116 (7) 81 (7) 15 N/A N/A

Eventfinda

Stadium

1800 (5) 527 (7) 517 (7) N/A N/A N/A N/A

Health New Lynn 2603 (5) 1258 (7) 1703 (7) 732 (7) 129 58 196

Henderson 940 (4) 645 (7) 634 (7) 351 (5) N/A N/A N/A

Mangere Town

Centre

1748 (3) 1684 (7) 1599 (7) 860 (7) 144 76 107

Manurewa Marae N/A 124 (4) 268 (6) 110 (2) N/A N/A N/A

Northcare A&M 253 (2) 463 (7) 527 (7) 741 (7) 57 N/A N/A

Otara CTC 3221 (5) 1712 (7) 1429 (7) 930 (7) 126 100 93

Pukekohe CTC N/A 131 (4) 226 (6) 298 (6) N/A N/A N/A

St Lukes 1368 (5) 1045 (7) 1414 (7) 797 (7) 99 95 117

Takanini Urgent

Care

1886 (5) 1216 (7) 1153 (7) 684 (7) 92 73 63

Waiheke Medical

Centre

312 (5) 145 (7) 220 (7) 98 (7) 13 N/A N/A

Whanau House 2502 (5) 1371 (7) 1442 (7) 928 (7) 261 117 442

Whanau Ora -

Central

1957 (5) 964 (7) 1583 (7) 937 (7) 142 104 139

Whanau Ora -

North

1442 (5) 669 (7) 637 (7) 982 (7) 139 101 174

Whanau Ora -

South

2945 (5) 1250 (7) 718 (7) 677 (7) 103 60 83

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12

Point England Pop

Up

N/A N/A 88 (3) N/A N/A N/A N/A

Randwick Park Pop

Up

N/A N/A 303 (5) N/A N/A N/A N/A

Ranui Pop Up N/A N/A 409 (5) N/A N/A N/A N/A

Mt Smart Stadium

Pop Up

N/A N/A 219 (3) N/A N/A N/A N/A

Massey Pop Up N/A N/A 787 (5) N/A N/A N/A N/A

South Kaipara Pop

Up

N/A N/A 170 (4) N/A N/A N/A N/A

Clendon Pop Up N/A N/A 368 (3) N/A N/A N/A N/A

Mangere Pop Up N/A N/A 472 (2) N/A N/A N/A N/A

Mangere East Pop

Up

N/A N/A 109 (2) N/A N/A N/A N/A

Otara Pop Up N/A N/A 59 (2) N/A N/A N/A N/A

Otahuhu Pop Up N/A N/A 201 (2) N/A N/A N/A N/A

Mt Roskill Pop Up N/A N/A 217 (2) 164 (3) N/A N/A 138

Sandringham Pop

Up

N/A N/A N/A 189 (3) N/A N/A N/A

Ranui League Club

Pop Up

N/A N/A N/A 172 (3) N/A N/A N/A

Glen Eden Pop Up N/A N/A N/A 127 (4) N/A N/A N/A

Southmall Pop Up N/A N/A N/A 291 (3) N/A N/A N/A

Orakei Pop Up N/A N/A N/A 118 (3) N/A N/A N/A

Papatoetoe Pop

Up

N/A N/A N/A 74 (3) N/A N/A N/A

Te Atatu Pop Up N/A N/A N/A 65 (3) N/A N/A N/A

Mangere East

Marae Pop Up

N/A N/A N/A No

Data

N/A N/A N/A

Mangere Leagues

Club

N/A N/A N/A No

Data

N/A N/A N/A

Tamaki College

Pop Up

N/A N/A N/A 109 (2) N/A N/A N/A

Papatoetoe EFKS

Pop Up

N/A N/A N/A 74 (1) N/A N/A N/A

Botany Town

Centre Pop Up

N/A N/A N/A 121 (2) N/A N/A N/A

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13

Sylvia Park Pop Up N/A N/A N/A 21 (2) N/A N/A N/A

East Tamaki Pop

Up

N/A N/A N/A 161 (1) N/A N/A N/A

Rowandale Pop Up N/A N/A N/A 41 (1) N/A N/A N/A

Henderson EFKS

Pop Up

N/A N/A N/A N/A 43 40 No

Data

Mangere Central

Community Hall

Pop Up

N/A N/A N/A N/A N/A 12 30

Waipuna Targeted

Site

143 (2) 549 (7) 376 (7) 219 (7) 44 34 41

Blockhouse Bay

Targeted Site

N/A 277 (7) 921 (7) 161 (5) N/A N/A N/A

Henderson

Targeted Site

N/A N/A N/A N/A 6 6 170

Total 26,148 16,781 21,215 13,002 1748 1102 1939 * 09/09 day still in progress N/A = not open as a CTC () = Days open as a CTC

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14

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 10 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3239 6680 8570 18618 326 37,433

Bay of Plenty 2417 271 525 6063 56 9332

Canterbury 1520 592 1570 12724 190 16,596

Capital and Coast 1359 1034 1215 8530 182 12,320

Counties Manukau 6836 18847 8343 11783 407 46,216

Hawkes Bay 1305 271 197 3354 49 5176

Hutt Valley 728 417 505 2883 38 4571

Lakes 2213 287 442 3033 84 6059

MidCentral 979 247 344 3973 78 5621

Nelson Marlborough 546 142 246 3909 49 4892

Northland 2906 196 241 3829 41 7213

South Canterbury 137 33 75 1597 13 1855

Southern 998 313 629 8975 78 10,993

Tairāwhiti 822 52 56 754 19 1703

Taranaki 650 63 154 2464 41 3372

Waikato 4074 957 1312 9423 200 15,966

Wairarapa 215 35 36 993 7 1286

Waitematā 4243 4476 6905 22644 289 38,557

West Coast 46 8 13 307 6 380

Whanganui 614 72 62 1374 14 2136

Unknown 1334 672 722 3855 1512 8095

Total 37,181 35,665 32,162 131,086 3679 239,773

15

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 10 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 74.5 119.1 45.8 71.2 68.3

Bay of Plenty 40.4 61 26.8 38.5 38.7

Canterbury 29 41.7 25.8 28.5 28.9

Capital and Coast 37.2 46.6 24.2 40.1 38.3

Counties Manukau 76.8 156.9 55.2 56.3 81.2

Hawkes Bay 30.2 42.2 21.5 31 31

Hutt Valley 27.9 35.7 26.9 30.6 30.3

Lakes 57.5 112.3 45.4 50.6 54.7

MidCentral 26.9 44.5 22.2 32.1 31

Nelson Marlborough 34 57.5 33.1 31.1 32.2

Northland 47.8 52.1 29.1 35.1 39.7

South Canterbury 25.8 67.6 31.7 30.9 31

Southern 29.7 45.5 24.4 33.6 32.9

Tairāwhiti 33.2 46.5 48 34.1 34.6

Taranaki 27.8 45.2 24.7 27.4 27.9

Waikato 42.3 71.8 29.7 35 37.7

Wairarapa 27 42.1 28.9 27.8 28.1

Waitematā 67.8 100.4 48 59.2 60.9

West Coast 11.9 31.7 14.1 11.4 11.9

Whanganui 35.4 47.3 21.2 31.9 32.9

Total 47.8 111.5 42 42.3 48.3

1

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SITREP 049

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 11 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

1

MIQ CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

99

104

COMMUNITY CASES

ACTIVE

75 TOTAL CASES SINCE 11 AUG

176

39

TOTAL CASES SINCE 9 JUN

143

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 114

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

10 September

8,953

LABORATORY TESTS

04 to 10 Sep

50,430

LABORATORY TESTS

TOTAL

848,420

CASES DECEASED

2

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 11 September 2020

Case Status Active Recovered Deceased Total

Confirmed 114* (-6) 1309 (+7) 19 1442 (+1)

Probable 0 346 5 351

Total 114* (-6) 1655 (+7) 24 1793 (+1)

*1 new case identified, 7 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 11 September 20201

New community cases since 0900 10 September 20202

1. One new community case has been reported, as at 0900 11 September.

o The case has an epidemiological link to an existing case and is associated with the Mt

Roskill Evangelical Church bereavement sub-cluster.

Community cases linked to the Auckland Community Cluster August 20203

2. 174 of the 176 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 11 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

1 EpiSurv Database, 0900 10 September 2020

2 EpiSurv Database, 0900 11 September 2020

3 EpiSurv Database, 0900 11 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 76 52 46 (+1) 1 175 (+1)

Probable 1 0 0 0 1

Total 77 52 46 (+1) 1 176 (+1)

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3

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.4 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 11 September there are 70 people isolating in Jet Park from the community.

55 are confirmed cases, the remaining 15 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 10 September 20206

5. There have been no new cases detected at the border, as at 0900 11 September. In

total 143 cases have been detected at the border since the establishment of

MIFs/MIQs.

Cases in hospital

6. As at 0800 11 September there are three cases in hospital with COVID-19.7

o New case reported today was admitted to Auckland City Hospital 10 September.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 11 September 2020

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 11 September 2020

6 EpiSurv Database, 0900 11 September 2020

7 NRHCC Morning Report 08 September 2020 and COVID-19 Hospital Summary, 0900 08 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 1

Waikato Waikato 0 1

Total - 1 2

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Figure 1: Daily number of confirmed and probable cases of COVID-19 as at 0900 11 September

Source: NZ COVID-19 Dashboard

Current outbreak overview8

o The recent rate of increase in new cases observed during the last report has stabilised.

There are currently two sub-clusters which most new community cases are linked to

(Mount Roskill Evangelical Church and Botany sub-clusters). There are currently 43

confirmed cases in the Mount Roskill Evangelical Church sub-cluster and 5 confirmed

cases in the Botany sub-cluster.

Current outbreak investigation priorities9

o Contact tracing and containment around Mount Roskill Evangelical Church sub-cluster

and more recent bereavement events.

o Contact tracing and containment around Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

8 ARPHS Strategic Report 09 September 2020

9 ARPHS Strategic Report 09 September 2020

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5

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

Sub-clusters and settings of interest

A new sub-cluster and exposure events were identified (on 7 September) within Mt

Roskill with epidemiological links to Mt Roskill Evangelical Church sub-cluster.10 A death

(not COVID-19 related) . Between 24 August and 2 September,

there were multiple gatherings associated with the bereavement including the funeral

on . There were multiple other exposure events associated with the

bereavement. The investigation is ongoing. There is good engagement with the church

leadership who are assisting with the investigation.11

48 people attended the funeral on . All 48 close contacts from the funeral

have been identified, with 4612 tested. A mobile testing service has been arranged to

test the remaining two contacts.12 10 have tested positive, 35 have tested negative and

one is pending.5 As of 0800 11 September, of 332 Mt Roskill Evangelical Church

members 273 have been tested. Five have tested positive, 245 have tested negative and

23 are pending.5

A new sub-cluster has been created for cases associated with the bereavement events

to include cases whose source of infection occurred at the bereavement events. Within

this sub-cluster there are 13 cases and 33 cases remain in the Mt Roskill Evangelical

Church sub-cluster.5

8. A new setting of interest, St Dominic’s College in Henderson, Auckland, was identified

on 8 September. A confirmed case attended the school.13

. The school has

been informed and communications have been sent. The case is linked to the new sub-

cluster associated with the bereavement events. A list of all contacts has been gathered

by the school. Testing of all school students and staff is in progress with approximately

500 tested as at 1500 10 September.14 There are also 87 students and 11 teachers

identified as close contacts. As of 0800 11 September, of these 98 people, 63 have been

tested with 47 returning negative results so far.5

ARPHS actions:13

o Maintain positive relationships with Church leaders and liaise with Church members

about their need for financial and welfare support if asked to isolate.

o Scope new cases.

o Quarantine and test household contacts of the new cases. Testing is underway for

household contacts, including repeat testing as needed for people previously tested

from the Mt Roskill church.

10 ARPHS, Waikato DHB and MoH teleconference 0830 08 September 2020

11 NRHCC Morning report, 0900 10 September 2020

12 NRHCC Morning report, 0900 11 September 2020

13 ARPHS, Waikato DHB and MoH teleconference 0830 08 September 2020

14 ARPHS, Waikato DHB and MoH teleconference 1500 10 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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6

o All contacts have been stood down. They were being tested on 8

September and are in isolation.

o Develop and implement a testing strategy which includes communication with

church leaders around the reason for testing and who should be tested.

9. The Botany sub-cluster is still being investigated to determine the index case. As at 9

September no clear epidemiological link had been identified. The first case detected is

not the index case in this community. Source investigation is ongoing but there are

indications that the earliest symptom onset is around 3 August (based on a family

member with positive serology and earlier influenza-like-illness). Whole genome

sequencing results from 30 August showed a link back to the Americold sequences.15

Case investigation

10. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

11. The case in Tokoroa reported on 29 August is a contact of an existing case from

Tokoroa who is linked to the Auckland cluster. The case works at a medical centre in

Tokoroa and it is believed they had contact with the existing case

The centre has had a final deep clean and has reopened with reduced

staff and are completing most consultations virtually. Contact tracing is being

completed back to 20 August. This is a precautionary timeframe due to the case’s long

incubation period and radiological findings suggesting more advanced disease despite

the 27 August symptom onset date. To date, all contacts tested have received negative

results. Day 12 testing so far have also all returned negative results.

15 COVID-19 Auckland Outbreak II Strategic report 09 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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s 9(2)(a)

s 9(2)(a)

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ESR and wider testing16 12. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).17

13.

14. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

15. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

16.

Contact tracing18 17. Since the 11 August, 3623 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 3608 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest. Please note that the

total number and number successfully contacted can decrease due to records being

marked as invalid in the system.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 11 September 2020

08/09/2020 09/09/2020 10/09/2020 11/09/2020

Number of close contacts

identified1 3274 3346 3372 3623

Number of close contacts

successfully contacted (and are

self-isolating)

3228 3305 3354 3608

16 ESR Whole Genome Sequencing Report 02 September 2020

17 ESR email update 0900 08 September 2020

18 COVID-19 NCCS Analytics and Reporting 0956 10 September 2020

s 9(2)(a) s 9(2)(a)

s 9(2)(g)(i)

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9

Number of close contacts

referred to "finding services"2 0 0 0 3

Number of close contacts

awaiting contact 46 41 18 12

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing Unit or the Public Health Units. Contacts from MIQ and overseas cases are not

included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close contacts we do not have the correct contact details for. These services utilise

internal Ministry of Health databases along with Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from the system.

COVID-19 Tracer App usage19 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

10 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

19 Response Analyst – Digital Channels, 1617 08 September 2020

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10

Testing20 Table 6: Testing by functional groups, as at 0900 10 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers21 Table 7: Number of laboratory tests processed nationally as at 0900 11 September 2020

Testing supply update22

18. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

20 ÉCLAIR/MoH Public Health Intelligence, 1015 09 September 2020

21 Daily Lab Report, 0932 10 September 2020

22 Testing supply email, 1001 09 September 2020

Reason for test 09 September 03 – 09 September

GPs and other primary health 3768 20842

CBACs and pop-ups 3191 24779

Border workers - air crew 54 237

Border workers - airport staff 140 1259

Border workers - maritime crew 0 39

Border workers – Port of Tauranga staff 0 364

Border workers – Remaining Port staff 30 329

Border workers - MIF 132 1290

Border workers - MIQ 47 301

Travellers - Staying at MIF 587 2174

Travellers - Staying at MIQ 1 123

Total 7950 51737*

Time period Number of laboratory tests

10 September 8953

Last 7 days (04 Sep to 10 Sep) 50,430

Total 848,420

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Testing activity by region

Focus areas

19. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.23

Healthline updates24 20. On 10 September there were 2520 contacts in Healthline. Of those calls, 1246 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 719 contacts (16% higher than forecast).

21. On 10 September the new scripts to support the testing strategy went live with staff

being briefed on them. This followed clarification and consultation with the Ministry of

Health over 07 – 09 September on how a phone-based service should support the new

strategy.

22. The main themes yesterday/today:

o Most of the callers are calling because they are symptomatic and want to get a test,

o Calls relating to the latest exposure events,

o Confusion around Alert Level rules (i.e. crowd sizes in Auckland, around the rest of

the country etc) it is recommended to reemphasise this given recent media

confusion.

Logistics

Health Workforce25

23. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

24. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

25. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

23 Community Testing Centres report, 1800 08 September 2020

24 National Telehealth Service Coronavirus Update, 0914 11 September 2020

25 Health Workforce Directorate, 0832 01 September 2020

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12

Hospital capacity26 Table 8: Number and occupancy of hospital beds by type as at 0800 11 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 343 219 (63.8%)

Ventilators 305 61 (20.0%)

Ward beds 6968 5567 (79.9%)

26 COVID-19 Hospital Summary, 0927 11 September 2020

13

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Appendix 1: Case summary

Table 9: All community cases reported between 0900 10 September and 0900 11 September

s 9(2)(a)

14

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification18 Data for cases in the community

Indicator (as per Table 9832) Refined Indicator description Target 2-Sep 3-Sep 4-Sep 5 Sept ** 6 Sept ** 7 Sept ** 8 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

100% 100% 100% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

86% 100% 100% - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 100% 100% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

0% *

(0/2) 100% 33% 100% 50% 50% -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% 0% *

(0/1) 25%

0% *

(0/1) 20% 75% 80%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 100% 100% - 100% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% 100% 100% - 100% 97% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 100% 100% - 100% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% 0% 0% - 0% 5% 0%

Note: • * The numerator and denominator are provided in some instances to provide context for low percentages.

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15

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

Data for cases in Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 2-Sep ** 3-Sep 4-Sep ** 5 Sept ** 6 Sept ** 7 Sept ** 8 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

- 100% - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

- 0% - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

71% 100% 40% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

- 0% * (0/1)

- - - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% 100% 100% - 0% * (0/2)

100% -

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

71% 100% 40% - 100% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 0% * (0/1)

100% 100% -

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

71% 100% 40% - 100% 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

71% 100% 40% - 100% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% 67% 0% - 0% 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

16

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 10 September 2020

Table 1. Metro Auckland Summary Total of Testing for 09 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 2217 195 534 138 23 3107

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and reported later than

this; tests only included if coded and received and acknowledged by lab, result not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 08/09 09/09 10/09*

MIQ Staff 2132 659 1488 912 88 75 251 195

Guests 2972 3767 3600 3406 483 609 345 534

Border Airport 2129 933 1349 1158 153 68 154 138

Port 1588 678 161 392 19 15 39 23

* 10/09 day still in progress

Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site

reports at 4pm

The number of mobile testing sites change frequently please see

https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information.

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 335 268 603 19.8% 35,034 17.7%

Maori 282 166 448 14.7% 28,506 14.4%

Other 621 517 1138 37.5% 83,569 42.2%

Pacific 471 246 687 22.6% 46,420 23.4%

Unknown 38 124 162 5.3% 4425 2.2%

Total 1747 1291 3038 197,954

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17

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 10: Number of people tested for COVID-19 from 12 August to 10 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3239 6680 8570 18618 326 37,433

Bay of Plenty 2417 271 525 6063 56 9332

Canterbury 1520 592 1570 12724 190 16,596

Capital and Coast 1359 1034 1215 8530 182 12,320

Counties Manukau 6836 18847 8343 11783 407 46,216

Hawkes Bay 1305 271 197 3354 49 5176

Hutt Valley 728 417 505 2883 38 4571

Lakes 2213 287 442 3033 84 6059

MidCentral 979 247 344 3973 78 5621

Nelson Marlborough 546 142 246 3909 49 4892

Northland 2906 196 241 3829 41 7213

South Canterbury 137 33 75 1597 13 1855

Southern 998 313 629 8975 78 10,993

Tairāwhiti 822 52 56 754 19 1703

Taranaki 650 63 154 2464 41 3372

Waikato 4074 957 1312 9423 200 15,966

Wairarapa 215 35 36 993 7 1286

Waitematā 4243 4476 6905 22644 289 38,557

West Coast 46 8 13 307 6 380

Whanganui 614 72 62 1374 14 2136

Unknown 1334 672 722 3855 1512 8095

Total 37,181 35,665 32,162 131,086 3679 239,773

18

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Table 11: Rate per 1000 people tested for COVID-19 from 12 August to 10 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 74.5 119.1 45.8 71.2 68.3

Bay of Plenty 40.4 61 26.8 38.5 38.7

Canterbury 29 41.7 25.8 28.5 28.9

Capital and Coast 37.2 46.6 24.2 40.1 38.3

Counties Manukau 76.8 156.9 55.2 56.3 81.2

Hawkes Bay 30.2 42.2 21.5 31 31

Hutt Valley 27.9 35.7 26.9 30.6 30.3

Lakes 57.5 112.3 45.4 50.6 54.7

MidCentral 26.9 44.5 22.2 32.1 31

Nelson Marlborough 34 57.5 33.1 31.1 32.2

Northland 47.8 52.1 29.1 35.1 39.7

South Canterbury 25.8 67.6 31.7 30.9 31

Southern 29.7 45.5 24.4 33.6 32.9

Tairāwhiti 33.2 46.5 48 34.1 34.6

Taranaki 27.8 45.2 24.7 27.4 27.9

Waikato 42.3 71.8 29.7 35 37.7

Wairarapa 27 42.1 28.9 27.8 28.1

Waitematā 67.8 100.4 48 59.2 60.9

West Coast 11.9 31.7 14.1 11.4 11.9

Whanganui 35.4 47.3 21.2 31.9 32.9

Total 47.8 111.5 42 42.3 48.3

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1

SITREP 050

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 12 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

2

MIQ CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

106

105

COMMUNITY CASES

ACTIVE

70 TOTAL CASES SINCE 11 AUG

178

38

TOTAL CASES SINCE 9 JUN

143

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 108

MIQ CASES

TOTAL RECOVERED

MIQ CASES

ACTIVE

LABORATORY TESTS

11 September

8,838

LABORATORY TESTS

05 to 11 Sep

49,789

LABORATORY TESTS

TOTAL

857,258

CASES DECEASED

2

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 12 September 2020

Case Status Active Recovered Deceased Total

Confirmed 108* (-6) 1317 (+8) 19 1444 (+2)

Probable 0 346 5 351

Total 108* (-6) 1663 (+8) 24 1795 (+2)

*2 new case identified, 8 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 12 September 20201

New community cases since 0900 11 September 20202

1. Two new community case has been reported, as at 0900 12 September.

o Both cases have an epidemiological link to an existing case and are associated with

the Mt Roskill Evangelical Church bereavement sub-cluster.

Community cases linked to the Auckland Community Cluster August 20203

2. 176 of the 178 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 12 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

1 EpiSurv Database, 0900 10 September 2020

2 EpiSurv Database, 0900 11 September 2020

3 EpiSurv Database, 0900 11 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 76 54 (+2) 46 1 177 (+2)

Probable 1 0 0 0 1

Total 77 54 (+2) 46 1 178 (+2)

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3

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. Subsequently the case tested positive on

21 August after being swabbed at a mobile testing clinic in Auckland. Despite using

two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.4 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 12 September there are 63 people isolating in Jet Park from the community.

47 are confirmed cases, the remaining 16 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 12 September 20206

5. There have been no new cases detected at the border, as at 0900 12 September. In

total 143 cases have been detected at the border since the establishment of

MIFs/MIQs.

Cases in hospital

6. As at 0800 11 September there are three cases in hospital with COVID-19.7

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 12 September 2020

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 12 September 2020

6 EpiSurv Database, 0900 12 September 2020

7 NRHCC Morning Report 12 September 2020 and COVID-19 Hospital Summary, 0900 12 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 1

Waikato Waikato 0 1

Total - 1 2

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview8

o The recent rate of increase in new cases observed during the last report has stabilised.

There are currently two sub-clusters which most new community cases are linked to

(Mount Roskill Evangelical Church and Botany sub-clusters). There are currently 43

confirmed cases in the Mount Roskill Evangelical Church sub-cluster and 5 confirmed

cases in the Botany sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment around Mount Roskill Evangelical Church sub-cluster

and more recent bereavement events.

o Contact tracing and containment around Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

Sub-clusters and settings of interest9

8. New exposure events were identified (on 7 September) within Mt Roskill with

epidemiological links to Mt Roskill Evangelical Church sub-cluster. Between 24 August

and 2 September there were multiple gatherings associated with bereavement of a

(non COVID-19 related) death, including a funeral on

9. A new sub-cluster has been created to include cases whose source of infection

occurred at the bereavement events. There are 15 cases in the bereavement sub-cluster

and 33 cases remain in the Mt Roskill Evangelical Church sub-cluster.

10. 47 people attended the funeral on . Everyone who visited the households

during bereavement events are also on the funeral list. 46 of the 47 have been tested.

10 have tested positive, 32 have tested negative and four are pending. 10

8 ARPHS Strategic Report 08 September 2020

9 ARPHS Strategic Report 08 September 2020

10 NRHCC Morning Report 12 September 2020

s 9(2)(a)

s 9(2)(a)

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5

11. St Dominic’s College in Henderson, Auckland, was identified as a setting of interest on 8

September. A confirmed case linked to the bereavement sub-cluster

The school has

been informed and communications have been sent. A list of contacts has been

gathered by the school and includes 87 students and 11 teachers. As of 0800 12

September, 80 of the students have been tested with 1 positive result, 62 negative, and

17 results pending. All 11 of the teachers have tested negative.11 Testing of the wider

school community is ongoing with 1,399 people tested so far. 1,371 results are negative

and 28 results pending as at 1800 11 September.12

12. One of the cases that attended the funeral worked as a bus driver for two days while

infectious but pre-symptomatic. wore a facemask and had 2m distance from

passengers due to AT policy. A contact tracing exercise based on HOP card data is

ongoing.

o There were 293 individuals who rode these routes on 03/09 and 04/09, all of whom

are casual contacts. No individual rode the bus for more than two hours cumulatively

over these two days.

o There are two close contacts, they are in self-isolation.

13. As of 0800 12 September, of the 311 Mt Roskill Evangelical Church members 304 have

been tested. 4 have tested positive, 270 have tested negative and 30 are pending.

14. All five of the confirmed cases in the Botany sub-cluster were in Jet Park but have been

released. Two workplaces associated with the cases have been identified and close

contacts have been scoped. Three at one of the of a case

are close contacts and have been stood down, self-isolated, and tested negative. All

three have been released from isolation. One case is a and no close

contacts were identified at the second workplace. Four members of one of the families

in the sub-cluster has had serology testing on 11 September, results are pending.

15. ARPHS actions:13

o Maintain positive relationships with Church leaders and liaise with Church members

about their need for financial and welfare support if asked to isolate.

o Scope new cases.

o Quarantine and test household contacts of the new cases. Testing is underway for

household contacts, including repeat testing as needed for people previously tested

from the Mt Roskill church.

o Develop and implement a testing strategy which includes communication with

church leaders around the reason for testing and who should be tested.

o MoH have signed off on two medical officers of health to support ARPHS.

Case investigation

11 RHCC Morning Report 12 September 2020

12 ARPHS email 1800 11 September 2020

13 ARPHS Strategic Report 08 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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6

16. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing.

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

Self-isolation compliance14

17. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

o Engagement of the kaimanaaki workforce (community champions employed by our

Maaori providers in the community). Kaimanaaki have access to clinical

support/advice. Development of an implementation plan in progress. The aim of

kaimanaaki is to support and enable whaanau wellbeing through the pandemic. They

have specific skills to help whaanau cope with isolation. They are also trained in the

use of PPE so would be able to do house visits and/or contact whaanau by phone for

the duration of their isolation. Daily contact would be anticipated and kaimanaaki

would report back to the DHB/public health officials on a daily basis

14 ADHB Email, 100 11 September 2020

s 9(2)(a)

s 9(2)(a)

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s 9(2)(a)s 9(2)(a)

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s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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ESR and wider testing15 18. ESR now has an arrangement in place with Massey University for genome sequencing.

ESR will still validate all results, however this arrangement is predicted to speed up

genome testing.

19. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).16

20.

21. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

22. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

23.

Contact tracing17 24. Between 03 and 09 September 89% (352/394) of Community close contacts and 82%

(14/17) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0900 11 September 2020

09/09/2020 10/09/2020 11/09/2020 12/09/2020

Number of close contacts

identified1 3346 3372 3623 3647

15 ESR Whole Genome Sequencing Report 02 September 2020, Email 1859 11 September 2020

16 ESR email update 0900 08 September 2020

17 COVID-19 NCCS Analytics and Reporting 0906 12 September 2020

s 9(2)(a) s 9(2)(a)

s 9(2)(g)(i)

s 9(2)(g)(i)

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10

Number of close contacts

successfully contacted (and are

self-isolating)

3305 3354 3608 3640

Number of close contacts

referred to "finding services"2 0 0 3 0

Number of close contacts

awaiting contact 41 18 12 7

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation

and Tracing Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this

report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details

for close contacts we do not have the correct contact details for. These services utilise internal Ministry of Health

databases along with Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being

removed from the system.

COVID-19 Tracer App usage18 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

11 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

18 Response Analyst – Digital Channels, 1621 11 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

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06

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06

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04/

07

07/

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07

22/

07

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08

09/

08

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27/

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30/

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11/

09

Usa

ge

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing19 Table 6: Testing by functional groups, as at 0900 12 September 2020

3. *Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers20 Table 7: Number of laboratory tests processed nationally as at 0900 12 September 2020

Testing supply update21

25. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

19 ÉCLAIR/MoH Public Health Intelligence, 1000 12 September 2020

20 Daily Lab Report, 0807 12 September 2020

21 Testing supply email, 1001 09 September 2020

Reason for test 11 September 05 – 11 September

GPs and other primary health 3899 19975

CBACs and pop-ups 3994 24444

Border workers - air crew 34 222

Border workers - airport staff 202 1024

Border workers - maritime crew 0 1

Border workers – Port of Tauranga staff 6 127

Border workers – Remaining Port staff 59 266

Border workers - MIF 110 1076

Border workers - MIQ 109 294

Travellers - Staying at MIF 356 2242

Travellers - Staying at MIQ 69 78

Total 8838 49749

Time period Number of laboratory tests

11 September 8838

Last 7 days (05 Sep to 11 Sep) 49,789

Total 857,258

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12

Testing activity by region

Focus areas

26. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.22

Healthline updates23 27. On 11 September there were 2,249 contacts in Healthline. Of those calls, 1,015 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 623 contacts (slightly lower than forecast).

28. The main themes yesterday/today:

o Most of the callers are calling because they are symptomatic and want to get a test,

o Calls relating to the latest exposure events,

o Confusion around Alert Level rules (i.e. crowd sizes in Auckland, around the rest of

the country etc) it is recommended to reemphasise this given recent media

confusion.

Logistics

Health Workforce24

29. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

30. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

31. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

22 Community Testing Centres report, 1800 08 September 2020

23 National Telehealth Service Coronavirus Update, 0932 12 September 2020

24 Health Workforce Directorate, 0832 01 September 2020

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13

Hospital capacity25 Table 8: Number and occupancy of hospital beds by type as at 0800 12 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 325 185 (56.9%)

Ventilators 265 46 (17.4%)

Ward beds 6541 5075 (77.6%)

25 COVID-19 Hospital Summary, 1012 12 September 2020

14

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Appendix 1: Case summary

Table 5: All community cases reported between 0900 11 September and 0900 12 September

s 9(2)(a)

15

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification17 Table 6: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 4 Sept 5 Sept ** 6 Sept 7 Sept 8 Sept ** 9 Sept ** 10 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours

100% - 100% 30% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours

100% - 0% *

(0/2) 77% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

73% - 100% 82% 4% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours

33% 100% 50% 50% 33% 0% *

(0/1) -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours

25% 0% *

(0/1) 20% 75% 80%

0% *

(0/2) 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours

73% - 100% 93% 88% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours

82% - 100% 96% 97% 100% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% - 100% 98% 88% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 0% - 0% 4% 1% 0% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

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16

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

Table 7 NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 4 Sept 5 Sept ** 6 Sept 7 Sept 8 Sept ** 9 Sept ** 10 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

- - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

- - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

40% - 100% 100% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

- - - - - 0% * (0/1)

-

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% - 0% * (0/2)

100% - 100% -

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

40% - 100% 100% - 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% - 100% 100% - 100% -

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

40% - 100% 100% - 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

40% - 100% 100% - 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% - 0% 0% - 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 11 September 2020

Table 1. Metro Auckland Summary Total of Testing for 11 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1294 256 342 141 34 2067

Table 2. Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and reported later than

this; tests only included if coded and received and acknowledged by lab, result not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 3. Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 08/09 09/09 10/09 11/09*

MIQ Staff 2132 659 1488 912 88 75 251 195 221

Guests 2972 3767 3600 3406 483 609 345 534 342

Border Airport 2129 933 1349 1158 153 68 154 138 141

Port 1588 678 161 392 19 15 39 23 34

* 11/09 day still in progress

Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site

reports at 4pm

The number of mobile testing sites change frequently please see

https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information.

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 373 494 867 21.4% 36,126 17.8%

Maori 253 287 540 13.3% 29,163 14.3%

Other 696 878 1574 38.8% 85,897 42.3%

Pacific 461 432 893 22.0% 47,480 23.4%

Unknown 25 157 182 4.5% 4595 2.3%

Total 1808 2248 4056 203,261

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18

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed. There is an error in the source data and these

results are from 12 August to 10 September. This is being rectified and the below table will be

updated when this has been corrected.

Table 8: Number of people tested for COVID-19 from 12 August to 10 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3239 6680 8570 18618 326 37,433

Bay of Plenty 2417 271 525 6063 56 9332

Canterbury 1520 592 1570 12724 190 16,596

Capital and Coast 1359 1034 1215 8530 182 12,320

Counties Manukau 6836 18847 8343 11783 407 46,216

Hawkes Bay 1305 271 197 3354 49 5176

Hutt Valley 728 417 505 2883 38 4571

Lakes 2213 287 442 3033 84 6059

MidCentral 979 247 344 3973 78 5621

Nelson Marlborough 546 142 246 3909 49 4892

Northland 2906 196 241 3829 41 7213

South Canterbury 137 33 75 1597 13 1855

Southern 998 313 629 8975 78 10,993

Tairāwhiti 822 52 56 754 19 1703

Taranaki 650 63 154 2464 41 3372

Waikato 4074 957 1312 9423 200 15,966

Wairarapa 215 35 36 993 7 1286

Waitematā 4243 4476 6905 22644 289 38,557

West Coast 46 8 13 307 6 380

Whanganui 614 72 62 1374 14 2136

Unknown 1334 672 722 3855 1512 8095

Total 37,181 35,665 32,162 131,086 3679 239,773

19

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Table 9: Rate per 1000 people tested for COVID-19 from 12 August to 10 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 74.5 119.1 45.8 71.2 68.3

Bay of Plenty 40.4 61 26.8 38.5 38.7

Canterbury 29 41.7 25.8 28.5 28.9

Capital and Coast 37.2 46.6 24.2 40.1 38.3

Counties Manukau 76.8 156.9 55.2 56.3 81.2

Hawkes Bay 30.2 42.2 21.5 31 31

Hutt Valley 27.9 35.7 26.9 30.6 30.3

Lakes 57.5 112.3 45.4 50.6 54.7

MidCentral 26.9 44.5 22.2 32.1 31

Nelson Marlborough 34 57.5 33.1 31.1 32.2

Northland 47.8 52.1 29.1 35.1 39.7

South Canterbury 25.8 67.6 31.7 30.9 31

Southern 29.7 45.5 24.4 33.6 32.9

Tairāwhiti 33.2 46.5 48 34.1 34.6

Taranaki 27.8 45.2 24.7 27.4 27.9

Waikato 42.3 71.8 29.7 35 37.7

Wairarapa 27 42.1 28.9 27.8 28.1

Waitematā 67.8 100.4 48 59.2 60.9

West Coast 11.9 31.7 14.1 11.4 11.9

Whanganui 35.4 47.3 21.2 31.9 32.9

Total 47.8 111.5 42 42.3 48.3

1

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SITREP 051

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 13 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

1

IMPORTED MIQ

CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

119

105

COMMUNITY CASES

ACTIVE

58 TOTAL CASES SINCE 11 AUG

179

39

TOTAL IMPORTED MIQ CASES

144

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 97

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

12 September

7,211

LABORATORY TESTS

06 to 12 Sep

49,831

LABORATORY TESTS

TOTAL

864,469

CASES DECEASED

2

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 13 September 2020

Case Status Active Recovered Deceased Total

Confirmed 97* (-11) 1330 (+13) 19 1446 (+2)

Probable 0 346 5 351

Total 97* (-11) 1676 (+13) 24 1797 (+2)

*2 new case identified, 13 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 13 September 20201

New community cases since 0900 12 September 20202

1. One new community case has been reported, as at 0900 13 September.

o The case is a health worker at a quarantine facility in Auckland.

Community cases linked to the Auckland Community Cluster August 20203

2. 177 of the 179 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 13 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. The case subsequently tested positive

1 EpiSurv Database, 0900 10 September 2020

2 EpiSurv Database, 0900 11 September 2020

3 EpiSurv Database, 0900 11 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 76 55 (+1) 46 1 178 (+1)

Probable 1 0 0 0 1

Total 77 55 (+1) 46 1 179 (+1)

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3

on 21 August after being swabbed at a mobile testing clinic in Auckland. Despite

using two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.4 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 13 September there are 63 people isolating in Jet Park from the community.

38 are confirmed cases, the remaining 25 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 12 September 20206

5. There has been one new case detected at the border, as at 0900 13 September. In total

144 cases have been detected at the border since the establishment of MIFs/MIQs.

o The case arrived from South Africa on 08 September and is in managed isolation in

Canterbury.

Cases in hospital

6. As at 0800 11 September there are three cases in hospital with COVID-19.7

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 13 September 2020

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 13 September 2020

6 EpiSurv Database, 0900 13 September 2020

7 NRHCC Morning Report 13 September 2020 and COVID-19 Hospital Summary, 0900 12 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 1

Waikato Waikato 0 1

Total - 1 2

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4

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview8

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment of Mount Roskill Evangelical Church sub-cluster and

recent bereavement events.

o Contact tracing and containment of Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

o Waikato PHU will scope any positive cases in MIFs in the Auckland region for the next

week to alleviate some workload pressure at ARPHS.

Sub-clusters and settings of interest9

8. The new case in the community reported today is a healthcare worker in a quarantine

facility. The swab is being transported to ESR this morning for whole genome

sequencing on Monday 14 September. Scoping by ARPHS is underway to identify close

and casual contacts. The case is isolating at Jet Park facility. The case has three

household close contacts who are self-isolating at home. All staff at the quarantine

facility will be tested and staff who are considered close contacts have been stood

down. CCTV footage at the facility will be reviewed as part of the scoping process.

Community contact tracing is underway.10

9. On 7 September several exposure events were identified with epidemiological links to

Mt Roskill Evangelical Church sub-cluster. Between 24 August and 2 September there

were multiple gatherings associated with bereavement of a (non COVID-19 related)

death, including a funeral

10. A sub-cluster has been created to include cases whose source of infection occurred at

the bereavement events. There are 15 cases in the bereavement sub-cluster and 33

cases in the Mt Roskill Evangelical Church sub-cluster.

11. St Dominic’s College in Henderson, Auckland, was identified as a setting of interest on 8

September. A confirmed case linked to the bereavement sub-cluster

The school has

8 ARPHS Strategic Report 08 September 2020

9 ARPHS Strategic Report 08 September 2020

10 ARPHS text 1000 13 September 2020

s 9(2)(a)

s 9(2)(a)

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5

been informed and communications have been sent. A list of contacts has been

gathered by the school and includes 87 students and 11 teachers.11

12. A confirmed case linked to the bereavement sub-cluster worked as a bus driver for two

days while infectious but pre-symptomatic. wore a facemask and had 2m distance

from passengers due to AT policy. A contact tracing exercise based on HOP card data is

ongoing.

o 293 individuals rode these routes on 3 and 4 September, all of whom are casual

contacts. No individual rode the bus for more than two hours cumulatively over

these two days.

o There are two close contacts, they are in self-isolation.

13. All five of the confirmed cases in the Botany sub-cluster were in Jet Park but have been

released. Two workplaces associated with the Botany cases have been identified and

close contacts have been scoped. Three at one of the of a

case are close contacts and had been stood down, self-isolated, and tested negative. All

three have since been released from isolation. The second is related to a

case who is a and no close contacts were identified. Four members of one

of the families in the sub-cluster have had serology testing on 11 September, results

are pending.

14. ARPHS actions:12

o Maintain positive relationships with Church leaders and liaise with Church members

about their need for financial and welfare support if asked to isolate.

o Scope new cases.

o Quarantine and test household contacts of the new cases. Testing is underway for

household contacts, including repeat testing as needed for people previously tested

from the Mt Roskill church.

o Develop and implement a testing strategy which includes communication with

church leaders around the reason for testing and who should be tested.

o MoH have signed off on two medical officers of health to support ARPHS.

Case investigation

15. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

11 ARPHS email 1800 11 September 2020

12 ARPHS Strategic Report 08 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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o The Botany case

Self-isolation compliance13

16. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

o Engagement of the Kaimanaaki workforce (community champions employed by our

Maaori providers in the community). Kaimanaaki have access to clinical

support/advice. And will support and enable whaanau wellbeing through the

pandemic. They have specific skills to help whaanau cope with isolation. They are

also trained in the use of PPE so can make house visits and/or contact whaanau by

phone for the duration of their isolation. Daily contact is anticipated and Kaimanaaki

will report back to the DHB/public health officials on a daily basis. An

implementation plan is being developed and will be stood up from Monday.

13 ADHB Email, 1000 11 September 2020

7

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s 9(2)(a)

s 9(2)(a)

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8

s 9(2)(a)

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9

s 9(2)(a)

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ESR and wider testing14 17. ESR now has an arrangement in place with Massey University for genome sequencing.

ESR will still validate all results, however this arrangement is predicted to speed up

genome testing.

18. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).15

19.

20. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

21. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

22.

Contact tracing16 23. Between 04 and 10 September 86% (357/413) of Community close contacts and 79%

(11/14) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0900 11 September 2020

10/09/2020 11/09/2020 12/09/2020 13/09/2020

Number of close contacts

identified1 3372 3623 3647 3664

14 ESR Whole Genome Sequencing Report 02 September 2020, Email 1859 11 September 2020

15 ESR email update 0900 08 September 2020

16 COVID-19 NCCS Analytics and Reporting 0909 13 September 2020

s 9(2)(a) s 9(2)(a)

s 9(2)(g)(i)

s 9(2)(g)(i)

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11

Number of close contacts

successfully contacted (and are

self-isolating)

3354 3608 3640 3650

Number of close contacts

referred to "finding services"2 0 3 0 0

Number of close contacts

awaiting contact 18 12 7 14

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation

and Tracing Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this

report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details

for close contacts we do not have the correct contact details for. These services utilise internal Ministry of Health

databases along with Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being

removed from the system.

COVID-19 Tracer App usage17 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1045

12 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

17 Response Analyst – Digital Channels, 1056 12 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

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07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

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08

24/

08

27/

08

30/

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02/

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05/

09

08/

09

11/

09

Usa

ge

Day and month

Cumulative App registrations Daily scans and manual entries

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12

Testing18 Table 6: Testing by functional groups, as at 0900 13 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 7: Number of laboratory tests processed nationally as at 0900 13 September 2020

Testing supply update20

24. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

18 ÉCLAIR/MoH Public Health Intelligence, 1012 13 September 2020

19 Daily Lab Report, 0834 13 September 2020

20 Testing supply email, 1001 09 September 2020

Reason for test 12 September 06 – 12 September

GPs and other primary health 3515 20856

CBACs and pop-ups 2824 23659

Border workers - air crew 21 214

Border workers - airport staff 205 1113

Border workers - maritime crew 0 1

Border workers – Port of Tauranga staff 0 127

Border workers – Remaining Port staff 19 222

Border workers - MIF 226 946

Border workers - MIQ 54 325

Travellers - Staying at MIF 186 2196

Travellers - Staying at MIQ 161 242

Total 7211 49901

Time period Number of laboratory tests

12 September 7211

Last 7 days (06 Sep to 12 Sep) 49,831

Total 864,469

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13

Testing activity by region

Focus areas

25. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.21

Healthline updates22 26. On 12 September there were 2,354 contacts in Healthline. Of those calls, 1,082 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 545 contacts (lower than forecast).

27. The main themes yesterday/today:

o Most of the callers are calling because they are symptomatic and want to get a test,

o Calls relating to the latest exposure events,

o Confusion around Alert Level rules (i.e. crowd sizes in Auckland, around the rest of

the country etc) it is recommended to reemphasise this given recent media

confusion.

Logistics

Health Workforce23

28. Health Workforce have identified a small group of people on the surge workforce who

have indicated they would be willing to work in an ARC facility in the event of an

outbreak – this week we will work on whether this pool can be expanded and actions to

keep the group “warm” in the event ARC employers require them.

29. Upskilling of alternative workforces for testing continues to progress, including plans

for a training package and scoping of micro-credentialing, in addition to understanding

where this workforce would be obtained from. It is anticipated this training package will

be available within four weeks (estimated).

30. Health Workforce continue to work with TAS and all 20 GMsHR on workforce needs and

issues – regular workforce intelligence information will be provided to Health

Workforce, which will be incorporated into frequent dashboard reports.

21 Community Testing Centres report, 1800 08 September 2020

22 National Telehealth Service Coronavirus Update, 0933 13 September 2020

23 Health Workforce Directorate, 0832 01 September 2020

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Hospital capacity24 Table 8: Number and occupancy of hospital beds by type as at 0800 12 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 325 185 (56.9%)

Ventilators 265 46 (17.4%)

Ward beds 6541 5075 (77.6%)

24 COVID-19 Hospital Summary, 1012 12 September 2020

15

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Appendix 1: Case summary Table 9: All community cases reported between 0900 12 September and 0900 13 September. Source: ESR EpiSurv Estract 0900 13 September 2020

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16

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification16 Table 10:NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 5 Sept ** 6 Sept 7 Sept 8 Sept 9 Sept ** 10 Sept ** 11 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours

- 100% 27% 4% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours

- 0% *

(0/2) 70% 4% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

- 100% 74% 4% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours

100% 50% 50% 33% 0% *

(0/1) 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours

0% *

(0/1) 20% 75% 80%

0% *

(0/2) 100% 67%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours

- 100% 84% 87% 100% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours

- 100% 89% 97% 100% 100% 94%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

- 100% 91% 88% 100% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% 4% 1% 0% 0% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

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17

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

Table 11: NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 5 Sept ** 6 Sept ** 7 Sept ** 8 Sept ** 9 Sept ** 10 Sept ** 11 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

- - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

- - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

- 100% 100% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

- - - - 0% * (0/1)

- -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

- 0% * (0/2)

100% - 100% - -

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

- 100% 100% - 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours

- 100% 100% - 100% - -

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

- 100% 100% - 100% - -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

- 100% 100% - 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% - 0% 0% - 0% - -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19) Table 12: Metro Auckland Summary Total of Testing for 11 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1294 256 342 141 34 2067

Table 13: Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and reported later than

this; tests only included if coded and received and acknowledged by lab, result not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 14: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 08/09 09/09 10/09 11/09*

MIQ Staff 2132 659 1488 912 88 75 251 195 221

Guests 2972 3767 3600 3406 483 609 345 534 342

Border Airport 2129 933 1349 1158 153 68 154 138 141

Port 1588 678 161 392 19 15 39 23 34

* 11/09 day still in progress

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the

most up-to-date information on CTCs and mobile testing sites in the Auckland region.

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 373 494 867 21.4% 36,126 17.8%

Maori 253 287 540 13.3% 29,163 14.3%

Other 696 878 1574 38.8% 85,897 42.3%

Pacific 461 432 893 22.0% 47,480 23.4%

Unknown 25 157 182 4.5% 4595 2.3%

Total 1808 2248 4056 203,261

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19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 12 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3393 6974 9094 19625 365 39451

Bay of Plenty 2549 287 555 6442 56 9889

Canterbury 1596 623 1709 13384 209 17521

Capital and Coast 1452 1099 1354 9092 197 13194

Counties Manukau 7196 19593 8893 12433 423 48538

Hawkes Bay 1376 284 212 3504 54 5430

Hutt Valley 793 462 542 3095 40 4932

Lakes 2288 299 452 3142 93 6274

MidCentral 1014 251 358 4125 81 5829

Nelson Marlborough 581 174 258 4193 52 5258

Northland 3028 207 256 4003 45 7539

South Canterbury 145 34 77 1717 11 1984

Southern 1074 338 682 9696 85 11875

Tairāwhiti 853 54 63 779 21 1770

Taranaki 677 67 168 2587 44 3543

Waikato 4262 980 1456 9992 224 16914

Wairarapa 231 37 45 1075 8 1396

Waitematā 4664 5078 7932 24607 315 42596

West Coast 47 10 13 326 6 402

Whanganui 639 77 68 1426 14 2224

Unknown 1388 697 698 4090 1741 8614

Total 39246 37625 34885 139334 4084 255174

20

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 12 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 78 124.4 48.6 75.1 72

Bay of Plenty 42.6 64.6 28.3 40.9 41

Canterbury 30.4 43.9 28.1 30 30.5

Capital and Coast 39.8 49.6 27 42.7 41

Counties Manukau 80.8 163.2 58.8 59.4 85.2

Hawkes Bay 31.8 44.3 23.1 32.4 32.5

Hutt Valley 30.4 39.6 28.9 32.8 32.7

Lakes 59.5 117 46.5 52.4 56.7

MidCentral 27.9 45.2 23.1 33.3 32.2

Nelson Marlborough 36.2 70.4 34.8 33.3 34.6

Northland 49.8 55.1 31 36.7 41.5

South Canterbury 27.3 69.6 32.5 33.2 33.2

Southern 32 49.1 26.4 36.2 35.6

Tairāwhiti 34.4 48.3 54 35.2 36

Taranaki 29 48.1 27 28.8 29.3

Waikato 44.2 73.5 33 37.1 40

Wairarapa 29 44.5 36.1 30.1 30.5

Waitematā 74.5 113.9 55.2 64.3 67.3

West Coast 12.1 39.6 14.1 12.1 12.5

Whanganui 36.8 50.6 23.2 33.1 34.3

Total 50.5 117.6 45.5 45 51.4

1

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SITREP 052

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 14 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

1

IMPORTED MIQ

CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

121

105

COMMUNITY CASES

ACTIVE

57 TOTAL CASES SINCE 11 AUG

180

39

TOTAL IMPORTED MIQ CASES

144

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 96

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

3,573

LABORATORY TESTS

LAST SEVEN DAYS

49,413

LABORATORY TESTS

TOTAL

868,042

CASES DECEASED

2

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 14 September 2020

Case Status Active Recovered Deceased Total

Confirmed 96* (-1) 1332 (+2) 19 1447 (+1)

Probable 0 346 5 351

Total 96* (-1) 1678 (+2) 24 1798 (+1)

*1 new case identified, 2 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 14 September 20201

New community cases since 0900 13 September 20202

1. One new community case has been reported, as at 0900 14 September.

o The case has an epidemiological link to an existing case associated with the Botany

sub-cluster. The case is and has been in isolation since 30 August due

to household contact being a confirmed case.

Community cases linked to the Auckland Community Cluster August 20203

2. 177 of the 180 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 14 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

o The quarantine facility healthcare worker case reported 13 September is currently

under investigation for an epidemiological and genomic link. Genomic sequencing is

currently underway with ESR.

1 EpiSurv Database, 0900 14 September 2020

2 EpiSurv Database, 0900 14 September 2020

3 EpiSurv Database, 0900 14 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 77 (+1) 55 46 1 179 (+1)

Probable 1 0 0 0 1

Total 78 (+1) 55 46 1 180 (+1)

s 9(2)(a)

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3

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. The case subsequently tested positive

on 21 August after being swabbed at a mobile testing clinic in Auckland. Despite

using two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.4 Their epidemiological link to the community cluster is still under

investigation.

Community cases and household contacts at Jet Park

4. As at 0800 14 September there are 53 people isolating in Jet Park from the community.

29 are confirmed cases, the remaining 24 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 13 September 20206

5. There have been no new cases detected at the border, as at 0900 14 September. In

total 144 cases have been detected at the border since the establishment of

MIFs/MIQs.

Cases in hospital

6. As at 0800 14 September there are three cases in hospital with COVID-19.7

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 14 September 2020

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 14 September 2020

6 EpiSurv Database, 0900 14 September 2020

7 NRHCC Morning Report 14 September 2020 and COVID-19 Hospital Summary, 0900 14 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 1

Waikato Waikato 0 1

Total - 1 2

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview8

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment of Mount Roskill Evangelical Church sub-cluster and

recent bereavement events.

o Contact tracing and containment of Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

o Waikato PHU will scope any positive cases in MIFs in the Auckland region for the next

week to alleviate some workload pressure at ARPHS.

Sub-clusters and settings of interest9

8. A healthcare worker at Jet Park was reported 13 September Sitrep. The swab is with ESR

for whole genome sequencing. Scoping by ARPHS is underway to identify close and

casual contacts. The case is isolating at Jet Park facility. The case has five household

close contacts who are self-isolating at home. Four of five household contacts have

returned negative test results, one is pending. All staff at Jet Park will be tested and

staff who are considered close contacts have been stood down. Testing is underway

and results are pending. CCTV footage at the facility will be reviewed as part of the

scoping process. Community contact tracing is underway.10 As at 0800 14 September

there has been close contacts identified at three exposure events at Les Mills gym

8 ARPHS Strategic Report 08 September 2020

9 ARPHS Strategic Report 08 September 2020

10 ARPHS text 1000 13 September 2020

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5

classes on 9 and 10 September. Contacts at exposure events at The Warehouse,

Starbucks and Countdown are all considered casual contacts only.11

9. On 7 September several exposure events were identified with epidemiological links to

Mt Roskill Evangelical Church sub-cluster. Between 24 August and 2 September there

were multiple gatherings associated with bereavement of a (non COVID-19 related)

death, including a funeral on . Active monitoring and follow up of

compliance with self-isolation is ongoing with contacts associated with these events.12

10. A sub-cluster has been created to include cases whose source of infection occurred at

the bereavement events. There are 15 cases in the bereavement sub-cluster and 33

cases in the Mt Roskill Evangelical Church sub-cluster.

11. St Dominic’s College in Henderson, Auckland, was identified as a setting of interest on 8

September. A confirmed case linked to the bereavement sub-cluster

The school has

been informed and communications have been sent. A list of contacts has been

gathered by the school and includes 87 students and 11 teachers.13 The school will be

reopened today (14 September) and casual contacts will be able to attend.14

12. A confirmed case linked to the bereavement sub-cluster worked as a bus driver for two

days while infectious but pre-symptomatic. wore a facemask and had 2m distance

from passengers due to Auckland Transport policy. A contact tracing exercise based on

HOP card data is ongoing.

o 293 individuals rode these routes on 3 and 4 September, all of whom are casual

contacts. No individual rode the bus for more than two hours cumulatively over

these two days.

o There are two close contacts, they are in self-isolation.

13. All five of the confirmed cases in the Botany sub-cluster were in Jet Park but have been

released. Two workplaces associated with the Botany cases have been identified and

close contacts have been scoped. Three at one of the of a

case are close contacts and had been stood down, self-isolated, and tested negative. All

three have since been released from isolation. The second is related to a

case who is a and no close contacts were identified. Four members of one

of the families in the sub-cluster have had serology testing on 11 September, results

are pending.

14. ARPHS actions:15

o Maintain positive relationships with Church leaders and liaise with Church members

about their need for financial and welfare support if asked to isolate.

o Scope new cases.

11 NRHCC Morning Report 0900 14 September 2020

12 NRHCC Morning Report 0900 14 September 2020

13 ARPHS email 1800 11 September 2020

14 NRHCC Morning Report 0900 14 September 2020

15 ARPHS Strategic Report 08 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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o Quarantine and test household contacts of the new cases. Testing is underway for

household contacts, including repeat testing as needed for people previously tested

from the Mt Roskill church.

o Develop and implement a testing strategy which includes communication with

church leaders around the reason for testing and who should be tested.

o MoH have signed off on two medical officers of health to support ARPHS.

Case investigation

15. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

Self-isolation compliance16

16. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

o Engagement of the Kaimanaaki workforce (community champions employed by our

Māori providers in the community). Kaimanaaki have access to clinical

support/advice. And will support and enable whaanau wellbeing through the

pandemic. They have specific skills to help whaanau cope with isolation. They are

also trained in the use of PPE so can make house visits and/or contact whaanau by

phone for the duration of their isolation. Daily contact is anticipated and Kaimanaaki

will report back to the DHB/public health officials on a daily basis. An

implementation plan is being developed and will be stood up from Monday.

16 ADHB Email, 1000 11 September 2020

s 9(2)(a)

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1.

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ESR and wider testing17 17. ESR now has an arrangement in place with Massey University for genome sequencing.

ESR will still validate all results, however this arrangement is predicted to speed up

genome testing.

18. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).18

19.

20. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

21. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

22.

23. Genomic sequencing of the Jet Park case is under way.

Contact tracing19 24. Between 05 and 11 September 89% (372/418) of Community close contacts and 100%

(9/9) MIQ close contacts have been contacted within 48 hours of being determined to

be a contact. KPI for this metric is 80% of close contacts within 48 hours.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 14 September 2020

11/09/2020 12/09/2020 13/09/2020 14/09/2020

Number of close contacts

identified1 3623 3647 3664 3708

17 ESR Whole Genome Sequencing Report 02 September 2020, Email 1859 11 September 2020

18 ESR email update 0900 08 September 2020

19 COVID-19 NCCS Analytics and Reporting 0846 14 September 2020

s 9(2)(a)s 9(2)(a)

s 9(2)(g)(i)

s 9(2)(g)(i)

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10

Number of close contacts

successfully contacted (and are

self-isolating)

3608 3640 3650 3697

Number of close contacts

referred to "finding services"2 3 0 0 0

Number of close contacts

awaiting contact 12 7 14 11

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation

and Tracing Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this

report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details

for close contacts we do not have the correct contact details for. These services utilise internal Ministry of Health

databases along with Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being

removed from the system.

COVID-19 Tracer App usage20 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 0835

14 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20 Response Analyst – Digital Channels, 1056 13 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/0

523

/05

26/0

529

/05

01/0

604

/06

07/0

610

/06

13/0

616

/06

19/0

622

/06

25/0

628

/06

01/0

704

/07

07/0

710

/07

13/0

716

/07

19/0

722

/07

25/0

728

/07

31/0

703

/08

06/0

809

/08

12/0

815

/08

18/0

821

/08

24/0

827

/08

30/0

802

/09

05/0

908

/09

11/0

9

Da

ily

sca

ns

an

d m

an

ua

l e

ntr

ies

Cu

mu

lati

ve

Ap

p r

eg

istr

ati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing21 Table 6: Testing by functional groups, as at 0900 14 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers22 Table 7: Number of laboratory tests processed nationally as at 0900 14 September 2020

Testing supply update23

25. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

21 ÉCLAIR/MoH Public Health Intelligence, 0954 14 September 2020

22 Daily Lab Report, 0834 13 September 2020

23 Testing supply email, 1001 09 September 2020

Reason for test 13 September 07 – 13 September

GPs and other primary health 1528 19,386

CBACs and pop-ups 1541 24,694

Border workers - air crew 25 234

Border workers - airport staff 139 1143

Border workers - maritime crew 0 0

Border workers – Port of Tauranga staff 1 51

Border workers – Remaining Port staff 4 154

Border workers - MIF 108 978

Border workers - MIQ 83 426

Travellers - Staying at MIF 141 2248

Travellers - Staying at MIQ 3 241

Total 3573 49,555

Time period Number of laboratory tests

13 September 3573

Last 7 days (07 Sep to 13 Sep) 49,413

Total 868,042

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12

Testing activity by region

Focus areas

26. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.24

Healthline updates25 27. On 13 September there were 2,590 contacts in Healthline. Of those calls, 1,112 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 605 contacts (lower than forecast).

28. The main themes yesterday/today:

o National Telehealth Service (Healthline) received over 160 calls related to the

exposures in the community at Les Mills and the locations in Milford. From these

calls we have identified 53 casual contacts and 87 close contacts who have been sent

to the contact tracing service and referred for testing. A number of close contacts

reported being symptomatic.

o Over the weekend in response to various media items we had a number of calls from

the public expressing anger towards the lack of compliance by various religious

groups and close contacts not being honest with officials during interviews.

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

o Calls relating to the latest exposure events

o Confusion around alert leave rules (i.e. crowd sizes in Auckland, around the rest of

the country etc).

Logistics

Health Workforce26

29. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

30. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

24 Community Testing Centres report, 1800 08 September 2020

25 National Telehealth Service Coronavirus Update, 0937 14 September 2020

26 Health Workforce Directorate, 0945 14 September 2020

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13

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

31. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity27 Table 8: Number and occupancy of hospital beds by type as at 0800 14 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 355 178 (50.1%)

Ventilators 314 55 (17.5%)

Ward beds 7502 5706 (76.1%)

27 COVID-19 Hospital Summary, 0916 14 September 2020

14

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Appendix 1: Case summary Table 9: All community cases reported between 0900 13 September and 0900 14 September. Source: ESR EpiSurv Extract 0900 14 September 2020

s 9(2)(a)

15

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification19 Table 10:NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 6 Sept 7 Sept 8 Sept 9 Sept 10 Sept ** 11 Sept ** 12 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours

100% 27% 4% 0% *

(0/4) - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours

0% *

(0/2) 70% 4%

0% *

(0/4) - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 80% 4% 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours

50% 50% 33% 0% *

(0/1) 100% 67% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours

20% 75% 80% 0% *

(0/2) 100% 67% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours

100% 90% 87% 100% 100% 94% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% 100% 100% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours

100% 96% 97% 100% 100% 94% 89%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 98% 88% 100% 100% 94% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 0% 4% 1% 0% 0% 0% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Table 11: NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 6 Sept ** 7 Sept ** 8 Sept ** 9 Sept ** 10 Sept ** 11 Sept ** 12 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

- - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

- - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% 100% - 100% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

- - - 0% * (0/1)

- - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

0% * (0/2)

100% - 100% - - 0% * (0/1)

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% 100% - 100% - - -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% 100% - 100% - - 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% 100% - 100% - - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% 100% - 100% - - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% 0% - 0% - - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 11 September Table 12: Metro Auckland Summary Total of Testing for 11 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port TOTAL

5:00pm 1294 256 342 141 34 2067

Table 13: Totals tests receipted from 12 August 2020, by ethnicity (as at 5pm)

*Swab taken in last 24 hours taken between midnight and midnight, may have been receipted and reported later than

this; tests only included if coded and received and acknowledged by lab, result not required

*Includes GP clinics, Urgent Care Centres, Designated practices

Table 14: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 08/09 09/09 10/09 11/09*

MIQ Staff 2132 659 1488 912 88 75 251 195 221

Guests 2972 3767 3600 3406 483 609 345 534 342

Border Airport 2129 933 1349 1158 153 68 154 138 141

Port 1588 678 161 392 19 15 39 23 34

* 11/09 day still in progress

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the

most up-to-date information on CTCs and mobile testing sites in the Auckland region.

Tests Last 24 hours Total since 12/8*

Ethnicity CTC

Non-

CTC

Total

% Tests %

Asian 174 137 311 15.8% 38,159 17.9%

Maori 149 125 274 13.9% 30,397 14.3%

Other 433 406 839 42.6% 90,099 42.3%

Pacific 253 94 347 17.6% 49,269 23.1%

Unknown 1 199 200 10.1% 5032 2.4%

Total 1010 961 1971 212,956

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18

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 13 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3416 7036 9208 19,804 371 39,835

Bay of Plenty 2569 291 564 6488 59 9971

Canterbury 1603 626 1721 13,462 210 17,622

Capital and Coast 1460 1100 1367 9165 204 13,296

Counties Manukau 7255 19,713 8957 12,535 428 48,888

Hawkes Bay 1380 284 213 3512 60 5449

Hutt Valley 792 467 547 3111 44 4961

Lakes 2293 300 452 3153 94 6292

MidCentral 1017 251 358 4131 83 5840

Nelson Marlborough 584 174 257 4209 53 5277

Northland 3038 208 264 4050 46 7606

South Canterbury 145 34 78 1720 11 1988

Southern 1078 338 683 9719 86 11,904

Tairāwhiti 859 54 63 782 21 1779

Taranaki 687 67 173 2647 45 3619

Waikato 4288 985 1474 10,058 228 17,033

Wairarapa 233 39 46 1082 8 1408

Waitematā 4707 5162 8031 24,837 322 43,059

West Coast 47 10 13 327 6 403

Whanganui 639 77 68 1427 14 2225

Unknown 1398 709 741 4144 1820 8812

Total 39,488 37,925 35,278 140,364 4213 257,268

19

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 13 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 78.5 125.5 49.2 75.8 72.7

Bay of Plenty 43 65.5 28.8 41.2 41.3

Canterbury 30.6 44.1 28.3 30.2 30.7

Capital and Coast 40 49.6 27.2 43.1 41.3

Counties Manukau 81.5 164.2 59.3 59.9 85.8

Hawkes Bay 31.9 44.3 23.2 32.5 32.7

Hutt Valley 30.4 40 29.1 33 32.9

Lakes 59.6 117.4 46.5 52.6 56.8

MidCentral 28 45.2 23.1 33.4 32.2

Nelson Marlborough 36.4 70.4 34.6 33.4 34.8

Northland 49.9 55.3 31.9 37.2 41.8

South Canterbury 27.3 69.6 33 33.3 33.2

Southern 32.1 49.1 26.5 36.3 35.7

Tairāwhiti 34.7 48.3 54 35.4 36.2

Taranaki 29.4 48.1 27.8 29.4 29.9

Waikato 44.5 73.9 33.4 37.4 40.3

Wairarapa 29.2 46.9 36.9 30.3 30.8

Waitematā 75.2 115.8 55.9 65 68

West Coast 12.1 39.6 14.1 12.1 12.6

Whanganui 36.8 50.6 23.2 33.2 34.3

Total 50.8 118.6 46 45.3 51.9

1

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SITREP 053

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 15 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ

CASES

NEW LAST 24 hrs

3

COMMUNITY CASES

TOTAL RECOVERED

123

119

COMMUNITY CASES

ACTIVE

55 TOTAL CASES SINCE 11 AUG

180

28

TOTAL IMPORTED MIQ CASES

147

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 83

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

4,402

LABORATORY TESTS

LAST SEVEN DAYS

49,290

LABORATORY TESTS

TOTAL

872,444

CASES DECEASED

2

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 15 September 20201

Case Status Active Recovered Deceased Total

Confirmed 83* (-13) 1348 (+16) 19 1450 (+3)

Probable 0 346 5 351

Total 83* (-13) 1694 (+16) 24 1801 (+3)

*3 new case identified, 16 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 15 September 20201

New community cases since 0900 14 September 20202

1. No new community cases have been reported, as at 0900 15 September.

Community cases linked to the Auckland Community Cluster August 20203

2. 178 of the 180 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 15 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster and there is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. The case subsequently tested positive

on 21 August after being swabbed at a mobile testing clinic in Auckland. Despite

1 EpiSurv Database, 0900 15 September 2020

2 EpiSurv Database, 0900 15 September 2020

3 EpiSurv Database, 0900 15 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 77 55 46 1 179

Probable 1 0 0 0 1

Total 78 55 46 1 180

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3

using two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.4 Their epidemiological link to the community cluster is still under

investigation. As at 15 September no additional information has been revealed by

the investigation.11

Community cases and household contacts at Jet Park

4. As at 0800 15 September there are 56 people isolating in Jet Park from the community.

26 are confirmed cases, the remaining 30 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 14 September 20206

5. Three new cases detected at the border, as at 0900 15 September. In total 147 cases

have been detected at the border since the establishment of MIFs/MIQs.

Cases in hospital

6. As at 0800 15 September there are three cases in hospital with COVID-19.7

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 15 September 2020

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 15 September 2020

6 EpiSurv Database, 0900 15 September 2020

7 NRHCC Morning Report 15 September 2020 and COVID-19 Hospital Summary, 0900 15 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 1

Waikato Waikato 0 1

Total - 1 2

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview8

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment of Mount Roskill Evangelical Church sub-cluster and

recent bereavement events.

o Contact tracing and containment of Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

o Waikato PHU will scope any positive cases in MIFs in the Auckland region for the next

week to alleviate some workload pressure at ARPHS.

o Investigation and close contact tracing of Jet Park healthcare worker9

Sub-clusters and settings of interest8

8. A healthcare worker at Jet Park was reported as a case on the 13 September Sitrep. The

case has been genomically linked to the Auckland Community Cluster however a clear

epidemiological link is still being investigated. The case was working in the facility

where other confirmed community cases were completing managed isolation however

a clear link to an existing case is not yet determined (see para 15 for further information

on genomic sequencing). Scoping by ARPHS is underway to identify close and casual

contacts. The case is isolating at Jet Park facility. The case has five household close

contacts who are self-isolating at home. All five household contacts have returned

negative test results.9 All staff at Jet Park staff who are considered close contacts have

been stood down and have returned negative results so far.9 CCTV footage at the

facility will be reviewed as part of the scoping process. Community contact tracing is

8 ARPHS Strategic Report 08 September 2020

9 NRHCC Morning Report, 0900 15 September 2020

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5

underway.10 A total of 29311 gym users have been identified between three exposure

events at Les Mills gym classes on 9 and 10 September (See table 4 for further details).

These people are in the process of being contacted by NCTS and are all being

encouraged to be tested.12 Contacts at exposure events at The Warehouse, Starbucks

and Countdown are all considered casual contacts only.13

9. On 7 September several exposure events were identified with epidemiological links to

Mt Roskill Evangelical Church sub-cluster. Between 24 August and 2 September there

were multiple gatherings associated with bereavement of a (non COVID-19 related)

death, including a funeral on Active monitoring and follow up of

compliance with self-isolation is ongoing with contacts associated with these events.13

10. St Dominic’s College in Henderson, Auckland, was identified as a setting of interest on 8

September. A confirmed case linked to the bereavement sub-cluster

The school has

been informed and communications have been sent. A list of contacts has been

gathered by the school and includes 87 students and 11 teachers.14 The school was

reopened on 14 September and casual contacts will be able to attend.13

11. A confirmed case linked to the bereavement sub-cluster worked as a bus driver for two

days while infectious but pre-symptomatic. wore a facemask and had 2m distance

from passengers due to Auckland Transport policy. A contact tracing exercise based on

HOP card data is ongoing. No further contacts have been identified as of 14 September

regarding this case.15

o 293 individuals rode these routes on 3 and 4 September, all of whom are casual

contacts. No individual rode the bus for more than two hours cumulatively over

these two days.

o There are two close contacts, they are in self-isolation.

12. members of one of the families in the Botany sub-cluster had serology testing on

11 September and all returned negative results.11 A case reported in 14 September

SitRep is also associated with the Botany sub-cluster. The case is and has

been in isolation at Jet Park since 30 August due to being a household contact of a

confirmed case. The case and their close contacts will remain in isolation for a further

14 days.11

Case investigation

10 ARPHS text 1000 13 September 2020

11 Email update from ARPHS 0848 15 September 2020

12 MoH, ARPHS teleconference 1500 14 September 2020

13 NRHCC Morning Report 0900 14 September 2020

14 ARPHS email 1800 11 September 2020

15 NRHCC Morning Report, 0900 15 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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6

13. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

o Jet Park healthcare worker

Self-isolation compliance16

14. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

o Engagement of the Kaimanaaki workforce (community champions employed by our

Māori providers in the community). Kaimanaaki have access to clinical

support/advice. And will support and enable whaanau wellbeing through the

pandemic. They have specific skills to help whaanau cope with isolation. They are

also trained in the use of PPE so can make house visits and/or contact whaanau by

phone for the duration of their isolation. Daily contact is anticipated and Kaimanaaki

will report back to the DHB/public health officials on a daily basis. An

implementation plan is being developed and will was stood up on 14 September.

16 ADHB Email, 1000 11 September 2020

s 9(2)(a)

s 9(2)(a)

7

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s 9(2)(a)

s 9(2)(a)

8

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing17 15. Whole genome sequencing was undertaken on a sample from a confirmed COVID-19

case in a health care worker at Auckland’s quarantine facility Jet Park. The sequencing

results indicate that the case is linked to the Auckland community cluster and is most

closely genomically related to three community cases that have been isolated in the Jet

Park quarantine facility. This sequence information indicates that the health care worker

was most likely exposed at Jet Park and the Public Health Unit are continuing to

investigate how the infection occurred.

16. ESR now has an arrangement in place with Massey University for genome sequencing.

ESR will still validate all results, however this arrangement is predicted to speed up

genome testing.

17. A further 34 community cases are genomically linked with the Auckland cluster. These

cases are from the following known sub-clusters; Church 1 (6 cases), Church 2 (4 cases),

Church 3 (9 cases), Finance Now HH (1 case), Americold HH (3 cases), Botany (4 cases),

(4 cases) and (3 cases).18

18.

19. Work is underway to analyse how the whole genome sequencing can be used to tell us

how COVID-19 has been transmitted through the community cluster and to further

inform its management.

20. No direct links have been found between the community outbreak genome

sequencing, with the 67 genomes currently available from cases in managed isolation

facilities (MIFs).

21.

Contact tracing19 22. Between 06 and 12 September 91% (471/516) of Community close contacts and 100%

(29/29) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

17 ESR Whole Genome Sequencing Report 02 September 2020, Email 1859 11 September 2020

18 ESR email update 0900 08 September 2020

19 COVID-19 NCCS Analytics and Reporting 0836 15 September 2020

s 9(2)(a)s 9(2)(a)

s 9(2)(g)(i)

s 9(2)(g)(i)

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9

Table 4: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 15 September 2020

12/09/2020 13/09/2020 14/09/2020 15/09/2020

Number of close contacts

identified1 3647 3664 3708 3779

Number of close contacts

successfully contacted (and are

self-isolating)

3640 3650 3697 3772

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 7 14 11 7

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage20 Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1610

14 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20 Response Analyst – Digital Channels, 1614 14 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

23/0

526

/05

29

/05

01/0

604

/06

07

/06

10/0

613

/06

16

/06

19/0

622

/06

25

/06

28/0

601

/07

04

/07

07/0

710

/07

13

/07

16/0

719

/07

22

/07

25/0

728

/07

31

/07

03/0

806

/08

09

/08

12/0

815

/08

18

/08

21/0

824

/08

27

/08

30/0

802

/09

05

/09

08/0

911

/09

14

/09

Da

ily

sca

ns

an

d m

an

ua

l e

ntr

ies

Cu

mu

lati

ve

Ap

p r

eg

istr

ati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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10

Testing21 Table 5: Testing by functional groups, as at 0900 15 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers22 Table 6: Number of laboratory tests processed nationally as at 0900 15 September 2020

Testing supply update23

23. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

21 ÉCLAIR/MoH Public Health Intelligence, 1000 15 September 2020

22 Daily Lab Report, 0913 15 September 2020

23 Testing supply email, 1001 09 September 2020

Reason for test 14 September 08–14 September

GPs and other primary health 1904 19,287

CBACs and pop-ups 1908 24,263

Border workers - air crew 16 216

Border workers - airport staff 87 1168

Border workers - maritime crew 0 0

Border workers – Port of Tauranga staff 0 12

Border workers – Remaining Port staff 5 128

Border workers - MIF 137 986

Border workers - MIQ 145 504

Travellers - Staying at MIF 194 2134

Travellers - Staying at MIQ 6 243

Total 4402 48,941

Time period Number of laboratory tests

14 September 4402

Last 7 days (08 Sep to 14 Sep) 49,290

Total 872,444

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11

Testing activity by region

Focus areas

24. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.24

Healthline updates25 25. On 14 September there were 3,176 contacts in Healthline. Of those calls, 1,112 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 675 contacts (slightly higher than forecast).

26. The main themes yesterday/today:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure events.

o National Telehealth Service (Healthline) continued to have a number of calls from the

public expressing anger towards the lack of compliance by various religious groups

and close contacts not being honest with officials during interviews.

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

o Calls relating to the latest exposure events

o Confusion around alert leave rules (i.e. crowd sizes in Auckland, around the rest of

the country etc).

Logistics

Health Workforce26

27. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

28. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

29. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

24 Community Testing Centres report, 1800 08 September 2020

25 National Telehealth Service Coronavirus Update, 0903 15 September 2020

26 Health Workforce Directorate, 0945 14 September 2020

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12

Hospital capacity27 Table 7: Number and occupancy of hospital beds by type as at 0800 15 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 365 208 (57.0%)

Ventilators 320 58 (18.1%)

Ward beds 7728 6351 (82.2%)

27 COVID-19 Hospital Summary, 0918 15 September 2020

13

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Appendix 1: Case summary Table 8: All community cases reported between 0900 14 September and 0900 15 September. Source: ESR EpiSurv Extract 0900 15 September 2020

Cumulative

Number

Date tested

positive Onset date

Case

status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification19 Table 9:NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 7 Sept 8 Sept 9 Sept 10 Sept 11 Sept

** 12 Sept

** 13 Sept

**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 28% 4% 0% *

(0/4) 100% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 72% 4% 0% *

(0/4) 100% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours 83% 4% 100% 100% 89% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 50% 33% 0% *

(0/1) 100% 67% 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 75% 80% 0% *

(0/2) 100% 67% 100% -

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 93% 87% 100% 100% 89% 98% -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% 100% -

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours 97% 97% 100% 100% 100% 98% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 98% 88% 100% 100% 100% 98% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 4% 1% 0% 0% 0% 0% -

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Table 10: NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 7 Sept ** 8 Sept ** 9 Sept ** 10 Sept ** 11 Sept ** 12 Sept ** 13 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours

- - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours

- - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours

100% - 100% - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours

- - 0% * (0/1)

- - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours

100% - 100% - - 0% * (0/1)

-

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours

100% - 100% - - 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours

100% - 100% - - 100% -

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours

100% - 100% - - 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours

100% - 100% - - 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20% 0% - 0% - - 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 14 September

Table 11: Metro Auckland Summary Total of Testing for 11 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime

port

Ship’s

Crew

TOTAL

12/09/2020

5:00pm

1004 75 461 93 23 0 1656

13/09/2020

5:00pm

922 92 650 106 No Testing 0 1770

14/09/2020

5:00pm

1482 118 648 156 90 0 2494

Table 12: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

12/09 13/09 14/09*

MIQ Staff 2132 659 1488 912 1086 75 92 118

Guests 2972 3767 3600 3406 3424 461 650 648

Border Airport 2129 933 1349 1158 853 93 106 156

Port 1588 678 161 392 153 23 0 90

* 14/09 day still in progress

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the

most up-to-date information on CTCs and mobile testing sites in the Auckland region.

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Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 13: Number of people tested for COVID-19 from 12 August to 14 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Unknown Total

Auckland 3441 7066 9312 19950 380 40,149

Bay of Plenty 2580 292 569 6516 62 10,019

Canterbury 1614 627 1769 13581 211 17,802

Capital and Coast 1466 1110 1377 9211 205 13,369

Counties Manukau 7286 19774 9053 12617 435 49,165

Hawkes Bay 1398 287 219 3559 60 5523

Hutt Valley 794 515 553 3134 45 5041

Lakes 2305 300 456 3164 94 6319

MidCentral 1038 258 369 4215 86 5966

Nelson Marlborough 584 174 259 4235 53 5305

Northland 3044 208 266 4085 50 7653

South Canterbury 145 35 78 1724 11 1993

Southern 1090 369 694 9980 88 12,221

Tairāwhiti 875 55 64 796 22 1812

Taranaki 688 68 174 2665 45 3640

Waikato 4306 988 1490 10100 232 17,116

Wairarapa 234 39 46 1093 8 1420

Waitematā 4750 5210 8142 25117 324 43,543

West Coast 47 10 13 329 6 405

Whanganui 645 77 72 1458 14 2266

Unknown 1415 706 724 4177 1851 8873

Total 39,745 38,168 35,699 141,707 4282 259,601

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Table 14: Rate per 1000 people tested for COVID-19 from 12 August to 14 September

Prioritised Ethnicity MPAO

DHB of Domicile Māori Pacific Asian Other Total

Auckland 79.1 126 49.8 76.3 73.2

Bay of Plenty 43.1 65.7 29 41.4 41.5

Canterbury 30.8 44.2 29.1 30.4 31

Capital and Coast 40.1 50.1 27.4 43.3 41.6

Counties Manukau 81.8 164.7 59.9 60.3 86.3

Hawkes Bay 32.3 44.7 23.9 32.9 33.1

Hutt Valley 30.5 44.1 29.5 33.3 33.4

Lakes 59.9 117.4 46.9 52.8 57.1

MidCentral 28.5 46.5 23.8 34.1 32.9

Nelson Marlborough 36.4 70.4 34.9 33.7 35

Northland 50 55.3 32.2 37.5 42.1

South Canterbury 27.3 71.7 33 33.4 33.3

Southern 32.5 53.6 26.9 37.3 36.6

Tairāwhiti 35.3 49.2 54.8 36 36.9

Taranaki 29.5 48.8 27.9 29.6 30.1

Waikato 44.7 74.1 33.8 37.5 40.5

Wairarapa 29.3 46.9 36.9 30.6 31.1

Waitematā 75.9 116.8 56.6 65.7 68.7

West Coast 12.1 39.6 14.1 12.2 12.6

Whanganui 37.1 50.6 24.6 33.9 34.9

Total 51.1 119.3 46.6 45.8 52.3

1

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SITREP 054

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 16 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ

CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

125

121

COMMUNITY CASES

ACTIVE

52 TOTAL CASES SINCE 11 AUG

180

27

TOTAL IMPORTED MIQ CASES

148

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 79

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

9,088

LABORATORY TESTS

LAST SEVEN DAYS

50,015

LABORATORY TESTS

TOTAL

881,532

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 16 September 20201

Case Status Active Recovered Deceased Total

Confirmed 79* (-4) 1352 (+4) 20 (+1) 1451 (+1)

Probable 0 346 5 351

Total 79* (-4) 1698 (+4) 25 (+1) 1802 (+1)

*1 new case identified, 4 cases classified as recovered, 1 case deceased.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 16 September 20201

New community cases since 0900 15 September 20202

1. No new community cases have been reported, as at 0900 16 September.

Community cases linked to the Auckland Community Cluster August 20203

2. 178 of the 180 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 16 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case (reported 21 August) came through the border on 18 June. The case tested

negative at Day 3 and Day 12 of quarantine. The case subsequently tested positive

on 21 August after being swabbed at a mobile testing clinic in Auckland. Despite

1 EpiSurv Database, 0900 16 September 2020

2 EpiSurv Database, 0900 16 September 2020

3 EpiSurv Database, 0900 16 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 77 55 46 1 179

Probable 1 0 0 0 1

Total 78 55 46 1 180

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3

using two different whole genome sequencing protocols only a partial genome was

obtained. There is insufficient data to confirm the case is genomically linked to the

community cluster.4 Their epidemiological link to the community cluster is still under

investigation. As at 15 September no additional information has been revealed by

the investigation.11

Community cases and household contacts at Jet Park

4. As at 0800 16 September there are 57 people isolating in Jet Park from the community.

27 are confirmed cases, the remaining 30 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 15 September 20206

5. One new case detected at the border, as at 0900 16 September. In total 148 cases have

been detected at the border since the establishment of MIFs/MIQs.

Cases in hospital

6. As at 0800 16 September there are three cases in hospital with COVID-19.7

o One death was reported. The case was in ICU at Waikato Hospital on 15 September.

o The case in Middlemore ICU is receiving ward level treatment and will be transferred

to a general ward.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 16 September 2020

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 16 September 2020

6 EpiSurv Database, 0900 16 September 2020

7 NRHCC Morning Report 16 September 2020 and COVID-19 Hospital Summary, 0900 16 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 1

Counties Manukau Middlemore 0 1

Waikato Waikato 0 0

Total - 1 2

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4

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview8

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment of Mount Roskill Evangelical Church sub-cluster and

recent bereavement events.

o Contact tracing and containment of Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

o Waikato PHU will scope any positive cases in MIFs in the Auckland region for the next

week to alleviate some workload pressure at ARPHS.

o Investigation and close contact tracing of Jet Park healthcare worker9

Sub-clusters and settings of interest8

8. A healthcare worker at Jet Park was reported as a case on the 13 September Sitrep. The

case has been genomically linked to the Auckland Community Cluster. The

epidemiological link has been identified to a community case who was completing

isolation at Jet Park and required hospitalisation. A review is underway of the processes

at Jet Park with a focus on lessons learnt by this situation.

The case is isolating at Jet Park facility. Scoping by ARPHS is underway to identify close

and casual contacts. The case has five household close contacts who are self-isolating

at home. All five household contacts initially returned negative test results and were

retested on 15 September, results expected today (16 September)9 All staff at Jet Park

staff who are considered close contacts have been stood down and have returned

8 ARPHS Strategic Report 08 September 2020

9 NRHCC Morning Report, 0900 16 September 2020

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5

negative results so far.9 CCTV footage at the facility will be reviewed as part of the

scoping process. Community contact tracing is underway.10 A total of 29311 gym users

have been identified between three exposure events at Les Mills gym classes on 9 and

10 September (See table 4 for further details). These people are in the process of being

contacted by NCTS and are all being encouraged to be tested.12 Contacts at exposure

events at The Warehouse, Starbucks and Countdown are all considered casual contacts

only.13

9. On 7 September several exposure events were identified with epidemiological links to

Mt Roskill Evangelical Church sub-cluster. Between 24 August and 2 September there

were multiple gatherings associated with bereavement of a (non COVID-19 related)

death, including a funeral on Active monitoring and follow up of

compliance with self-isolation is ongoing with contacts associated with these events.13

10. St Dominic’s College in Henderson, Auckland, was identified as a setting of interest on 8

September. A confirmed case linked to the bereavement sub-cluster

The school has

been informed and communications have been sent. A list of contacts has been

gathered by the school and includes 87 students and 11 teachers.14 The school was

reopened on 14 September and casual contacts will be able to attend.13

11. A confirmed case linked to the bereavement sub-cluster worked as a bus driver for two

days while infectious but pre-symptomatic. wore a facemask and had 2m distance

from passengers due to Auckland Transport policy. A contact tracing exercise based on

HOP card data is ongoing. No further contacts have been identified as of 14 September

regarding this case.15

o 293 individuals rode these routes on 3 and 4 September, all of whom are casual

contacts. No individual rode the bus for more than two hours cumulatively over

these two days.

o There are two close contacts, they are in self-isolation.

12. members of one of the families in the Botany sub-cluster had serology testing on

11 September and all returned negative results.11 A case reported in 14 September

SitRep is also associated with the Botany sub-cluster. The case is and has

been in isolation at Jet Park since 30 August due to being a household contact of a

confirmed case. The case and their close contacts will remain in isolation for a further

14 days.11

10 ARPHS text 1000 13 September 2020

11 Email update from ARPHS 0848 15 September 2020

12 MoH, ARPHS teleconference 1500 14 September 2020

13 NRHCC Morning Report 0900 14 September 2020

14 ARPHS email 1800 11 September 2020

15 NRHCC Morning Report, 0900 15 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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6

Case investigation

13. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

Self-isolation compliance16

14. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

o Engagement of the Kaimanaaki workforce (community champions employed by our

Māori providers in the community). Kaimanaaki have access to clinical

support/advice. And will support and enable whānau wellbeing through the

pandemic. They have specific skills to help whānau cope with isolation. They are also

trained in the use of PPE so can make house visits and/or contact whānau by phone

for the duration of their isolation. Daily contact is anticipated and Kaimanaaki will

report back to the DHB/public health officials on a daily basis. An implementation

plan is being developed and will be stood up on 14 September.

16 ADHB Email, 1000 11 September 2020

s 9(2)(a)

s 9(2)(a)

7

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s 9(2)(a)

s 9(2)(a)

8

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ESR and wider testing17 15. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

16.

17. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

18. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

19.

Table 5: Sub-cluster sequencing table as at 14 September 202018

Sub-cluster Sequenced and

Genomically Clustered

Sequence Not

available

Total

Americold 9 1 10

Americold HH 24 3 27

7 1 8

Botany 4 1 5

3 0 3

Church 1 22 4 26

17 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

18 ESR email 1608 14 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(g)(i)

s 9(2)(g)(i)

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9

Church 2 14 5 19

Church 3 24 9 33

Finance Now 6 1 7

Finance Now HH 4 1 5

Household 1 5 0 5

Household 2 2 0 2

Household 3 3 0 3

MREF-Bereavement 2 13 15

GP 5 0 5

NZ Courier Post 1 1 2

Pending 0 2 2

Warehouse 1 0 1

Contact tracing19 20. Between 07 and 13 September 70% (465/663) of Community close contacts and 100%

(25/25) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 16 September 2020

13/09/2020 14/09/2020 15/09/2020 16/09/2020

Number of close contacts

identified1 3664 3708 3779 4139

Number of close contacts

successfully contacted (and are

self-isolating)

3650 3697 3772 4046

Number of close contacts

referred to "finding services"2 0 0 0 8

Number of close contacts

awaiting contact 14 11 7 85

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

19 COVID-19 NCCS Analytics and Reporting 0924 16 September 2020

s 9(2)(a)

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10

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage20 21. Since 20 May 2020, a total of 18 contact alerts have been sent out from the NCTS

system for exposure events. These exposure events are ones where contact tracers

deem a positive case to have been in a location where a risk of transmission warrants

releasing a contact alert (these are also notified on the Ministry of Health website).

22. Since 03 September 2020 (Release 4 of the app), we have measured that the app has

notified 113 people where a contact alert was presented because they had been in a

location of interest (we were not recording this before Release 4).

Figure 1: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

15 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20 Response Analyst – Digital Channels, 1618 15 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/0

523

/05

26/0

529

/05

01/0

604

/06

07/0

610

/06

13/0

616

/06

19/0

622

/06

25/0

628

/06

01/0

704

/07

07/0

710

/07

13/0

716

/07

19/0

722

/07

25/0

728

/07

31/0

703

/08

06/0

809

/08

12/0

815

/08

18/0

821

/08

24/0

827

/08

30/0

802

/09

05/0

908

/09

11/0

914

/09

Da

ily

sca

ns

an

d m

an

ua

l e

ntr

ies

Cu

mu

lati

ve

Ap

p r

eg

istr

ati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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Testing21 Table 7: Testing by functional groups, as at 0900 16 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers22 Table 8: Number of laboratory tests processed nationally as at 0900 16 September 2020

Testing supply update23

23. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

21 ÉCLAIR/MoH Public Health Intelligence, 1000 16 September 2020

22 Daily Lab Report, 0952 16 September 2020

23 Testing supply email, 1001 09 September 2020

Reason for test 15 September 09–15 September

GPs and other primary health 2841 18,333

CBACs and pop-ups 2971 23,201

Border workers - air crew 29 206

Border workers - airport staff 152 1114

Border workers - maritime crew 13 13

Border workers – Port of Tauranga staff 34 43

Border workers – Remaining Port staff 4 121

Border workers - MIF 165 1006

Border workers - MIQ 21 462

Travellers - Staying at MIF 255 1989

Travellers - Staying at MIQ 4 244

Total 6489* 46,732

Time period Number of laboratory tests

15 September 9088*

Last 7 days (09 Sep to 15 Sep) 50,015

Total 881,532

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12

Testing activity by region

Focus areas

24. As at 1700 08 September there are 28 Community testing Centres in the Metro

Auckland area. Three of these are closed CTC's for close contacts only.24

Healthline updates25 25. On 15 September there were 2,579 contacts in Healthline. Of those calls, 1,208 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 659 contacts (in line with forecast).

26. The main themes yesterday/today:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure events and media reporting caused confusion on this. It maybe timely to

clarify close and casual contact information again.

o Ongoing confusion around alert leave rules (i.e. crowd sizes in Auckland, around the

rest of the country etc).

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

Logistics

Health Workforce26

27. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

28. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

29. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

24 Community Testing Centres report, 1800 08 September 2020

25 National Telehealth Service Coronavirus Update, 0939 16 September 2020

26 Health Workforce Directorate, 0945 14 September 2020

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13

Hospital capacity27 Table 9: Number and occupancy of hospital beds by type as at 0800 16 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 365 228 (62.5%)

Ventilators 323 51 (15.8%)

Ward beds 7847 6439 (82.1%)

27 COVID-19 Hospital Summary, 0938 16 September 2020

14

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Appendix 1: Case summary Table 10: All community cases reported between 0900 15 September and 0900 16 September. Source: ESR EpiSurv Extract 0900 16 September 2020

Cumulative

Number

Date tested

positive Onset date

Case

status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

15

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification19 Table 11: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 8 Sept 9 Sept 10 Sept 11 Sept 12 Sept

** 13 Sept

** 14 Sept

**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 4% 0% 100% 5% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 4% 0% 100% 58% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours 4% 100% 100% 89% 38% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 33% 0% 100% 67% 100% - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 80% 0% 100% 67% 100% - 0%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 87% 100% 100% 89% 38% - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% - 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours 97% 100% 100% 100% 79% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 88% 100% 100% 100% 87% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 1% 0% 0% 0% 0% - 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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16

Table 12:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 8 Sept ** 9Sept ** 10 Sept ** 11 Sept ** 12 Sept ** 13 Sept ** 14 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 0% - - - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 100% - - 0% - 0%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - - 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - 100% - 0%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours 100% 100% - - 89% - -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

0% 0% - - 0% - -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 15 September

Table 13: Metro Auckland Summary Total of Testing for 15 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime

port

Ship’s

Crew

TOTAL

5:00pm 1558 113 688 137 18* 0 2514

*Note: the Port was an afternoon start and is running through until 8pm tonight

Table 14: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-16/08 17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 15/09*

MIQ Staff 2132 659 1488 912 1086 136 113

Guests 2972 3767 3600 3406 3424 648 688

Border Airport 2129 933 1349 1158 853 156 137

Port 1588 678 161 392 153 90 18

Crew 0 0 0 0 0 0 0

* 15/09 day still in progress

Table 15: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site

reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 15/09*

Airport Oaks 1148 515 366 265 181 27 19

Botany CTC 1151 948 905 749 681 126 151

Health New Lynn 2603 1258 1703 732 889 148 125

Mangere Town Centre 1748 1684 1599 860 660 75 109

Otara CTC 3221 1712 1429 930 699 91 78

St Lukes 1368 1045 1414 797 666 204 132

Takanini Urgent Care 1886 1216 1153 684 440 93 108

Whanau House 2502 1371 1442 928 1613 219 174

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18

Whanau Ora - Central 1957 964 1583 937 783 100 84

Whanau Ora - North 1442 669 637 982 947 208 186

Whanau Ora - South 2945 1250 718 677 620 48 69

Henderson (EFKS

Church) Pop Up

N/A N/A N/A N/A 460 43 46

Henderson (Te

Wananga O Aotearoa)

Pop Up

N/A N/A N/A N/A N/A 44 22

Manurewa (Netball

Courts) Pop Up

N/A N/A N/A N/A N/A 44 50

Mt Wellington Pop Up N/A N/A N/A N/A N/A N/A 53

Wairau Valley Pop Up N/A N/A N/A N/A N/A N/A 60

Otahuhu Pop Up N/A N/A N/A N/A N/A N/A 22

Papatoetoe Pop Up N/A N/A N/A N/A N/A N/A 10

Waipuna Targeted Site 143 549 376 219 251 28 46

Henderson Targeted

Site

N/A N/A N/A N/A 631 20 14

Total 26,148 16,781 21,215 13,002 10,475 1518 1558

*15/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not

included in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the

most up-to-date information on CTCs and mobile testing sites in the Auckland region.

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19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 16: Number of people tested for COVID-19 from 12 August to 15 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3467 7103 9433 20,264 388 40,655

Bay of Plenty 2622 297 585 6647 63 10,214

Canterbury 1624 631 1775 13,683 212 17,925

Capital and Coast 1485 1114 1398 9358 213 13,568

Counties Manukau 7392 19,936 9139 12,774 440 49,681

Hawkes Bay 1426 301 232 3620 60 5639

Hutt Valley 815 533 564 3189 43 5144

Lakes 2324 302 463 3227 95 6411

MidCentral 1037 259 369 4232 89 5986

Nelson Marlborough 602 187 277 4332 58 5456

Northland 3059 208 270 4125 50 7712

South Canterbury 146 35 79 1749 11 2020

Southern 1108 383 717 10,191 92 12,491

Tairāwhiti 875 56 64 800 23 1818

Taranaki 693 69 175 2683 46 3666

Waikato 4361 1005 1522 10,293 243 17,424

Wairarapa 235 39 46 1108 8 1436

Waitematā 4832 5274 8295 25,758 341 44,500

West Coast 47 10 13 330 6 406

Whanganui 647 77 72 1459 15 2270

Unknown 1429 711 728 4246 1891 9009

Total 40,226 38,530 36,216 144,069 4387 263,432

20

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Table 17: Rate per 1000 people tested for COVID-19 from 12 August to 15 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 79.7 126.7 50.4 77.5 74.2

Bay of Plenty 43.9 66.8 29.9 42.2 42.4

Canterbury 31 44.5 29.2 30.7 31.3

Capital and Coast 40.7 50.2 27.9 44 42.2

Counties Manukau 83 166 60.5 61 87.2

Hawkes Bay 33 46.9 25.3 33.5 33.8

Hutt Valley 31.3 45.6 30.1 33.8 34.1

Lakes 60.4 118.2 47.6 53.8 57.9

MidCentral 28.5 46.7 23.8 34.2 33

Nelson Marlborough 37.5 75.7 37.3 34.4 35.9

Northland 50.3 55.3 32.6 37.8 42.4

South Canterbury 27.5 71.7 33.4 33.9 33.8

Southern 33 55.6 27.8 38.1 37.4

Tairāwhiti 35.3 50.1 54.8 36.2 37

Taranaki 29.7 49.5 28.1 29.8 30.3

Waikato 45.2 75.4 34.5 38.2 41.2

Wairarapa 29.5 46.9 36.9 31.1 31.4

Waitematā 77.2 118.3 57.7 67.4 70.3

West Coast 12.1 39.6 14.1 12.2 12.7

Whanganui 37.3 50.6 24.6 33.9 35

Total 51.7 120.5 47.3 46.5 53.1

1

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SITREP 055

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 17 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ

CASES

NEW LAST 24 hrs

7

COMMUNITY CASES

TOTAL RECOVERED

133

122

COMMUNITY CASES

ACTIVE

44 TOTAL CASES SINCE 11 AUG

180

33

TOTAL IMPORTED MIQ CASES

155

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 77

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

8,185

LABORATORY TESTS

LAST SEVEN DAYS

50,250

LABORATORY TESTS

TOTAL

889,717

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 17 September 20201

Case Status Active Recovered Deceased Total

Confirmed 77* (-2) 1361 (+9) 20 1458 (+7)

Probable 0 346 5 351

Total 77* (-2) 1707 (+9) 25 1809 (+7)

*7 new case identified, 9 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 17 September 20201

New community cases since 0900 16 September 20202

1. No new community cases have been reported, as at 0900 17 September.

Community cases linked to the Auckland Community Cluster August 20203

2. 178 of the 180 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 17 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at Day 3

and Day 12 of quarantine. The case subsequently tested positive on 21 August.

Despite using two different whole genome sequencing protocols only there is

1 EpiSurv Database, 0900 17 September 2020

2 EpiSurv Database, 0900 17 September 2020

3 EpiSurv Database, 0900 17 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 77 55 46 1 179

Probable 1 0 0 0 1

Total 78 55 46 1 180

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3

insufficient data to confirm the case is genomically linked to the community cluster.4

Their epidemiological link to the community cluster is still under investigation. As at

15 September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

4. As at 0800 17 September there are 54 people isolating in Jet Park from the community.

23 are confirmed cases, the remaining 31 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 16 September 20206

5. Seven new cases detected at the border, as at 0900 17 September. In total 155 cases

have been detected at the border since the establishment of MIFs/MIQs.

o One case is in managed isolation in Wellington, arriving from the United States of

America and was identified through routine day 3 testing.

o Three cases were in managed isolation in Hamilton upon arriving from India and

were identified through routine day 3 testing. The cases have been transferred to Jet

Park, Auckland for quarantine due to positive test results.

o One case was managed isolation in Hamilton upon arriving from Uzbekistan and was

identified through testing due to showing symptoms. The case has been transferred

to Jet Park, Auckland for quarantine due to positive test.

o One case is in managed isolation in Christchurch, arriving from the Indonesia and

was identified through routine day 3 testing.

o One case is in managed isolation in Hamilton upon arriving from India and were

identified through routine day 3 testing.

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 17 September 2020

6 EpiSurv Database, 0900 17 September 2020

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4

Cases in hospital

6. As at 0800 17 September there are four cases in hospital with COVID-19.7

o Case in Waitematā ICU was transferred to a general ward on 16 September.

o One new admission to Counties Manukau overnight of an existing case from Jet Park.

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 17 September 2020

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview8

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment of Mount Roskill Evangelical Church sub-cluster and

recent bereavement events.

o Contact tracing and containment of Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

7 NRHCC Morning Report 17 September 2020

8 ARPHS Strategic Report 08 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 0 2

Total - 2 2

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5

o Waikato PHU will scope any positive cases in MIFs in the Auckland region for the next

week to alleviate some workload pressure at ARPHS.

o Investigation and close contact tracing of Jet Park healthcare worker9

Sub-clusters and settings of interest8

8. A healthcare worker at Jet Park was reported as a case on the 13 September Sitrep. The

case has been genomically linked to the Auckland Community Cluster. The

epidemiological link has been identified to a community case who was completing

isolation at Jet Park and required hospitalisation. A review is underway of the processes

at Jet Park with a focus on lessons learnt by this situation.

The case is isolating at Jet Park facility. Scoping by ARPHS is underway to identify close

and casual contacts. The case has five household close contacts who are self-isolating

at home. All five household contacts initially returned negative test results and were

retested on 15 September, results are pending.9 All staff at Jet Park staff who are

considered close contacts have been stood down and have returned negative results so

far.9 CCTV footage at the facility will be reviewed as part of the scoping process.

9. members of one of the families in the Botany sub-cluster had serology testing on

11 September and all returned negative results. A case reported in 14 September

SitRep is also associated with the Botany sub-cluster.

10. An existing confirmed case has been identified as attending school for

prior to been taken home due to feeling unwell.10 The school

has been closed for 3 days as a precaution while close contact tracing is completed.

Part of the investigation will focus on what the child did while at school.

Case investigation

11. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

Self-isolation compliance11

12. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

9 NRHCC Morning Report, 0900 16 September 2020

10 NRHCC Morning Report 17 September 2020

11 ADHB Email, 1000 11 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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6

o Engagement of the Kaimanaaki workforce (community champions employed by our

Māori providers in the community). Kaimanaaki have access to clinical

support/advice. And will support and enable whānau wellbeing through the

pandemic. They have specific skills to help whānau cope with isolation. They are also

trained in the use of PPE so can make house visits and/or contact whānau by phone

for the duration of their isolation. Daily contact is anticipated and Kaimanaaki will

report back to the DHB/public health officials on a daily basis. An implementation

plan is being developed and will be stood up on 14 September.

7

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s 9(2)(a)

s 9(2)(a)

8

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing12 13. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

14.

15. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

16. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

17.

12 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

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9

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202013

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing14 18. Between 08 and 14 September 62% (363/584) of Community close contacts and 100%

(22/22) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Note: This metric is low for community cases as it includes some casual contacts associated with

the Les Mills exposure events. This will be rectified in reporting tomorrow.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 17 September 2020

14/09/2020 15/09/2020 16/09/2020 17/09/2020

Number of close contacts

identified1 3708 3779 4139 4043

Number of close contacts

successfully contacted (and are

self-isolating)

3697 3772 4046 4036

Number of close contacts

referred to "finding services"2 0 0 8 1

13 ESR email 1608 14 September 2020

14 COVID-19 NCCS Analytics and Reporting 0924 16 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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10

Number of close contacts

awaiting contact 11 7 85 6

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage15 19. Since 20 May 2020, a total of 18 contact alerts have been sent out from the NCTS

system for exposure events. These exposure events are ones where contact tracers

deem a positive case to have been in a location where a risk of transmission warrants

releasing a contact alert (these are also notified on the Ministry of Health website).

20. Since 03 September 2020 (Release 4 of the app), we have measured that the app has

notified 113 people where a contact alert was presented because they had been in a

location of interest (we were not recording this before Release 4).

Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

16 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

15 Response Analyst – Digital Channels, 1625 16 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/0

523

/05

26/0

529

/05

01/0

604

/06

07/0

610

/06

13/0

616

/06

19/0

622

/06

25/0

628

/06

01/0

704

/07

07/0

710

/07

13/0

716

/07

19/0

722

/07

25/0

728

/07

31/0

703

/08

06/0

809

/08

12/0

815

/08

18/0

821

/08

24/0

827

/08

30/0

802

/09

05/0

908

/09

11/0

914

/09

Da

ily

sca

ns

an

d m

an

ua

l e

ntr

ies

Cu

mu

lati

ve

Ap

p r

eg

istr

ati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing16 Table 6: Testing by functional groups, as at 0900 17 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers17 Table 7: Number of laboratory tests processed nationally as at 0900 17 September 2020

Testing supply update18

21. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

16 ÉCLAIR/MoH Public Health Intelligence, 1000 17 September 2020

17 Daily Lab Report, 0843 16 September 2020

18 Testing supply email, 1001 09 September 2020

Reason for test 16 September 10–16 September

GPs and other primary health 3641 20,104

CBACs and pop-ups 3587 24,762

Border workers - air crew 44 225

Border workers - airport staff 221 1288

Border workers - maritime crew 2 15

Border workers – Port of Tauranga staff 88 131

Border workers – Remaining Port staff 34 130

Border workers - MIF 161 1101

Border workers - MIQ 22 455

Travellers - Staying at MIF 376 1887

Travellers - Staying at MIQ 9 253

Total 8185 50,351*

Time period Number of laboratory tests

16 September 8185

Last 7 days (10 Sep to 16 Sep) 50,250*

Total 889,717

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12

Healthline updates19 22. On 16 September there were 2,275 contacts in Healthline. Of those calls, 933 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 695 contacts (slightly higher than forecast).

23. The main themes yesterday/today:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure events and media reporting caused confusion on this. It maybe timely to

clarify close and casual contact information again.

o Ongoing confusion around alert leave rules (i.e. crowd sizes in Auckland, around the

rest of the country etc).

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

Logistics

Health Workforce20

24. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

25. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

26. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity21 Table 8: Number and occupancy of hospital beds by type as at 0800 17 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 337 210 (62.3%)

Ventilators 296 59 (19.9%)

Ward beds 7219 5862 (81.2%)

19 National Telehealth Service Coronavirus Update, 0948 17 September 2020

20 Health Workforce Directorate, 0945 14 September 2020

21 COVID-19 Hospital Summary, 1000 17 September 2020

13

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Appendix 1: Case summary Table 9: All community cases reported between 0900 16 September and 0900 17 September. Source: ESR EpiSurv Extract 0900 17 September 2020

Cumulative

Number

Date tested

positive Onset date

Case

status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

14

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification14 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 8 Sept 9 Sept 10 Sept 11 Sept 12 Sept

** 13 Sept

** 14 Sept

**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 4% 0% 100% 5% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 4% 0% 100% 58% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours 4% 100% 100% 89% 38% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 33% 0% 100% 67% 100% - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 80% 0% 100% 67% 100% - 0%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 87% 100% 100% 89% 38% - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% 100% 100% - 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours 97% 100% 100% 100% 79% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 88% 100% 100% 100% 87% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 1% 0% 0% 0% 0% - 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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15

Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 8 Sept ** 9Sept ** 10 Sept ** 11 Sept ** 12 Sept ** 13 Sept ** 14 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 0% - - - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 100% - - 0% - 0%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - - 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - 100% - 0%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours 100% 100% - - 89% - -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

0% 0% - - 0% - -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 16 September

Table 12: Metro Auckland Summary Total of Testing for 16 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime

port

Ship’s

Crew

TOTAL

5:00pm 1109 202 522 194 123 0 2150

*Note: the Port was an afternoon start and is running through until 8pm tonight

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 15/09 16/09*

MIQ Staff 2132 659 1488 912 1086 136 133 202

Guests 2972 3767 3600 3406 3424 648 688 522

Border Airport 2129 933 1349 1158 853 156 137 194

Port 1588 678 161 392 153 90 18 123

Crew 0 0 0 0 0 0 0 0

* 16/09 day still in progress

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site

reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09

13/09

14/09 15/09 16/09*

Airport Oaks 1148 515 366 265 181 27 19 25

Botany CTC 1151 948 905 749 681 126 151 86

Health New Lynn 2603 1258 1703 732 889 148 125 82

Mangere Town

Centre

1748 1684 1599 860 660 75 109 79

Otara CTC 3221 1712 1429 930 699 91 78 62

St Lukes 1368 1045 1414 797 666 204 132 111

Takanini Urgent Care 1886 1216 1153 684 440 93 108 62

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17

Whanau House 2502 1371 1442 928 1613 219 174 134

Whanau Ora - Central 1957 964 1583 937 783 100 99 45

Whanau Ora - North 1442 669 637 982 947 208 221 133

Whanau Ora - South 2945 1250 718 677 620 48 79 54

Henderson (EFKS

Church) Pop Up

N/A N/A N/A N/A 460 43 46 35

Henderson (Te

Wananga O

Aotearoa) Pop Up

N/A N/A N/A N/A N/A 44 22 21

Manurewa Pop Up N/A N/A N/A N/A N/A 44 50 36

Mt Wellington Pop

Up

N/A N/A N/A N/A N/A N/A 53 42

Wairau Valley Pop Up N/A N/A N/A N/A N/A N/A 60 50

Port Waikato Pop Up N/A N/A N/A N/A N/A N/A N/A 17

Waipuna Targeted

Site

143 549 376 219 251 28 39 No

Data

Henderson Targeted

Site

N/A N/A N/A N/A 631 20 14 35

Total 26,148 16,781 21,215 13,002 10,475 1518 1622 1109

*16/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not

included in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the

most up-to-date information on CTCs and mobile testing sites in the Auckland region.

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18

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 16 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3543 7211 9665 20,732 402 41,553

Bay of Plenty 2654 360 595 6770 68 10,447

Canterbury 1667 658 1848 14,093 223 18,489

Capital and Coast 1520 1145 1481 9678 221 14,045

Counties Manukau 7533 20,247 9390 13,062 449 50,681

Hawkes Bay 1445 320 237 3688 63 5753

Hutt Valley 829 548 585 3282 46 5290

Lakes 2349 306 470 3269 97 6491

MidCentral 1085 264 402 4368 96 6215

Nelson Marlborough 617 237 290 4490 61 5695

Northland 3115 214 278 4258 52 7917

South Canterbury 146 38 81 1780 11 2056

Southern 1134 394 768 10,482 98 12,876

Tairāwhiti 906 57 67 826 23 1879

Taranaki 703 71 182 2782 50 3788

Waikato 4448 1018 1554 10,508 251 17,779

Wairarapa 240 42 47 1165 8 1502

Waitematā 4952 5406 8566 26,551 352 45,827

West Coast 47 10 13 340 6 416

Whanganui 655 81 73 1490 15 2314

Unknown 1453 722 759 4364 1969 9267

Total 41,041 39,349 37,351 147,979 4561 270,281

19

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 16 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 81.5 128.6 51.6 79.3 75.8

Bay of Plenty 44.4 81 30.4 43 43.3

Canterbury 31.8 46.4 30.4 31.6 32.2

Capital and Coast 41.6 51.6 29.5 45.5 43.7

Counties Manukau 84.6 168.6 62.1 62.4 89

Hawkes Bay 33.4 49.9 25.9 34.1 34.5

Hutt Valley 31.8 46.9 31.2 34.8 35.1

Lakes 61.1 119.8 48.3 54.5 58.6

MidCentral 29.8 47.6 25.9 35.3 34.3

Nelson Marlborough 38.5 95.9 39.1 35.7 37.5

Northland 51.2 56.9 33.6 39.1 43.5

South Canterbury 27.5 77.8 34.2 34.5 34.4

Southern 33.8 57.2 29.8 39.2 38.6

Tairāwhiti 36.6 51 57.4 37.4 38.2

Taranaki 30.1 51 29.2 30.9 31.3

Waikato 46.1 76.4 35.2 39 42

Wairarapa 30.1 50.5 37.7 32.7 32.8

Waitematā 79.1 121.2 59.6 69.4 72.4

West Coast 12.1 39.6 14.1 12.6 13

Whanganui 37.7 53.2 24.9 34.6 35.7

Total 52.8 123 48.7 47.8 54.5

1

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SITREP 056

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 18 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ

CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

140

122

COMMUNITY CASES

ACTIVE

37 TOTAL CASES SINCE 11 AUG

180

33

TOTAL IMPORTED MIQ CASES

155

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 70

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

7,360

LABORATORY TESTS

LAST SEVEN DAYS

48,657

LABORATORY TESTS

TOTAL

897,077

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 18 September 20201

Case Status Active Recovered Deceased Total

Confirmed 70* (-7) 1368 (+7) 20 1458

Probable 0 346 5 351

Total 70* (-7) 1714 (+7) 25 1809

*0 new cases identified, 7 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 18 September 20201

New community cases since 0900 17 September 20202

1. No new community cases have been reported, as at 0900 18 September.

Community cases linked to the Auckland Community Cluster August 20203

2. 178 of the 180 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 18 September. The unlinked cases are summarised as follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 3).

Community cases under investigation to determine a link to the Auckland community

cluster

3. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at Day 3

and Day 12 of quarantine. The case subsequently tested positive on 21 August.

Despite using two different whole genome sequencing protocols only there is

1 EpiSurv Database, 0900 18 September 2020

2 EpiSurv Database, 0900 18 September 2020

3 EpiSurv Database, 0900 18 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 77 55 46 1 179

Probable 1 0 0 0 1

Total 78 55 46 1 180

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3

insufficient data to confirm the case is genomically linked to the community cluster.4

Their epidemiological link to the community cluster is still under investigation. As at

15 September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

4. As at 0800 18 September there are 54 people isolating in Jet Park from the community.

22 are confirmed cases, the remaining 32 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

MIQ cases since 0900 17 September 20206

5. No new cases detected at the border, as at 0900 18 September. In total 155 cases have

been detected at the border since the establishment of MIFs/MIQs.

Cases in hospital

6. As at 0800 18 September there are four cases in hospital with COVID-19.7

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 18 September 2020

Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

4 ESR WGS report 03 September 2020

5 NRHCC Morning Report, 0900 17 September 2020

6 EpiSurv Database, 0900 18 September 2020

7 NRHCC Morning Report 17 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 1

Total - 3 1

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4

Current outbreak overview8

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster.

Current outbreak investigation priorities

o Contact tracing and containment of Mount Roskill Evangelical Church sub-cluster and

recent bereavement events.

o Contact tracing and containment of Botany sub-cluster.

o Clarify whether June border case is a new infection and clarify strain.

o Seek to identify epidemiological link for index case in Mount Roskill Evangelical Church

sub-cluster.

o Waikato PHU will scope any positive cases in MIFs in the Auckland region for the next

week to alleviate some workload pressure at ARPHS.

o Investigation and close contact tracing of Jet Park healthcare worker9

Sub-clusters and settings of interest8

8. A healthcare worker at Jet Park was reported as a case on the 13 September Sitrep. The

case has been genomically linked to the Auckland Community Cluster. The

epidemiological link has been identified to a community case who was completing

isolation at Jet Park and required hospitalisation. A review is underway of the processes

at Jet Park with a focus on lessons learnt by this situation.

The case is isolating at Jet Park facility. Scoping by ARPHS is underway to identify close

and casual contacts. The case has five household close contacts who are self-isolating

at home. All five household contacts initially returned negative test results and were

retested on 15 September and were negative.9 All staff at Jet Park staff who are

considered close contacts have been stood down and have returned negative results so

far.9 CCTV footage at the facility will be reviewed as part of the scoping process.

9. members of one of the families in the Botany sub-cluster had serology testing on

11 September and all returned negative results. A case reported in 14 September

SitRep is also associated with the Botany sub-cluster. This case briefly attended school

on Monday 14 September prior to being notified of the positive test result.10 The school

has been closed as a precaution while close contact tracing and a deep clean is

completed.11 A total of four close contacts have been identified.12 All students who

attended school (about 470) on 14 September are considered to be casual contacts.

Letters have been sent asking students to be tested and to remain self-isolated at

8 ARPHS Strategic Report 08 September 2020

9 NRHCC Morning Report, 0900 16 September 2020

10 NRHCC Morning Report 17 September 2020

11 ARPHS email update – 1210 17 September 2020

12 NRHCC Morning Report, 0900 18 September 2020

s 9(2)(a)

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5

home until they receive a negative test result. They have also been asked to contact

Healthline if they become symptomatic.13 Onsite testing has been arranged from today

(18 September) until 20 September.14 The school will remain closed until at least

Monday 21 September. Students who receive a negative test will be able to attend.15

Part of the investigation will focus on what the child did while at school.

Case investigation

10. Source investigation for the epidemiological link to the main cluster for four cases that

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

Self-isolation compliance16

11. Discussions with a key representative from Ngaa Amokura have confirmed that the

option below will reinforce the trust/relationship between the health sector and the

fellowship whanau for supporting compliance with self-isolation requirements (to be

used if standard contact tracing cannot be established within 48 hrs).

o Engagement of the Kaimanaaki workforce (community champions employed by our

Māori providers in the community). Kaimanaaki have access to clinical

support/advice. And will support and enable whānau wellbeing through the

pandemic. They have specific skills to help whānau cope with isolation. They are also

trained in the use of PPE so can make house visits and/or contact whānau by phone

for the duration of their isolation. Daily contact is anticipated and Kaimanaaki will

report back to the DHB/public health officials on a daily basis. An implementation

plan is being developed and will be stood up on 14 September

13 ARPHS email update – 17 September 2020 1210

14 ARPHS email update – 17 September 2020 1210

15 ARPHS email update – 17 September 2020 1210

16 ADHB Email, 1000 11 September 2020

s 9(2)(a)

s 9(2)(a)

6

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s 9(2)(a)

s 9(2)(a)

7

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing17 12. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

13.

14. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

15. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

16.

17 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

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8

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202018

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing19 17. Between 09 and 15 September 78.1% (139/178) of Community close contacts and 100%

(14/14) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Note: Please note that the total number and number successfully contacted has decreased due

to casual contacts associated with the Les Mills exposure events being excluded.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 18 September 2020

15/09/2020 16/09/2020 17/09/2020 18/09/2020

Number of close contacts

identified1 3779 4139 4043 3912

Number of close contacts

successfully contacted (and are

self-isolating)

3772 4046 4036 3908

Number of close contacts

referred to "finding services"2 0 8 1 0

18 ESR email 1608 14 September 2020

19 COVID-19 NCCS Analytics and Reporting 0931 18 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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9

Number of close contacts

awaiting contact 7 85 6 4

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage20 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

17 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20 Response Analyst – Digital Channels, 1631 17 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

09

05/

09

08/

09

11/

09

14/

09

17/

09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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10

Testing21 Table 6: Testing by functional groups, as at 0900 18 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers22 Table 7: Number of laboratory tests processed nationally as at 0900 18 September 2020

Testing supply update23

18. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

21 ÉCLAIR/MoH Public Health Intelligence, 1000 18 September 2020

22 Daily Lab Report, 0917 18 September 2020

23 Testing supply email, 1001 09 September 2020

Reason for test 17 September 11–17 September

GPs and other primary health 3497 19,314

CBACs and pop-ups 3179 24,399

Border workers - air crew 34 243

Border workers - airport staff 169 1231

Border workers - maritime crew 3 18

Border workers – Port of Tauranga staff 29 158

Border workers – Remaining Port staff 24 154

Border workers - MIF 203 1175

Border workers - MIQ 51 499

Travellers - Staying at MIF 168 1802

Travellers - Staying at MIQ 3 257

Total 7360 49,250*

Time period Number of laboratory tests

17 September 7360

Last 7 days (11 Sep to 17 Sep) 48,657*

Total 897,077

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11

Healthline updates24 19. On 17 September there were 2,235 contacts in Healthline. Of those calls, 933 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 687 contacts (6% higher than forecast).

20. The main themes yesterday/today:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure events and media reporting caused confusion on this.

o Ongoing confusion around alert leave rules (i.e. crowd sizes in Auckland, around the

rest of the country etc).

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

Logistics

Health Workforce25

21. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

22. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

23. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity26 Table 8: Number and occupancy of hospital beds by type as at 0800 18 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 336 212 (63.1%)

Ventilators 298 64 (21.5%)

Ward beds 7182 5848 (81.4%)

24 National Telehealth Service Coronavirus Update, 0910 18 September 2020

25 Health Workforce Directorate, 0945 14 September 2020

26 COVID-19 Hospital Summary, 0926 18 September 2020

12

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Appendix 1: Case summary Table 9: All community cases reported between 0900 17 September and 0900 18 September. Source: ESR EpiSurv Extract 0900 18 September 2020

Cumulative

Number

Date tested

positive Onset date

Case

status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

13

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification19 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 10 Sept 11 Sept 12 Sept 13 Sept 14 Sept

** 15 Sept

** 16 Sept

**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 100% 5% 33% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 100% 58% 83% - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours 100% 95% 69% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 100% 67% 100% - - - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 100% 67% 100% - 0% - -

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 100% 95% 69% - 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% 100% - 100% - -

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours 100% 100% 98% - 100% - -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 100% 100% 83% - 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 0% 0% 0% - 0% - -

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

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Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 10 Sept ** 11Sept ** 11 Sept ** 12 Sept ** 13 Sept ** 14 Sept ** 15 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - - 100% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - - - - 33% - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - - 0% - 0% - 71%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - - 100% - 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - - 100% - 75% - 58%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - - 100% - 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - - 100% - 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- - 0% - 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

15

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 17 September

Table 12: Metro Auckland Summary Total of Testing for 17 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

5:00pm 1501 132 627 164 32 0 2456

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-23/08 24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 15/09 16/09 17/09*

MIQ Staff 2132 659 1488 912 1086 136 133 202 132

Guests 2972 3767 3600 3406 3424 648 688 522 627

Border Airport 2129 933 1349 1158 853 156 137 194 164

Port 1588 678 161 392 153 90 18 123 32

Crew 0 0 0 0 0 0 0 0 0

* 17/09 day still in progress

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09

13/09

14/09 15/09 16/09 17/09*

Airport Oaks 1148 515 366 265 181 27 19 25 40

Botany CTC 1151 948 905 749 681 126 151 86 184

Health New Lynn 2603 1258 1703 732 889 148 125 82 76

Mangere Town

Centre

1748 1684 1599 860 660 75 109 79 98

Otara CTC 3221 1712 1429 930 699 91 78 121 355

St Lukes 1368 1045 1414 797 666 204 132 111 131

Takanini Urgent

Care

1886 1216 1153 684 440 93 108 62 70

Whanau House 2502 1371 1442 928 1613 219 174 134 123

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16

Whanau Ora -

Central

1957 964 1583 937 783 100 99 45 55

Whanau Ora - North 1442 669 637 982 947 208 221 133 106

Whanau Ora - South 2945 1250 718 677 620 48 79 54 119

Manurewa Pop Up N/A N/A N/A N/A N/A 44 50 36 73

Mangere Pop Up N/A N/A N/A N/A N/A N/A N/A N/A 9

Beach Haven Pop

Up

N/A N/A N/A N/A N/A N/A N/A N/A 27

Westgate Pop Up N/A N/A N/A N/A N/A N/A N/A N/A 21

Waipuna Targeted

Site

143 549 376 219 251 28 39 29 No

Data

Henderson Targeted

Site

N/A N/A N/A N/A 631 20 14 35 14

Total 26,148 16,781 21,215 13,002 10,475 1518 1622 1228 1501

*17/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included in

this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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17

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 17 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3594 7308 9825 21,053 407 42,187

Bay of Plenty 2704 367 609 6900 66 10,646

Canterbury 1684 667 1884 14270 227 18,732

Capital and Coast 1549 1169 1512 9907 228 14,365

Counties Manukau 7664 20,489 9539 13,217 456 51,365

Hawkes Bay 1467 321 244 3740 63 5835

Hutt Valley 847 564 603 3356 46 5416

Lakes 2375 313 479 3327 96 6590

MidCentral 1104 266 411 4418 97 6296

Nelson Marlborough 636 239 294 4563 63 5795

Northland 3174 219 282 4351 53 8079

South Canterbury 148 38 82 1791 11 2070

Southern 1159 408 785 10,675 99 13,126

Tairāwhiti 918 57 68 843 20 1906

Taranaki 715 72 182 2822 50 3841

Waikato 4531 1023 1595 10,688 254 18,091

Wairarapa 245 44 49 1188 9 1535

Waitematā 5035 5480 8737 27,017 360 46,629

West Coast 47 10 13 340 6 416

Whanganui 661 81 73 1515 15 2345

Unknown 1464 741 852 4465 2001 9523

Total 41,721 39,876 38,118 150,447 4627 274,789

18

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 17 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 82.6 130.3 52.5 80.5 77

Bay of Plenty 45.2 82.6 31.1 43.9 44.1

Canterbury 32.1 47 31 32 32.7

Capital and Coast 42.4 52.7 30.1 46.6 44.7

Counties Manukau 86.1 170.6 63.1 63.2 90.2

Hawkes Bay 33.9 50 26.6 34.6 35

Hutt Valley 32.5 48.3 32.1 35.6 35.9

Lakes 61.7 122.5 49.2 55.5 59.5

MidCentral 30.3 47.9 26.5 35.7 34.7

Nelson Marlborough 39.6 96.7 39.6 36.3 38.2

Northland 52.2 58.3 34.1 39.9 44.4

South Canterbury 27.9 77.8 34.6 34.7 34.6

Southern 34.5 59.2 30.4 39.9 39.3

Tairāwhiti 37 51 58.3 38.1 38.8

Taranaki 30.6 51.7 29.2 31.4 31.8

Waikato 47 76.7 36.1 39.7 42.8

Wairarapa 30.7 52.9 39.3 33.3 33.6

Waitematā 80.5 122.9 60.8 70.7 73.6

West Coast 12.1 39.6 14.1 12.6 13

Whanganui 38.1 53.2 24.9 35.2 36.2

Total 53.7 124.7 49.7 48.6 55.4

1

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SITREP 057

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 19 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

1

IMPORTED MIQ

CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

145

122

COMMUNITY CASES

ACTIVE

33 TOTAL CASES SINCE 11 AUG

181

34

TOTAL IMPORTED MIQ CASES

156

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 67

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

8,359

LABORATORY TESTS

LAST SEVEN DAYS

48,178

LABORATORY TESTS

TOTAL

905,436

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 19 September 20201

Case Status Active Recovered Deceased Total

Confirmed 67* (-3) 1373 (+5) 20 1460 (+2)

Probable 0 346 5 351

Total 67* (-3) 1719 (+5) 25 1811 (+2)

*2 new cases identified, 5 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 19 September 20201

New community cases since 0900 18 September 20202

1. One new community case has been reported, as at 0900 19 September. More

information on this case in paragraph 2 below.

New case under investigation since 0900 18 September 20203

2. The new case reported today (19 September) is a returnee who arrived in New Zealand

on 27 August and completed managed isolation in Christchurch. They tested negative

on day 3 and day 12. They left managed isolation on 11 September and returned home

to Auckland. They were tested after developing symptoms on 16 September. The test

returned positive on 18 September. The case and their household contacts have been

transferred to the Auckland Jet Park quarantine facility. The case is possibly a close

contact of a confirmed case from the same flight to New Zealand. Source of infection is

under investigation.

Community cases linked to the Auckland Community Cluster August 20204

3. 178 of the 181 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 19 September 2020. The unlinked cases are summarised as

follows:

1 EpiSurv Database, 0900 19 September 2020

2 EpiSurv Database, 0900 19 September 2020

3 EpiSurv Database, 0900 19 September 2020

4 EpiSurv Database, 0900 19 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 77 55 47 (+1) 1 180 (+1)

Probable 1 0 0 0 1

Total 78 55 47 (+1) 1 181 (+1)

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3

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 4).

o The third case is detailed in paragraph two.

Community cases under investigation to determine a link to the Auckland

community cluster

4. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at day 3 and

day 12 of quarantine. The case subsequently tested positive on 21 August. Despite

using two different whole genome sequencing protocols only there is insufficient

data to confirm the case is genomically linked to the community cluster.5 Their

epidemiological link to the community cluster is still under investigation. As at 15

September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

5. As at 0800 18 September there are 50 people isolating in Jet Park from the community.

20 are confirmed cases, the remaining 30 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.6

MIQ cases since 0900 18 September 20207

6. One new case detected at the border, as at 0900 19 September. In total 156 cases have

been detected at the border since the establishment of MIQ facilities.

Cases in hospital

7. As at 0800 19 September there are four cases in hospital with COVID-19.8

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 19 September 2020

5 ESR WGS report 03 September 2020

6 NRHCC Morning Report, 0900 19 September 2020

7 EpiSurv Database, 0900 19 September 2020

8 NRHCC Morning Report 19 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 2 0

Total - 4 0

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4

Health system response

Overall approach

8. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview

o There are two sub-clusters which most new community cases are linked to (Mount

Roskill Evangelical Church and Bereavements sub-clusters). There are 33 confirmed

cases in the Mount Roskill Evangelical Church sub-cluster and 15 confirmed cases in the

Bereavements sub-cluster. Ongoing scoping of community settings since 14 September

has revealed no major concerns.9

Current outbreak investigation priorities10

o Ongoing management of healthcare workers from Jet Park

o Ongoing management of Chapel Down’s Primary School associated with Botany Cluster.

o Investigation and scoping of new confirmed case.

Sub-clusters and settings of interest11

9. A healthcare worker at Jet Park was reported as a case on 13 September. The case has

been epidemiologically and genomically linked to the Auckland Community Cluster.

The case has been epidemiologically linked to a community case who was completing

isolation at Jet Park and required hospitalisation. A review of processes at Jet Park is

underway with a focus on lessons to be learnt from this situation.

10. The case is isolating at Jet Park facility. The case has five household close contacts who

are self-isolating at home. All five household contacts have tested negative twice. All

staff at Jet Park staff who are considered close contacts have been stood down and

have returned negative results so far.

11. members of a family in the Botany sub-cluster had serology testing on 11

September which returned negative results for all members. A case linked to the

Botany sub-cluster briefly attended school on 14 September, prior to being notified of

9 NRHCC Morning Report, 0900 19 September 2020

10NRHCC Morning Report, 0900 19 September 2020

11 NRHCC Morning Report, 0900 16 September 2020

s 9(2)(a)

s 9(2)(a)

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5

the positive test result that day.12 The school has been closed as a precaution while

close contact tracing and a deep clean is completed. A total of four close contacts have

been identified. All students who attended school (about 470) on 14 September are

considered to be casual contacts. Letters have been sent asking students to be tested

and to remain in self-isolation at home until they receive a negative test result. They

have also been asked to contact Healthline if they become symptomatic. Onsite testing

has been arranged from 18 September until 20 September. The school will remain

closed until at least Monday 21 September. Students who receive a negative test will be

able to attend school once it reopens. The investigation is also focusing on what the

child did while at school. 13

Case investigation

12. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

12 NRHCC Morning Report 17 September 2020

13 ARPHS email update – 1210 17 September 2020

s 9(2)(a)

s 9(2)(a)

6

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s 9(2)(a)

s 9(2)(a)

7

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing14 13. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

14.

15. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

16. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

17.

14 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

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8

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202015

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing16 18. Between 10 and 16 September 75.8% (119/157) of Community close contacts and 100%

(30/30) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Note: Please note that the total number and number successfully contacted has decreased due

to casual contacts associated with the Les Mills exposure events being excluded.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 19 September 2020

16/09/2020 17/09/2020 18/09/2020 19/09/2020

Number of close contacts

identified1 4139 4043 3912 3918

Number of close contacts

successfully contacted (and are

self-isolating)

4046 4036 3908 3912

Number of close contacts

referred to "finding services"2 8 1 0 0

15 ESR email 1608 14 September 2020

16 COVID-19 NCCS Analytics and Reporting 0928 19 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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9

Number of close contacts

awaiting contact 85 6 4 2

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

18 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

17 Response Analyst – Digital Channels, 1631 18 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

23

/05

26

/05

29

/05

01

/06

04

/06

07

/06

10

/06

13

/06

16

/06

19

/06

22

/06

25

/06

28

/06

01

/07

04

/07

07

/07

10

/07

13

/07

16

/07

19

/07

22

/07

25

/07

28

/07

31

/07

03

/08

06

/08

09

/08

12

/08

15

/08

18

/08

21

/08

24

/08

27

/08

30

/08

02

/09

05

/09

08

/09

11

/09

14

/09

17

/09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

regi

stra

tio

ns

Day and month

Cumulative App registrations Daily scans and manual entries

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10

Testing18 Table 6: Testing by functional groups, as at 0900 19 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 7: Number of laboratory tests processed nationally as at 0900 19 September 2020

Testing supply update20

19. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 19 September 2020

19 Daily Lab Report, 0847 19 September 2020

20 Testing supply email, 1001 09 September 2020

Reason for test 18 September 12–18 September

GPs and other primary health 4015 19,933

CBACs and pop-ups 3298 22,766

Border workers - air crew 49 242

Border workers - airport staff 295 1364

Border workers - maritime crew 13 31

Border workers – Port of Tauranga staff 138 290

Border workers – Remaining Port staff 50 144

Border workers - MIF 164 1227

Border workers - MIQ 41 461

Travellers - Staying at MIF 291 1696

Travellers - Staying at MIQ 5 192

Total 8359 48,346*

Time period Number of laboratory tests

18 September 8359

Last 7 days (12 Sep to 18 Sep) 48,178*

Total 905,436

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11

Healthline updates21 20. On 18 September there were 2,008 contacts in Healthline. Of those calls, 726 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 586 contacts (slightly lower than forecast).

21. The main themes on 18 September were:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure events.

o Ongoing confusion around alert leave rules (i.e. crowd sizes in Auckland, around the

rest of the country etc).

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

Logistics

Health Workforce22

22. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

23. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

24. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity23 Table 8: Number and occupancy of hospital beds by type as at 0800 19 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 336 218 (64.9%)

Ventilators 302 64 (21.2%)

Ward beds 7494 5781 (77.1%)

21 National Telehealth Service Coronavirus Update, 0958 19 September 2020

22 Health Workforce Directorate, 0945 14 September 2020

23 COVID-19 Hospital Summary, 0918 19 September 2020

12

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Appendix 1: Case summary Table 9: All community cases reported between 0900 18 September and 0900 19 September. Source: ESR EpiSurv Extract 0900 19 September 2020

s 9(2)(a)

13

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification16 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 11 Sept 12 Sept 13 Sept 14 Sept 15 Sept

** 16 Sept

** 17 Sept

**

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 5% 33% - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 58% 84% - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours 95% 70% - 100% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 67% 100% - - - - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 67% 100% - 0% - - -

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 95% 70% - 100% - - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% 100% - 100% - - -

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours 100% 98% - 100% - - -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 100% 83% - 100% - - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 0% 0% - 0% - - -

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

14

Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 11 Sept ** 12 Sept ** 13 Sept ** 14 Sept ** 15 Sept ** 16 Sept ** 17 Sept **

1 - (S001) Time from exp osure to contact isolation / quarantine

80% within 96 hours - - - 100% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - - - 100% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% - - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - - - 33% - 33% -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 0% - 71% 0%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% - 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - 75% - 58% 0%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% - 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% - 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% - 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

15

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 18 September

Table 12: Metro Auckland Summary Total of Testing for 18 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

5:00pm 1188 122 423 95 57 0 1885

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 15/09 16/09 17/09 18/09*

MIQ Staff 2132 659 1488 912 1086 136 133 202 132 122

Guests 2972 3767 3600 3406 3424 648 688 522 627 423

Border Airport 2129 933 1349 1158 853 156 137 194 164 95

Port 1588 678 161 392 153 90 18 123 32 57

Crew 0 0 0 0 0 0 0 0 0 0

* 18/09 day still in progress

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/0

9

15/09 16/09 17/09 18/09

*

Airport Oaks 1148 515 366 265 181 27 19 25 40 19

Botany CTC 1151 948 905 749 681 126 151 86 184 162

Health New

Lynn

2603 1258 1703 732 889 148 125 82 85 80

Mangere Town

Centre

1748 1684 1599 860 660 75 109 79 98 64

Otara CTC 3221 1712 1429 930 699 91 78 121 383 117

St Lukes 1368 1045 1414 797 666 204 132 111 131 89

Takanini Urgent

Care

1886 1216 1153 684 440 93 108 62 70 70

Whanau House 2502 1371 1442 928 1613 219 174 134 123 101

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16

Whanau Ora -

Central

1957 964 1583 937 783 100 99 45 64 50

Whanau Ora -

North

1442 669 637 982 947 208 221 133 114 88

Whanau Ora -

South

2945 1250 718 677 620 48 79 54 144 76

Manurewa Pop

Up**

N/A N/A N/A N/A N/A 44 50 36 73 24**

Beach Haven

Pop Up**

N/A N/A N/A N/A N/A N/A N/A N/A 27 1**

Westgate Pop

Up**

N/A N/A N/A N/A N/A N/A N/A N/A 21 5**

Henderson Pop

Up

N/A N/A N/A N/A N/A N/A N/A N/A N/A No

Data

Flat Bush Pop

Up

N/A N/A N/A N/A N/A N/A N/A N/A N/A 200

Waiuku Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A No

Data

Waipuna

Targeted Site

143 549 376 219 251 28 39 29 44 38

Henderson

Targeted Site

N/A N/A N/A N/A 631 20 14 35 14 4

Total 26,148 16,781 21,215 13,002 10,475 1518 1622 1228 1624 1188

*18/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included in

this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

IN CONFIDENCE – NOT FOR DISTRIBUTION

17

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 18 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3650 7387 9981 21,330 426 42,774

Bay of Plenty 2741 369 621 7010 67 10,808

Canterbury 1703 676 1956 14,474 238 19,047

Capital and Coast 1574 1200 1541 10,086 232 14,633

Counties Manukau 7848 21,048 9829 13,475 464 52,664

Hawkes Bay 1478 325 248 3794 63 5908

Hutt Valley 861 571 615 3419 47 5513

Lakes 2407 314 481 3357 100 6659

MidCentral 1116 270 418 4465 99 6368

Nelson Marlborough 641 240 298 4607 65 5851

Northland 3207 221 285 4412 54 8179

South Canterbury 150 42 87 1812 12 2103

Southern 1176 416 836 10,908 101 13,437

Tairāwhiti 921 58 70 852 21 1922

Taranaki 722 72 186 2848 52 3880

Waikato 4602 1027 1625 10,850 256 18,360

Wairarapa 246 47 49 1228 9 1579

Waitematā 5092 5550 8904 27,434 370 47,350

West Coast 48 10 13 345 6 422

Whanganui 662 82 73 1530 16 2363

Unknown 1485 747 801 4529 2063 9625

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18

Total 42,330 40,672 38,917 152,766 4761 279,446

19

IN CONFIDENCE – NOT FOR DISTRIBUTION

Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 18 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 83.9 131.7 53.3 81.6 78

Bay of Plenty 45.8 83 31.7 44.6 44.8

Canterbury 32.5 47.7 32.2 32.4 33.2

Capital and Coast 43.1 54.1 30.7 47.4 45.5

Counties Manukau 88.1 175.3 65 64.4 92.5

Hawkes Bay 34.2 50.6 27.1 35.1 35.4

Hutt Valley 33 48.9 32.8 36.3 36.6

Lakes 62.6 122.9 49.4 56 60.1

MidCentral 30.7 48.7 27 36.1 35.1

Nelson Marlborough 40 97.1 40.2 36.6 38.5

Northland 52.7 58.8 34.5 40.5 45

South Canterbury 28.2 86 36.8 35.1 35.2

Southern 35 60.4 32.4 40.8 40.3

Tairāwhiti 37.2 51.9 60 38.5 39.1

Taranaki 30.9 51.7 29.9 31.7 32.1

Waikato 47.7 77 36.8 40.3 43.4

Wairarapa 30.8 56.5 39.3 34.4 34.5

Waitematā 81.4 124.5 61.9 71.7 74.8

West Coast 12.4 39.6 14.1 12.8 13.2

Whanganui 38.1 53.9 24.9 35.6 36.4

Total 54.4 127.2 50.8 49.3 56.3

1

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SITREP 058

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 20 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

2

IMPORTED MIQ

CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

144

123

COMMUNITY CASES

ACTIVE

36 TOTAL CASES SINCE 11 AUG

183

35

TOTAL IMPORTED MIQ CASES

158

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 71

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

5,417

LABORATORY TESTS

LAST SEVEN DAYS

46,384

LABORATORY TESTS

TOTAL

910,853

CASES DECEASED

3

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 20 September 20201

Case Status Active Recovered Deceased Total

Confirmed 71* (+4) 1373 20 1464 (+4)

Probable 0 346 5 351

Total 71* (+4) 1719 25 1815 (+4)

*4 new cases identified, no cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 20 September 20201

New community cases since 0900 19 September 20202

1. Two new community cases have been reported, as at 0900 20 September. Both cases

are household contacts of the community case reported yesterday (see paragraph 2).

New case under investigation since 0900 19 September 20203

2. The new case reported yesterday (19 September) is a returnee who arrived in New

Zealand on 27 August and completed managed isolation in Christchurch. The case

tested negative on day 3 and day 12. They left managed isolation on 11 September and

returned home to Auckland. They were tested after developing symptoms on 16

September. The test returned positive on 18 September. The case and their household

contacts have been transferred to the Auckland Jet Park quarantine facility. The case’s

genome sequence is consistent with two confirmed cases from the same flight to New

Zealand. Source of infection is still under investigation. The two household contacts of

this case returned positive and are now confirmed cases. All three cases have been

isolating at Jet Park quarantine facility since 18 September. Three neighbours who are

close contacts, have all tested negative and been in self-isolation.

1 EpiSurv Database, 0900 20 September 2020

2 EpiSurv Database, 0900 20 September 2020

3 EpiSurv Database, 0900 20 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 (+2) 55 47 1 182 (+2)

Probable 1 0 0 0 1

Total 80 (+2) 55 47 1 183 (+2)

IN CONFIDENCE – NOT FOR DISTRIBUTION

3

Community cases linked to the Auckland Community Cluster August 20204

3. 178 of the 183 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 20 September 2020. The unlinked cases are summarised as

follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 4).

o The remaining three cases are detailed in paragraph 2.

Community cases under investigation to determine a link to the Auckland

community cluster

4. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at day 3 and

day 12 of quarantine. The case subsequently tested positive on 21 August. Despite

using two different whole genome sequencing protocols only there is insufficient

data to confirm the case is genomically linked to the community cluster.5 Their

epidemiological link to the community cluster is still under investigation. As at 15

September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

5. As at 0800 20 September there are 47 people isolating in Jet Park from the community.

20 are confirmed cases, the remaining 27 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.6

MIQ cases since 0900 19 September 20207

6. Two new cases have been detected at the border, as at 0900 20 September. In total 158

cases have been detected at the border since the establishment of MIQ facilities.

Cases in hospital

4 EpiSurv Database, 0900 20 September 2020

5 ESR WGS report 03 September 2020

6 NRHCC Morning Report, 0900 19 September 2020

7 EpiSurv Database, 0900 20 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

4

7. As at 0800 20 September there are three cases in hospital with COVID-19.8

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 20 September 2020

Health system response

Overall approach

8. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview

o There have been no new cases reported in the Auckland community cluster since 14

September. Ongoing scoping of community settings since 14 September has revealed

no major concerns.9

Current outbreak investigation priorities10

o Ongoing management of healthcare workers from Jet Park

o Ongoing management of Chapel Down’s Primary School associated with Botany Cluster.

o Investigation and scoping of the cases linked to the case reported yesterday from the

Christchurch MIF.

8 NRHCC Morning Report 19 September 2020

9 NRHCC Morning Report, 0900 19 September 2020

10NRHCC Morning Report, 0900 20 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 0

Total - 3 0

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

Sub-clusters and settings of interest11

9. The child of the case (paragraph 2) attended an Auckland primary school. As soon as

the developed symptoms, the whole family self-isolated and the child was kept

home from school. One of the close contacts

and attended the same school until 18 September (tested negative).12 The school is now

considered low risk. Further analysis of the symptoms of the is

underway this morning and any implications for the school will be clarified by early

afternoon.

10. A healthcare worker at Jet Park was reported as a case on 13 September. The case has

been epidemiologically and genomically linked to the Auckland Community Cluster.

The case has been epidemiologically linked to a community case who was completing

isolation at Jet Park and required hospitalisation. A review of processes at Jet Park is

underway with a focus on lessons to be learnt from this situation.

11. The healthcare worker is isolating at Jet Park facility. The case has five household close

contacts who are self-isolating at home. All five household contacts have tested

negative twice. All staff at Jet Park staff who are considered close contacts have been

stood down and have returned negative results so far.

12. members of a family in the Botany sub-cluster had serology testing on 11

September which returned negative results for all members. A case linked to the

Botany sub-cluster briefly attended school on 14 September, prior to being notified of

the positive test result that day.13 The school has been closed as a precaution while

close contact tracing and a deep clean is completed. A total of four close contacts have

been identified. All students who attended school (about 470) on 14 September are

casual contacts. Letters have been sent asking students to be tested and to remain in

self-isolation at home until they receive a negative test result. They have also been

asked to contact Healthline if they become symptomatic. Onsite testing has been

arranged from 18 September until 20 September. The school will remain closed until at

least Monday 21 September. Students who receive a negative test will be able to attend

school once it reopens. The investigation is also focusing on what the child did while at

school.14

Case investigation

13. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

11 NRHCC Morning Report, 0900 16 September 2020

12 NRHCC Morning Report, 0900 20 September 2020

13 NRHCC Morning Report 17 September 2020

14 ARPHS email update – 1210 17 September 2020

s 9(2)(a)

s 9(2)(a) s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

IN CONFIDENCE – NOT FOR DISTRIBUTION

)

s 9(2)(a)

s 9(2)(a)

7

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing15 14. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

15.

16. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

17. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

18.

15 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

IN CONFIDENCE – NOT FOR DISTRIBUTION

8

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202016

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing17 19. Between 11 and 17 September 75.0% (111/148) of Community close contacts and 100%

(32/32) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Note: Please note that the total number and number successfully contacted has decreased due

to casual contacts associated with the Les Mills exposure events being excluded.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 20 September 2020

17/09/2020 18/09/2020 19/09/2020 20/09/2020

Number of close contacts

identified1 4043 3912 3918 3916

Number of close contacts

successfully contacted (and are

self-isolating)

4036 3908 3912 3912

Number of close contacts

referred to "finding services"2 1 0 0 0

16 ESR email 1608 14 September 2020

17 COVID-19 NCCS Analytics and Reporting 0931 20 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

9

Number of close contacts

awaiting contact 6 4 2 4

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage18 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

18 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

18 Response Analyst – Digital Channels, 1631 18 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

23

/05

26

/05

29

/05

01

/06

04

/06

07

/06

10

/06

13

/06

16

/06

19

/06

22

/06

25

/06

28

/06

01

/07

04

/07

07

/07

10

/07

13

/07

16

/07

19

/07

22

/07

25

/07

28

/07

31

/07

03

/08

06

/08

09

/08

12

/08

15

/08

18

/08

21

/08

24

/08

27

/08

30

/08

02

/09

05

/09

08

/09

11

/09

14

/09

17

/09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

regi

stra

tio

ns

Day and month

Cumulative App registrations Daily scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

10

Testing19 Table 6: Testing by functional groups, as at 0900 20 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers20 Table 7: Number of laboratory tests processed nationally as at 0900 20 September 2020

Testing supply update21

20. There are no issues with regent supplies, and hologic supplies are now in labs around

the country. There are 43 days of reagent stocks on hand nationally.

19 ÉCLAIR/MoH Public Health Intelligence, 1000 20 September 2020

20 Daily Lab Report, 0818 20 September 2020

21 Testing supply email, 1001 09 September 2020

Reason for test 19 September 13–19 September

GPs and other primary health 3522 20,725

CBACs and pop-ups 1075 20,104

Border workers - air crew 31 245

Border workers - airport staff 207 1339

Border workers - maritime crew 1 32

Border workers – Port of Tauranga staff 183 473

Border workers – Remaining Port staff 57 182

Border workers - MIF 163 1175

Border workers - MIQ 48 465

Travellers - Staying at MIF 127 1686

Travellers - Staying at MIQ 3 33

Total 5417 46,459*

Time period Number of laboratory tests

19 September 5417

Last 7 days (13 Sep to 19 Sep) 46,384*

Total 910,853

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Healthline updates22 21. On 19 September there were 2,227 contacts in Healthline. Of those calls, 482 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 504 contacts (lower than forecast).

22. The main themes on 18 September were:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure events.

o Questions relating to the changes to Alert Levels that may occur this week.

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

Logistics

Health Workforce23

23. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

24. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

25. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity24 Table 8: Number and occupancy of hospital beds by type as at 0800 20 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 278 141 (50.7%)

Ventilators 188 29 (15.4%)

Ward beds 4586 3474 (75.8%)

22 National Telehealth Service Coronavirus Update, 0938 20 September 2020

23 Health Workforce Directorate, 0945 14 September 2020

24 COVID-19 Hospital Summary, 0916 20 September 2020

12

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 1: Case summary Table 9: All community cases reported between 0900 19 September and 0900 20 September. Source: ESR EpiSurv Extract 0900 20 September 2020

s 9(2)(a)

13

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification17 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 12 Sept 13 Sept

** 14 Sept ** 15 Sept ** 16 Sept **

17 Sept **

18 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours 19% - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours 84% - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours 70% - 100% - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours 100% - - - - - -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours 100% - 0% - - - 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours 70% - 100% - - - -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% - 100% - - - 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours 99% - 100% - - - 50%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 70% - 100% - - - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% 0% - 0% - - - 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

14

Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 1 Sept ** 13 Sept ** 14 Sept 15 Sept ** 16 Sept ** 17 Sept ** 18 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - - 100% - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - - 100% - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours 100% - 100% - 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - - 33% - 50% - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours 0% - 0% - 71% 0% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours 100% - 100% - 100% 100% -

7 – (P001) Time from notification to case interview 80% within 24 hours 100% - 75% - 58% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours 100% - 100% - 100% 100% -

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours 100% - 100% - 100% 100% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

0% - 0% - 0% 0% -

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

15

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 18 September

Note this report is not provided over the weekend Table 12: Metro Auckland Summary Total of Testing for 18 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

5:00pm 1188 122 423 95 57 0 1885

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 15/09 16/09 17/09 18/09*

MIQ Staff 2132 659 1488 912 1086 136 133 202 132 122

Guests 2972 3767 3600 3406 3424 648 688 522 627 423

Border Airport 2129 933 1349 1158 853 156 137 194 164 95

Port 1588 678 161 392 153 90 18 123 32 57

Crew 0 0 0 0 0 0 0 0 0 0

* 18/09 day still in progress

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/0

9

15/09 16/09 17/09 18/09

*

Airport Oaks 1148 515 366 265 181 27 19 25 40 19

Botany CTC 1151 948 905 749 681 126 151 86 184 162

Health New

Lynn

2603 1258 1703 732 889 148 125 82 85 80

Mangere Town

Centre

1748 1684 1599 860 660 75 109 79 98 64

Otara CTC 3221 1712 1429 930 699 91 78 121 383 117

St Lukes 1368 1045 1414 797 666 204 132 111 131 89

Takanini Urgent

Care

1886 1216 1153 684 440 93 108 62 70 70

Whanau House 2502 1371 1442 928 1613 219 174 134 123 101

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16

Whanau Ora -

Central

1957 964 1583 937 783 100 99 45 64 50

Whanau Ora -

North

1442 669 637 982 947 208 221 133 114 88

Whanau Ora -

South

2945 1250 718 677 620 48 79 54 144 76

Manurewa Pop

Up**

N/A N/A N/A N/A N/A 44 50 36 73 24**

Beach Haven

Pop Up**

N/A N/A N/A N/A N/A N/A N/A N/A 27 1**

Westgate Pop

Up**

N/A N/A N/A N/A N/A N/A N/A N/A 21 5**

Henderson Pop

Up

N/A N/A N/A N/A N/A N/A N/A N/A N/A No

Data

Flat Bush Pop

Up

N/A N/A N/A N/A N/A N/A N/A N/A N/A 200

Waiuku Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A No

Data

Waipuna

Targeted Site

143 549 376 219 251 28 39 29 44 38

Henderson

Targeted Site

N/A N/A N/A N/A 631 20 14 35 14 4

Total 26,148 16,781 21,215 13,002 10,475 1518 1622 1228 1624 1188

*18/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included in

this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

IN CONFIDENCE – NOT FOR DISTRIBUTION

17

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 19 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3676 7435 10,093 21,479 431 43,114

Bay of Plenty 2775 370 633 7098 68 10,944

Canterbury 1717 686 1983 14,644 248 19,278

Capital and Coast 1587 1213 1556 10,211 234 14,801

Counties Manukau 7998 21,263 9980 13,654 466 53,361

Hawkes Bay 1482 326 248 3804 63 5923

Hutt Valley 867 576 621 3438 47 5549

Lakes 2422 315 482 3391 100 6710

MidCentral 1119 270 420 4489 101 6399

Nelson Marlborough 656 242 302 4712 64 5976

Northland 3223 225 286 4436 54 8224

South Canterbury 151 42 87 1832 12 2124

Southern 1199 418 850 11,050 104 13,621

Tairāwhiti 931 59 70 858 23 1941

Taranaki 725 72 187 2871 52 3907

Waikato 4649 1031 1654 10975 261 18,570

Wairarapa 249 47 52 1249 9 1606

Waitematā 5128 5593 9013 27,687 375 47,796

West Coast 49 10 13 357 6 435

Whanganui 663 82 73 1536 16 2370

Unknown 1494 751 807 4577 2150 9779

Total 42,760 41,026 39,410 154,349 4884 282,429

18

IN CONFIDENCE – NOT FOR DISTRIBUTION

Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 19 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 84.5 132.6 53.9 82.2 78.7

Bay of Plenty 46.4 83.2 32.3 45.1 45.4

Canterbury 32.7 48.4 32.6 32.8 33.6

Capital and Coast 43.4 54.7 31 48 46

Counties Manukau 89.8 177.1 66 65.3 93.7

Hawkes Bay 34.3 50.8 27.1 35.2 35.5

Hutt Valley 33.3 49.3 33.1 36.5 36.8

Lakes 63 123.3 49.5 56.5 60.6

MidCentral 30.8 48.7 27.1 36.3 35.3

Nelson Marlborough 40.9 97.9 40.7 37.4 39.4

Northland 53 59.9 34.6 40.7 45.2

South Canterbury 28.4 86 36.8 35.5 35.5

Southern 35.7 60.7 32.9 41.3 40.8

Tairāwhiti 37.6 52.8 60 38.8 39.5

Taranaki 31.1 51.7 30 31.9 32.3

Waikato 48.2 77.3 37.5 40.8 43.9

Wairarapa 31.2 56.5 41.7 35 35.1

Waitematā 81.9 125.4 62.7 72.4 75.5

West Coast 12.6 39.6 14.1 13.2 13.6

Whanganui 38.2 53.9 24.9 35.7 36.5

Total 55 128.3 51.4 49.9 56.9

1

IN CONFIDENCE – NOT FOR DISTRIBUTION

SITREP 059

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 21 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ

CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

147

129

COMMUNITY CASES

ACTIVE

33 TOTAL CASES SINCE 11 AUG

183

29

TOTAL IMPORTED MIQ CASES

158

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 62

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

3,568

LABORATORY TESTS

LAST SEVEN DAYS

46,379

LABORATORY TESTS

TOTAL

914,421

CASES DECEASED

3

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 21 September 20201

Case Status Active Recovered Deceased Total

Confirmed 62* (-9) 1382 (+9) 20 1464

Probable 0 346 5 351

Total 62* (-9) 1728 (+9) 25 1815

*0 new cases identified, 9 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 21 September 20201

New community cases since 0900 20 September 20202

1. No new community cases have been reported, as at 0900 21 September.

New case under investigation since 0900 20 September 20203

2. The case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September. The test returned positive on 18 September. The case and

their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September. The

case’s genome sequence is consistent with two confirmed cases from the same flight to

New Zealand.4 Source of infection is still under investigation. Three neighbours who are

close contacts, have all tested negative and been in self-isolation. The 87 passengers of

the charter flight are being contacted and assessed. The first nine rows (who sat near

the case) have been asked to self-isolate and have been tested, with results pending.

1 EpiSurv Database, 0900 21 September 2020

2 EpiSurv Database, 0900 21 September 2020

3 EpiSurv Database, 0900 21 September 2020

4 WGS Interim Report, 0313 21 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 55 47 1 182

Probable 1 0 0 0 1

Total 80 55 47 1 183

IN CONFIDENCE – NOT FOR DISTRIBUTION

3

Community cases linked to the Auckland Community Cluster August 20205

3. 178 of the 183 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 21 September 2020. The unlinked cases are summarised as

follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 4).

o The three cases detailed in paragraph 2.

Community cases under investigation to determine a link to the Auckland

community cluster

4. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at day 3 and

day 12 of quarantine. The case subsequently tested positive on 21 August. Despite

using two different whole genome sequencing protocols only there is insufficient

data to confirm the case is genomically linked to the community cluster.6 Their

epidemiological link to the community cluster is still under investigation. As at 21

September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

5. As at 0800 21 September there are 40 people isolating in Jet Park from the community.

17 are confirmed cases, the remaining 23 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.7

MIQ cases since 0900 20 September 20208

6. No new cases have been detected at the border, as at 0900 21 September. In total 158

cases have been detected at the border since the establishment of MIQ facilities.

5 EpiSurv Database, 0900 21 September 2020

6 ESR WGS report 03 September 2020

7 NRHCC Morning Report, 0900 21 September 2020

8 EpiSurv Database, 0900 21 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

4

Cases in hospital

7. As at 0800 21 September there are three cases in hospital with COVID-19.9

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 21 September 2020

Health system response

Overall approach

8. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview

o There have been no new cases reported in the Auckland community cluster since 14

September. Ongoing scoping of community settings since 14 September has revealed

no major concerns.10

Current outbreak investigation priorities11

o Ongoing management of healthcare workers from Jet Park.

o Ongoing management of Auckland community cluster work.

o Ongoing source investigation and contact tracing linked to the case reported 19

September.

9 NRHCC Morning Report 21 September 2020

10 NRHCC Morning Report, 0900 19 September 2020

11NRHCC Morning Report, 0900 21 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 0

Total - 3 0

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

Sub-clusters and settings of interest12

9. The child of the case (paragraph 2) attended an Auckland primary school. As soon as

the developed symptoms, the whole family self-isolated and the child was kept

home from school. One of the close contacts

and attended the same school until 18 September (tested negative).13 The school is

considered low risk. Further analysis of the symptoms of the is

underway and any implications for the school will be clarified.

10. A healthcare worker at Jet Park was reported as a case on 13 September. The case has

been epidemiologically and genomically linked to the Auckland Community Cluster.

The case has been epidemiologically linked to a community case who was completing

isolation at Jet Park and required hospitalisation. A review of processes at Jet Park is

underway with a focus on lessons to be learnt from this situation.

11. The healthcare worker is isolating at Jet Park facility. The case has five household close

contacts who are self-isolating at home. All five household contacts have tested

negative twice. All staff at Jet Park staff who are considered close contacts have been

stood down and have returned negative results so far.

12. members of a family in the Botany sub-cluster had serology testing on 11

September which returned negative results for all members. A case linked to the

Botany sub-cluster briefly attended school on 14 September, prior to being notified of

the positive test result that day.14 The school has been closed as a precaution while

close contact tracing and a deep clean is completed. A total of four close contacts have

been identified. All students who attended school (about 470) on 14 September are

casual contacts. Letters have been sent asking students to be tested and to remain in

self-isolation at home until they receive a negative test result. They have also been

asked to contact Healthline if they become symptomatic. Onsite testing has been

arranged from 18 September until 20 September. The school is now open.

Case investigation

13. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

12 NRHCC Morning Report, 0900 16 September 2020

13 NRHCC Morning Report, 0900 20 September 2020

14 NRHCC Morning Report 17 September 2020

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

IN CONFIDENCE – NOT FOR DISTRIBUTION

1.

2.

s 9(2)(a)

s 9(2)(a)

7

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing15 14. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

15.

16. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

17. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

18.

15 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

IN CONFIDENCE – NOT FOR DISTRIBUTION

8

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202016

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing17 19. Between 12 and 18 September 77.2% (169/219) of Community close contacts and 100%

(32/32) MIQ close contacts have been contacted within 48 hours of being determined

to be a contact. KPI for this metric is 80% of close contacts within 48 hours.

o Note: Please note that the total number and number successfully contacted has decreased due

to casual contacts associated with the Les Mills exposure events being excluded.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 12 August as at

0830 21 September 2020

18/09/2020 19/09/2020 20/09/2020 21/09/2020

Number of close contacts

identified1 3912 3918 3916 3989

Number of close contacts

successfully contacted (and are

self-isolating)

3908 3912 3912 3978

Number of close contacts

referred to "finding services"2 0 0 0 0

16 ESR email 1608 14 September 2020

17 COVID-19 NCCS Analytics and Reporting 0928 21 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

9

Number of close contacts

awaiting contact 4 2 4 11

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage18 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 0900

21 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

18 Response Analyst – Digital Channels, 0912 21 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20

/05

23

/05

26

/05

29

/05

01

/06

04

/06

07

/06

10

/06

13

/06

16

/06

19

/06

22

/06

25

/06

28

/06

01

/07

04

/07

07

/07

10

/07

13

/07

16

/07

19

/07

22

/07

25

/07

28

/07

31

/07

03

/08

06

/08

09

/08

12

/08

15

/08

18

/08

21

/08

24

/08

27

/08

30

/08

02

/09

05

/09

08

/09

11

/09

14

/09

17

/09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

regi

stra

tio

ns

Day and month

Cumulative App registrations Daily scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

10

Testing19 Table 6: Testing by functional groups, as at 0900 21 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers20 Table 7: Number of laboratory tests processed nationally as at 0900 21 September 2020

Testing supply update21

20. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

19 ÉCLAIR/MoH Public Health Intelligence, 1000 20 September 2020

20 Daily Lab Report, 0923 21 September 2020

21 Testing supply email, 0939 21 September 2020

Reason for test 20 September 14–20 September

GPs and other primary health 1572 17,917

CBACs and pop-ups 1395 22,932

Border workers - air crew 25 246

Border workers - airport staff 104 1332

Border workers - maritime crew 0 32

Border workers – Port of Tauranga staff 1 473

Border workers – Remaining Port staff 3 181

Border workers - MIF 156 1212

Border workers - MIQ 54 435

Travellers - Staying at MIF 255 1770

Travellers - Staying at MIQ 4 34

Total 3569* 46,564*

Time period Number of laboratory tests

20 September 3568*

Last 7 days (14 Sep to 20 Sep) 46,379*

Total 914,421

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Healthline updates22 21. On 20 September there were 2,357 contacts in Healthline. Of those calls, 588 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 562 contacts (lower than forecast).

22. The main themes on 20 September were:

o National Telehealth Service (Healthline) continued to take calls related to the

exposure event, including in response to media reporting on possible school

students yesterday.

o Questions relating to the changes to Alert Levels that may occur this week. When

alert levels are changed it would be useful to ensure that this is supported by a single

source of information on the various alert levels being set and what it means.

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested.

Logistics

Health Workforce23

23. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

24. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

25. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

22 National Telehealth Service Coronavirus Update, 0921 21 September 2020

23 Health Workforce Directorate, 0945 14 September 2020

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12

Hospital capacity24 Table 8: Number and occupancy of hospital beds by type as at 0800 21 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 389 208 (53.5%)

Ventilators 299 53 (17.7%)

Ward beds 7257 5782 (79.7%)

24 COVID-19 Hospital Summary, 0904 21 September 2020

13

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Appendix 1: Case summary Table 9: All community cases reported between 0900 20 September and 0900 21 September. Source: ESR EpiSurv Extract 0900 21 September 2020

Cumulative

Number

Date tested

positive Onset date

Case

status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

14

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification17 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

15

Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

16

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1000 21 September

Table 12: Metro Auckland Summary Total of Testing for 18 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

19/09/2020 962 98 526 91 No testing No

testing 1677

20/09/2020 635 75 409 72 No testing No

testing 1191

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

19/09 20/09

MIQ Staff 2132 659 1488 912 1086 908 98 75

Guests 2972 3767 3600 3406 3424 3843 526 409

Border Airport 2129 933 1349 1158 853 951 91 72

Port 1588 678 161 392 153 320 No

testing

No

testing

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at

4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

19/09 20/09

Airport Oaks 1148 515 366 265 181 152 8 14

Botany CTC 1151 948 905 749 681 802 52 41

Health New Lynn 2603 1258 1703 732 889 613 45 48

Mangere Town

Centre

1748 1684 1599 860 660 487 41 21

Otara CTC 3221 1712 1429 930 699 938 86 62

St Lukes 1368 1045 1414 797 666 830 75 88

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17

Takanini Urgent

Care

1886 1216 1153 684 440 487 37 47

Whanau House 2502 1371 1442 928 1613 822 71 48

Whanau Ora -

Central

1957 964 1583 937 783 470 43 49

Whanau Ora -

North

1442 669 637 982 947 907 64 79

Whanau Ora -

South

2945 1250 718 677 620 470 46 12

Flat Bush Pop Up N/A N/A N/A N/A N/A 349 111 38

Pakuranga Pop Up N/A N/A N/A N/A N/A 59 30 29

Panmure Pop Up N/A N/A N/A N/A N/A 100 57 43

Beach Haven Pop

Up N/A N/A N/A N/A N/A 74 46 N/A

Henderson Pop Up N/A N/A N/A N/A N/A 46 45 N/A

Otara Pop Up N/A N/A N/A N/A N/A 73 73 N/A

Waipuna Targeted

Site

143 549 376 219 251 220 28 14

Henderson

Targeted Site

N/A N/A N/A N/A 631 93 4 2

Total 26,148 16,781 21,215 13,002 10,475 8,776 962 635

N/A = not open as a CTC; Previous sites that are no longer open are not included in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

IN CONFIDENCE – NOT FOR DISTRIBUTION

18

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 20 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3699 7480 10,198 21,644 441 43,462

Bay of Plenty 2789 373 634 7126 68 10,990

Canterbury 1723 687 2006 14,703 254 19,373

Capital and Coast 1596 1219 1576 10,266 239 14,896

Counties Manukau 8039 21,442 10,087 13,757 475 53,800

Hawkes Bay 1485 326 248 3809 64 5932

Hutt Valley 871 577 625 3457 50 5580

Lakes 2432 315 485 3400 101 6733

MidCentral 1125 271 420 4505 101 6422

Nelson Marlborough 657 242 304 4725 68 5996

Northland 3243 226 288 4470 57 8284

South Canterbury 151 43 87 1843 14 2138

Southern 1199 418 851 11,083 109 13,660

Tairāwhiti 933 59 70 861 23 1946

Taranaki 731 74 189 2911 53 3958

Waikato 4667 1040 1672 11,043 267 18,689

Wairarapa 250 47 52 1252 10 1611

Waitematā 5152 5653 9075 27,868 382 48,130

West Coast 49 10 13 357 6 435

Whanganui 663 82 73 1536 16 2370

Unknown 1514 755 825 4614 2223 9931

Total 42,968 41,339 39,778 155,231 5021 284,337

19

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 20 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 85 133.4 54.5 82.8 79.3

Bay of Plenty 46.6 83.9 32.4 45.3 45.6

Canterbury 32.9 48.4 33 33 33.8

Capital and Coast 43.7 55 31.4 48.3 46.3

Counties Manukau 90.3 178.5 66.7 65.7 94.5

Hawkes Bay 34.3 50.8 27.1 35.3 35.5

Hutt Valley 33.4 49.4 33.3 36.7 37

Lakes 63.2 123.3 49.9 56.7 60.8

MidCentral 30.9 48.8 27.1 36.4 35.4

Nelson Marlborough 41 97.9 41 37.5 39.5

Northland 53.3 60.1 34.8 41 45.5

South Canterbury 28.4 88.1 36.8 35.7 35.7

Southern 35.7 60.7 33 41.4 40.9

Tairāwhiti 37.7 52.8 60 38.9 39.6

Taranaki 31.3 53.1 30.3 32.4 32.7

Waikato 48.4 78 37.9 41 44.2

Wairarapa 31.3 56.5 41.7 35.1 35.2

Waitematā 82.3 126.8 63.1 72.9 76

West Coast 12.6 39.6 14.1 13.2 13.6

Whanganui 38.2 53.9 24.9 35.7 36.5

Total 55.3 129.3 51.9 50.1 57.3

1

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SITREP 060

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 22 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ

CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

148

129

COMMUNITY CASES

ACTIVE

32 TOTAL CASES SINCE 11 AUG

183

29

TOTAL IMPORTED MIQ CASES

158

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 61

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

3,278

LABORATORY TESTS

LAST SEVEN DAYS

45,255

LABORATORY TESTS

TOTAL

917,699

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 22 September 20201

Case Status Active Recovered Deceased Total

Confirmed 61* (-1) 1383 (+1) 20 1464

Probable 0 346 5 351

Total 61* (-1) 1729 (+1) 25 1815

*0 new cases identified, 1 case classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 22 September 20201

New community cases since 0900 21 September 20202

1. No new community cases have been reported, as at 0900 22 September.

Community cases under investigation since 0900 21 September 20203

2. The case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September. The test returned positive on 18 September. The case and

their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September. The

case’s genome sequence is consistent with two confirmed cases from the same flight to

New Zealand.4 Source of infection is still under investigation. Three neighbours who are

close contacts, have all tested negative and been in self-isolation.

3. The 87 passengers of the charter flight are being contacted and assessed. The first nine

rows (who sat near the case) have been asked to self-isolate and have been tested,

results in table 4 below. One of the passengers from the chartered flight returned a

positive test with a high CT value yesterday (21 September). They were retested and

returned a negative result this morning (22 September). This person was reported in

1 EpiSurv Database, 0900 22 September 2020

2 EpiSurv Database, 0900 22 September 2020

3 EpiSurv Database, 0900 22 September 2020

4 WGS Interim Report, 0313 21 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 55 47 1 182

Probable 1 0 0 0 1

Total 80 55 47 1 183

IN CONFIDENCE – NOT FOR DISTRIBUTION

3

the end of day report on 21 September and in the text message at 0900 22 September

as a confirmed case. However, the case status of this person has been reclassified as

under investigation, due to the subsequent negative test, to determine if it is an historic

case and if they were already reported as a case in India. A precautionary approach is

being taken and they have been transferred to the Auckland Jet Park facility. The case

was a close contact of the case reported on 19 September on the flight from Fiji to

Christchurch on 27 August and was also a passenger on the charter flight from

Christchurch to Auckland on 11 September.

4. An expert panel is being established to consider cases with high CT counts to

determine their status and develop a protocol for reporting, management, and

investigation of potentially historic infections. As a consequence, historic cases under

investigation will be included in future reporting.

Community cases linked to the Auckland Community Cluster August 20205

5. 178 of the 183 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 22 September 2020. The unlinked cases are summarised as

follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 4).

o The three cases detailed in paragraph 2.

Community cases under investigation to determine a link to the Auckland

community cluster

6. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at day 3 and

day 12 of quarantine. The case subsequently tested positive on 21 August. Despite

using two different whole genome sequencing protocols only there is insufficient

data to confirm the case is genomically linked to the community cluster.6 Their

epidemiological link to the community cluster is still under investigation. As at 21

September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

7. As at 0800 22 September there are 39 people isolating in Jet Park from the community.

18 are confirmed cases, the remaining 21 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.7

5 EpiSurv Database, 0900 22 September 2020

6 ESR WGS report 03 September 2020

7 NRHCC Morning Report, 0845 22 September 2020

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4

MIQ cases since 0900 21 September 20208

8. No new cases have been detected at the border, as at 0900 22 September. In total 158

cases have been detected at the border since the establishment of MIQ facilities.

Cases in hospital

9. As at 0800 22 September there are three cases in hospital with COVID-19.9

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 22 September 2020

Health system response

Overall approach

10. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview

o There have been no new cases reported in the Auckland community cluster since 14

September.

Current outbreak investigation priorities10

o Ongoing management of healthcare workers from Jet Park.

o Ongoing management of Auckland community cluster work.

8 EpiSurv Database, 0900 22 September 2020

9 NRHCC Morning Report, 0845 22 September 2020

10NRHCC Morning Report, 0845 22 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 0

Total - 3 0

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

o Ongoing source investigation and contact tracing linked to the case reported 19

September.

Sub-clusters and settings of interest11

11. The child of the case (paragraph 2) attended an Auckland primary school. As soon as

the developed symptoms, the whole family self-isolated and the child was kept

home from school. One of the close contacts

and attended the same school until 18 September (tested negative).12 The school is

considered low risk. Further analysis of the symptoms of the is

underway and any implications for the school will be clarified.

12. A healthcare worker at Jet Park was reported as a case on 13 September. The case has

been epidemiologically and genomically linked to the Auckland Community Cluster.

The case has been epidemiologically linked to a community case who was completing

isolation at Jet Park and required hospitalisation. A review of processes at Jet Park is

underway with a focus on lessons to be learnt from this situation.

13. The healthcare worker is isolating at Jet Park facility. The case has close

contacts who are self-isolating at home. All contacts have tested

negative twice. All staff at Jet Park staff who are considered close contacts have been

stood down and have returned negative results so far.

14. members of a family in the Botany sub-cluster had serology testing on 11

September which returned negative results for all members. A case linked to the

Botany sub-cluster briefly attended school on 14 September, prior to being notified of

the positive test result that day.13 The school has been closed as a precaution while

close contact tracing and a deep clean is completed. A total of four close contacts have

been identified. All students who attended school (about 470) on 14 September are

casual contacts. Letters have been sent asking students to be tested and to remain in

self-isolation at home until they receive a negative test result. They have also been

asked to contact Healthline if they become symptomatic. Onsite testing has been

arranged from 18 September until 20 September. The school is now open.

Case investigation

15. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

11 NRHCC Morning Report, 0900 16 September 2020

12 NRHCC Morning Report, 0900 20 September 2020

13 NRHCC Morning Report 17 September 2020

s 9(2)(a)

s 9(2)(a) s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

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1.

2.

s 9(2)(a)

s 9(2)(a)

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7

s 9(2)(a)

8

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing14 16. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

17.

18. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

19. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

20.

14 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

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9

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202015

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing16 21. Since the 11 August, 4003 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 3992 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 22 September 2020

19/09/2020 20/09/2020 21/09/2020 22/09/2020

Cumulative number of close

contacts identified1 3918 3916 3989 4003

Cumulative number of close

contacts successfully contacted 3912 3912 3978 3992

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 2 4 11 11

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

15 ESR email 1608 14 September 2020

16 COVID-19 NCCS Analytics and Reporting 0921 22 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

10

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1600

21 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

17 Response Analyst – Digital Channels, 1617 21 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

09

05/

09

08/

09

11/

09

14/

09

17/

09

20/

09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Testing18 Table 6: Testing by functional groups, as at 0900 22 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 7: Number of laboratory tests processed nationally as at 0900 22 September 2020

Testing supply update20

22. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 22 September 2020

19 Daily Lab Report, 0921 22 September 2020

20 Testing supply email, 0939 21 September 2020

Reason for test 21 September 15–21 September

GPs and other primary health 1488 17908

CBACs and pop-ups 1044 21600

Border workers - air crew 20 261

Border workers - airport staff 85 1288

Border workers - maritime crew 26 58

Border workers – Port of Tauranga staff 0 473

Border workers – Remaining Port staff 3 180

Border workers - MIF 95 1190

Border workers - MIQ 43 313

Travellers - Staying at MIF 312 1869

Travellers - Staying at MIQ 162 190

Total 3278* 45,330*

Time period Number of laboratory tests

21 September 3278*

Last 7 days (15 Sep to 21 Sep) 45,255*

Total 917,699

IN CONFIDENCE – NOT FOR DISTRIBUTION

12

Healthline updates21 23. On 21 September there were 2,510 contacts in Healthline. Of those calls, 1,121were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 647 contacts (in line with forecast).

24. The main themes on 21 September were:

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested. Increased level of people checking testing centre locations

and asking if family need to isolate with them.

o Some questions on pre-departure testing requirements.

o Questions relating to the changes to alert levels.

Logistics

Health Workforce22

25. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

26. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

27. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity23 Table 8: Number and occupancy of hospital beds by type as at 0800 22 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 422 282 (66.8%)

Ventilators 330 74 (22.4%)

Ward beds 7641 6228 (81.5%)

21 National Telehealth Service Coronavirus Update, 0940 22 September 2020

22 Health Workforce Directorate, 0945 14 September 2020

23 COVID-19 Hospital Summary, 0914 22 September 2020

13

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Appendix 1: Case summary Table 9: All community cases reported between 0900 21 September and 0900 22 September. Source: ESR EpiSurv Extract 0900 22 September 2020

Cumulative

Number

Date tested

positive Onset date

Case

status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

14

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification16 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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15

Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 21 September

Table 12: Metro Auckland Summary Total of Testing for 18 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

21/09/2020 1,013 118 599 112 49 0 1,891

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 – 06/09 07/09 – 13/09 14/09 –

20/09

21/09*

MIQ Staff 2132 659 1488 912 1086 908 118

Guests 2972 3767 3600 3406 3424 3843 599

Border Airport 2129 933 1349 1158 853 951 112

Port 1588 678 161 392 153 320 49

Crew 0 0 0 0 0 0 0

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09*

Airport Oaks 1148 515 366 265 181 152 18

Botany CTC 1151 948 905 749 681 802 99

Health New Lynn 2603 1258 1703 732 889 621 101

Mangere Town

Centre

1748 1684 1599 860 660 487 70

Otara CTC 3221 1712 1429 930 699 938 65

St Lukes 1368 1045 1414 797 666 830 158

Takanini Urgent Care 1886 1216 1153 684 440 487 65

Whanau House 2502 1371 1442 928 1613 870 129

Whanau Ora - Central 1957 964 1583 937 783 470 90

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Whanau Ora - North 1442 669 637 982 947 907 111

Whanau Ora - South 2945 1250 718 677 620 470 61

Takanini Pop Up N/A N/A N/A N/A N/A N/A 17

Waipuna Targeted

Site

143 549 376 219 251 220 28

Henderson Targeted

Site

N/A N/A N/A N/A 631 93 1

Total 26,148 16,781 21,215 13,002 10,475 8,832 1,013

N/A = not open as a CTC; Previous sites that are no longer open are not included in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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18

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 21 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3714 7504 10,287 21,759 447 43,711

Bay of Plenty 2799 374 636 7144 69 11,022

Canterbury 1726 688 2027 14,749 256 19,446

Capital and Coast 1613 1311 1598 10,364 243 15,129

Counties Manukau 8075 21,522 10,161 13,824 477 54,059

Hawkes Bay 1526 330 252 3893 65 6066

Hutt Valley 877 582 629 3468 50 5606

Lakes 2432 314 487 3410 102 6745

MidCentral 1150 273 430 4600 103 6556

Nelson Marlborough 657 243 310 4749 68 6027

Northland 3247 226 288 4476 56 8293

South Canterbury 151 43 88 1845 14 2141

Southern 1202 419 871 11,139 110 13,741

Tairāwhiti 938 59 70 877 23 1967

Taranaki 734 74 189 2923 53 3973

Waikato 4676 1044 1683 11,066 268 18,737

Wairarapa 252 47 52 1267 10 1628

Waitematā 5171 5667 9166 28,014 388 48,406

West Coast 49 10 13 357 6 435

Whanganui 671 83 75 1563 16 2408

Unknown 1518 752 840 4657 2246 10,013

Total 43,178 41,565 40,152 156,145 5070 286,110

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 21 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 85.4 133.8 55 83.2 79.7

Bay of Plenty 46.8 84.1 32.5 45.4 45.7

Canterbury 32.9 48.5 33.4 33.1 33.9

Capital and Coast 44.2 59.1 31.8 48.7 47

Counties Manukau 90.7 179.2 67.2 66.1 94.9

Hawkes Bay 35.3 51.4 27.5 36 36.4

Hutt Valley 33.7 49.8 33.5 36.8 37.2

Lakes 63.2 122.9 50.1 56.9 60.9

MidCentral 31.6 49.2 27.7 37.2 36.2

Nelson Marlborough 41 98.3 41.8 37.7 39.7

Northland 53.4 60.1 34.8 41.1 45.6

South Canterbury 28.4 88.1 37.2 35.7 35.8

Southern 35.8 60.8 33.8 41.6 41.2

Tairāwhiti 37.9 52.8 60 39.7 40

Taranaki 31.4 53.1 30.3 32.5 32.9

Waikato 48.5 78.3 38.1 41.1 44.3

Wairarapa 31.6 56.5 41.7 35.5 35.6

Waitematā 82.6 127.1 63.7 73.3 76.4

West Coast 12.6 39.6 14.1 13.2 13.6

Whanganui 38.6 54.5 25.6 36.3 37.1

Total 55.5 130 52.4 50.4 57.7

1

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SITREP 061

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 23 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

3

IMPORTED MIQ CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

149

130

COMMUNITY CASES

ACTIVE

34 TOTAL CASES SINCE 11 AUG

186

28

TOTAL IMPORTED MIQ CASES

158

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 62

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

6,938

LABORATORY TESTS

LAST SEVEN DAYS

43,105

LABORATORY TESTS

TOTAL

924,637

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 23 September 20201

Case Status Active Recovered Deceased Total

Confirmed 62* (+1) 1386 (+3) 20 1468 (+4)

Probable 0 351 (+5) 5 356 (+5)

Total 62* (+1) 1737 (+8) 25 1824** (+9)

*3 newly identified cases, 2 cases classified as recovered from the August 2020 Auckland outbreak

**6 historic community cases newly reported today (1 confirmed, 5 probable) all are recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 23 September 20201

New community cases since 0900 22 September 20202

1. Three new community cases have been reported, as at 0900 23 September.

o All three cases are within the same family unit. They were tested as contacts from the

charter flight from Christchurch to Auckland which had a confirmed case reported on

19 September. . All

have been in isolation since 20 September.

o There are also six newly reported historic cases. See paragraph 8 for details.

Community cases under investigation since 0900 22 September 20203

2. The case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September. The test returned positive on 18 September. The case and

their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September. The

case’s genome sequence is consistent with two confirmed cases from the same flight to

New Zealand.4 Source of infection is still under investigation.

1 EpiSurv Database, 0900 23 September 2020

2 EpiSurv Database, 0900 23 September 2020

3 EpiSurv Database, 0900 23 September 2020

4 WGS Interim Report, 0313 21 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 55 50 (+3) 1 185 (+3)

Probable 1 0 0 0 1

Total 80 55 50 (+3) 1 186 (+3)

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3

3. One of the passengers from the same chartered flight from Christchurch to Auckland as

the initially reported positive returnee returned a positive test with a high CT value on

21 September. They were retested and returned a negative result on 22 September.

This person was reported in the end of day report on 22 September and in the text

message at 0900 22 September as a confirmed case. However, the case status of this

person has been reclassified as under investigation, due to the subsequent negative

test, to determine if it is an historic case and if they were already reported as a case in

India. A precautionary approach is being taken and they have been transferred to the

Auckland Jet Park facility. The case was a close contact of the case reported on 19

September on the flight from Fiji to Christchurch on 27 August and was also a

passenger on the charter flight from Christchurch to Auckland on 11 September.

Additional investigations are underway today (23 September).

Community cases linked to the Auckland Community Cluster August 20205

4. 178 of the 186 community cases have been linked to the Auckland Community Cluster

August 2020, as at 0900 23 September 2020. The unlinked cases are summarised as

follows:

o The Rydges employee (this investigation has been closed).

o A case (reported 21 August) is still under investigation for an epidemiological link to

the community cluster. There is insufficient data to confirm a genomic link to the

community cluster (see 4).

o The third case is the case report on 19 September as detailed in paragraph 2.

o The final three are the three new cases reported today, see paragraph 1 for details.

Community cases under investigation to determine a link to the Auckland

community cluster

5. The case under investigation is summarised as follows:

o One case came through the border on 18 June. The case tested negative at day 3 and

day 12 of quarantine. The case subsequently tested positive on 21 August. Despite

using two different whole genome sequencing protocols only there is insufficient

data to confirm the case is genomically linked to the community cluster.6 Their

epidemiological link to the community cluster is still under investigation. As at 21

September no additional information has been revealed by the investigation.

Community cases and household contacts at Jet Park

6. As at 0800 23 September there are 37 people isolating in Jet Park from the community.

17 are confirmed cases, the remaining 20 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.7

5 EpiSurv Database, 0900 23 September 2020

6 ESR WGS report 03 September 2020

7 NRHCC Morning Report, 0845 22 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

4

MIQ cases since 0900 22 September 20208

7. No new cases have been detected at the border, as at 0900 23 September. In total 158

cases have been detected at the border since the establishment of MIQ facilities.

Historically reported cases

8. Six cases reported today (23 September), one confirmed and five probable, are historic

cases. This means they all have old infections which have been diagnosed

retrospectively. They are not included in the total cases since 11 August, as they are

historic cases. All members had positive serology tests, and one family member has

returned a positive PCR test result. All six cases are from the same family unit and have

recovered.

9. A member of the family arrived in New Zealand from Italy in February. became

symptomatic while in New Zealand however was not tested. Subsequently, all other

family members experienced symptoms in February/early March. The family were not

tested when they were unwell, as they did not meet the case definition in place at that

time. In July, the family member from Italy completed serology in Italy which was

returned positive. Of the six cases, the one confirmed case is a member of the family

who experienced mild symptoms recently so was tested on 10

September and returned a positive result. The result had a high Ct value, which means

low levels of viral load and indicates an old infection. The case has had four tests, all

with a high Ct value, which is consistent with an old infection together with positive

serology. The other family members had a negative PCR result but positive

serology and have been classified as probable cases.

Cases in hospital

10. Three cases in hospital with COVID-19 as at 0800 23 September.9

Table 3: Number of cases in hospital with COVID-19 by DHB as at 0800 23 September 2020

Health system response

Overall approach

11. Our investigation has two main focus areas that run in parallel:

8 EpiSurv Database, 0900 22 September 2020

9 NRHCC Morning Report, 0845 22 September 2020

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 0

Total - 3 0

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o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

Current outbreak overview

o There have been no new cases reported in the Auckland community cluster since 14

September.

Current outbreak investigation priorities10

o Ongoing management of healthcare workers from Jet Park.

o Ongoing management of Auckland community cluster work.

o Ongoing source investigation and contact tracing linked to the case reported 19

September.

Sub-clusters and settings of interest11

12. The child of the case (paragraph 2) attended an Auckland primary school. As soon as

the developed symptoms, the whole family self-isolated and the child was kept

home from school. One of the close contacts

and attended the same school until 18 September (tested negative).12 The school is

considered low risk. Further analysis of the symptoms of the is

underway and any implications for the school will be clarified.

13. A healthcare worker at Jet Park was reported as a case on 13 September. The case has

been epidemiologically and genomically linked to the Auckland Community Cluster.

The case has been epidemiologically linked to a community case who was completing

isolation at Jet Park and required hospitalisation. A review of processes at Jet Park is

underway with a focus on lessons to be learnt from this situation.

14. members of a family in the Botany sub-cluster had serology testing on 11

September which returned negative results for all members. A case linked to the

Botany sub-cluster briefly attended school on 14 September, prior to being notified of

the positive test result that day.13 The school has been closed as a precaution while

close contact tracing and a deep clean is completed. A total of four close contacts have

been identified. All students who attended school (about 470) on 14 September are

casual contacts. Letters have been sent asking students to be tested and to remain in

self-isolation at home until they receive a negative test result. They have also been

asked to contact Healthline if they become symptomatic. Onsite testing has been

arranged from 18 September until 20 September. The school is now open.

Case investigation

10NRHCC Morning Report, 0845 22 September 2020

11 NRHCC Morning Report, 0900 16 September 2020

12 NRHCC Morning Report, 0900 20 September 2020

13 NRHCC Morning Report 17 September 2020

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15. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

16. Investigation regarding the recent Christchurch flight case is ongoing. The 87

passengers of the charter flight are being contacted and assessed. The first nine rows

(who sat near the case) have been asked to self-isolate and have been tested, results in

table 4 below. Three neighbours who are close contacts, have all tested negative and

been in self-isolation.

17. One of the passengers from the same chartered flight from Christchurch to Auckland as

the initially reported positive returnee returned a positive test with a high CT value on

21 September. They were retested and returned a negative result this on 22 September.

This person was reported in the end of day report on 22 September and in the text

message at 0900 22 September as a confirmed case. However, the case status of this

person has been reclassified as under investigation, due to the subsequent negative

test, to determine if it is an historic case and if they were already reported as a case in

India. A precautionary approach is being taken and they have been transferred to the

Auckland Jet Park facility. The case was a close contact of the case reported on 19

September on the flight from Fiji to Christchurch on 27 August and was also a

passenger on the charter flight from Christchurch to Auckland on 11 September.

18. An expert panel is being established to consider cases with high CT counts to

determine their status and develop a protocol for reporting, management, and

investigation of potentially historic infections. As a consequence, historic cases under

investigation will be included in future reporting.

s 9(2)(a)

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1.

2.

3.

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8

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing14 19. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

20.

21. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

22. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

23.

14 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

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Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202015

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing16 24. Since the 11 August, 4014 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 4006 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest.

Table 5: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 23 September 2020

20/09/2020 21/09/2020 22/09/2020 23/09/2020

Cumulative number of close

contacts identified1 3916 3989 4003 4014

Cumulative number of close

contacts successfully contacted 3912 3978 3992 4006

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 4 11 11 8

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

15 ESR email 1608 14 September 2020

16 COVID-19 NCCS Analytics and Reporting 0934 23 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

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10

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

22 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

17 Response Analyst – Digital Channels, 1616 22 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

09

05/

09

08/

09

11/

09

14/

09

17/

09

20/

09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing18 Table 6: Testing by functional groups, as at 0900 23 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 7: Number of laboratory tests processed nationally as at 0900 23 September 2020

Testing supply update20

25. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 23 September 2020

19 Daily Lab Report, 0927 23 September 2020

20 Testing supply email, 0939 21 September 2020

Reason for test 22 September 16–22 September

GPs and other primary health 3139 17026

CBACs and pop-ups 3010 20796

Border workers - air crew 46 255

Border workers - airport staff 135 1285

Border workers - maritime crew 0 45

Border workers – Port of Tauranga staff 3 442

Border workers – Remaining Port staff 59 230

Border workers - MIF 154 1128

Border workers - MIQ 40 306

Travellers - Staying at MIF 351 1936

Travellers - Staying at MIQ 1 186

Total 6938 43635*

Time period Number of laboratory tests

22 September 6938

Last 7 days (16 Sep to 22 Sep) 43,105*

Total 924,637

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12

Healthline updates21 26. On 22 September there were 2,184 contacts in Healthline. Of those calls, 845 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 615 contacts (lower than forecast).

27. The main themes on 21 September were:

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested. Increased level of people checking testing centre locations.

o Some questions on pre-departure testing requirements.

o Questions relating to the changes to alert levels.

Logistics

Health Workforce22

28. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

29. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

30. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity23 Table 8: Number and occupancy of hospital beds by type as at 0800 23 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 334 228 (68.3%)

Ventilators 303 61 (20.1%)

Ward beds 7120 5888 (82.7%)

21 National Telehealth Service Coronavirus Update, 0839 23 September 2020

22 Health Workforce Directorate, 0945 14 September 2020

23 COVID-19 Hospital Summary, 0917 23 September 2020

13

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Appendix 1: Case summary Table 9: All new community cases reported between 0900 22 September and 0900 23 September. Source: ESR EpiSurv Extract 0900 23 September 2020

s 9(2)(a)

IN CONFIDENCE – NOT FOR DISTRIBUTION

14

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification16 Table 10: NCTS data for cases in the community

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Table 11:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

16

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 22 September

Table 12: Metro Auckland Summary Total of Testing for 22 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

22/09/2020 881 246 600 121 13 0 1861

Table 13: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09*

MIQ Staff 2132 659 1488 912 1086 908 118 246

Guests 2972 3767 3600 3406 3424 3843 599 600

Border Airport 2129 933 1349 1158 853 951 112 121

Port 1588 678 161 392 153 320 49 13 (PM

Start)

Crew 0 0 0 0 0 0 0 0

*22/09 day still in progress

Table 14: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09*

Airport Oaks 1148 515 366 265 181 152 18 25

Botany CTC 1151 948 905 749 681 802 99 95

Health New Lynn 2603 1258 1703 732 889 621 102 66

Mangere Town

Centre

1748 1684 1599 860 660 487 70

45

Otara CTC 3221 1712 1429 930 699 938 65 57

St Lukes 1368 1045 1414 797 666 830 158 101

Takanini Urgent

Care

1886 1216 1153 684 440 487 65

61

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17

Whanau House 2502 1371 1442 928 1613 870 129 126

Whanau Ora -

Central

1957 964 1583 937 783 470 75

62

Whanau Ora -

North

1442 669 637 982 947 907 113

116

Whanau Ora -

South

2945 1250 718 677 620 470 66

54

Takanini Pop Up N/A N/A N/A N/A N/A N/A 17 25

Mangere Pop Up N/A N/A N/A N/A N/A N/A N/A 12

Waipuna Targeted

Site

143 549 376 219 251 220 28

34

Henderson

Targeted Site

N/A N/A N/A N/A 631 93 1

2

Total 26,148 16,781 21,215 13,002 10,475 8,832 1,020 881

*22/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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18

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 15: Number of people tested for COVID-19 from 12 August to 22 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3755 7567 10,434 22,100 453 44,309

Bay of Plenty 2833 377 646 7233 69 11,158

Canterbury 1751 697 2042 14,919 261 19,670

Capital and Coast 1637 1359 1624 10,555 249 15,424

Counties Manukau 8181 21,745 10,307 14,046 487 54,766

Hawkes Bay 1545 335 257 3942 68 6147

Hutt Valley 893 595 651 3545 51 5735

Lakes 2461 316 490 3461 105 6833

MidCentral 1168 277 439 4652 104 6640

Nelson Marlborough 664 249 315 4831 68 6127

Northland 3276 227 299 4536 60 8398

South Canterbury 152 46 90 1863 16 2167

Southern 1224 422 882 11,314 110 13,952

Tairāwhiti 950 61 70 886 23 1990

Taranaki 745 75 191 2977 65 4053

Waikato 4734 1052 1722 11,219 275 19,002

Wairarapa 257 47 52 1294 12 1662

Waitematā 5242 5722 9304 28,421 390 49,079

West Coast 49 10 13 358 8 438

Whanganui 673 83 76 1576 16 2424

Unknown 1539 760 839 4740 2363 10,241

Total 43,729 42,022 40,743 158,469 5253 290,216

19

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Table 16: Rate per 1000 people tested for COVID-19 from 12 August to 22 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 86.3 134.9 55.7 84.5 80.8

Bay of Plenty 47.4 84.8 33 46 46.3

Canterbury 33.4 49.1 33.6 33.4 34.3

Capital and Coast 44.8 61.3 32.4 49.6 48

Counties Manukau 91.9 181.1 68.2 67.1 96.2

Hawkes Bay 35.7 52.2 28 36.5 36.8

Hutt Valley 34.3 50.9 34.7 37.6 38

Lakes 64 123.7 50.4 57.7 61.7

MidCentral 32.1 49.9 28.3 37.6 36.6

Nelson Marlborough 41.4 100.8 42.4 38.4 40.4

Northland 53.8 60.4 36.2 41.6 46.2

South Canterbury 28.6 94.2 38 36.1 36.2

Southern 36.5 61.3 34.2 42.3 41.8

Tairāwhiti 38.3 54.6 60 40.1 40.5

Taranaki 31.9 53.9 30.7 33.1 33.5

Waikato 49.1 78.9 39 41.7 44.9

Wairarapa 32.2 56.5 41.7 36.3 36.3

Waitematā 83.8 128.3 64.7 74.3 77.5

West Coast 12.6 39.6 14.1 13.3 13.7

Whanganui 38.8 54.5 26 36.6 37.4

Total 56.2 131.4 53.2 51.2 58.5

1

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SITREP 062

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 24 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ CASES

NEW LAST 24 hrs

3

COMMUNITY CASES

TOTAL RECOVERED

149

130

COMMUNITY CASES

ACTIVE

34 TOTAL CASES SINCE 11 AUG

186

31 TOTAL IMPORTED MIQ CASES

160*

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 65

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

6,142

LABORATORY TESTS

LAST SEVEN DAYS

41,062

LABORATORY TESTS

TOTAL

930,779

CASES DECEASED

3

*This number has been reviewed and revised to 160, by ESR.

IN CONFIDENCE – NOT FOR DISTRIBUTION

2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 24 September 20201

Case Status Active Recovered Deceased Total

Confirmed 65* (+3) 1386 20 1471 (+3)

Probable 0 351 5 356

Total 65* (+3) 1737 25 1827 (+3)

*3 newly identified cases, 0 cases classified as recovered.

Total community cases since 11 August

Table 2: Community cases by DHB and case status as at 0900 24 September 20201

New Cases in New Zealand since 0900 23 September 2020, as at 0900 24 September2

Imported in MIQ facilities

1. Three new cases have been detected at the border. In total 160 cases have been

detected at the border since the establishment of MIQ facilities.

o One case arrived on 18 September. Tested positive on day 3 in Auckland MIQ facility.

o One case arrived on 16 September. Tested positive as a contact of a confirmed case

in Auckland MIQ facility.

o One case arrived on 18 September. Tested positive on day 3 in Rotorua MIQ facility.

Historical

2. No new historical cases have been reported.

Community cases

3. No new community cases have been reported.

1 EpiSurv Database, 0900 24 September 2020

2 EpiSurv Database, 0900 24 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 55 50 1 185

Probable 1 0 0 0 1

Total 80 55 50 1 186

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3

Total community cases by DHB since 11 August

Table 3: Community cases by DHB and case status as at 0900 24 September 20203

Total community cases by outbreak since 11 August4

Table 4: Community cases by Outbreak as at 0900 24 September 2020

Community cases and household contacts at Jet Park

4. As at 0800 24 September there are 32 people isolating in Jet Park from the community.

15 are confirmed cases, the remaining 17 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.5

Cases in hospital

5. Three cases in hospital with COVID-19 as at 0800 24 September.6

Table 5: Number of cases in hospital with COVID-19 by DHB as at 0800 24 September 2020

3 EpiSurv Database, 0900 24 September 2020

4 EpiSurv Database, 0900 24 September 2020

5 NRHCC Morning Report, 0845 22 September 2020

6 NRHCC Morning Report, 0845 22 September 2020

Case

Status

Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 55 50 1 185

Probable 1 0 0 0 1

Total 80 55 50 1 186

Outbreak New Cases (last 24 hrs) Total Cases

Auckland August 0 178

Christchurch Returnees 0 6

Rydges Hotel (MIF) 0 1

Under Investigation 0 1

Total 0 186

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 0

Total - 3 0

s 9(2)(a)

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4

Health system response

Overall approach

6. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification – An expert panel has been established to consider cases with

high CT counts to determine their status and develop a protocol for reporting,

management, and investigation of potentially historic infections.

Current outbreak investigation priorities7

o Ongoing management of healthcare worker from Jet Park.

o Ongoing management of Auckland August outbreak.

o Ongoing source investigation and contact tracing of Christchurch Returnees outbreak.

Settings of interest8

7. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

8. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

Case investigation Christchurch Returnee Outbreak

9. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September. The test returned positive on 18 September. The case and

their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September. The

case’s genome sequence is consistent with two confirmed cases from the same flight to

New Zealand.9 Source of infection is still under investigation.

7NRHCC Morning Report, 0845 24 September 2020

8 NRHCC Morning Report, 0845 24 September 2020

9 WGS Interim Report, 0313 21 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

10. Another passenger from the same chartered flight returned a positive test with a high

CT value on 21 September. They were retested and returned a negative result on 22

September. They are classified as under investigation until it is determined if it is an

historic case and if they were already reported as a case in India.

11. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

. The family has

been in isolation since 20 September. Contact tracing has been underway for this family

since 20 September. The family visited Tāupo from 18 to 20 September and met

parties from across the country. They also had dinner with a family

outside of the Tāupo trip.

12. 31 contacts have been identified in total to date, and all have been tested. As at 1000,

25 contacts are isolating. Relevant PHUs have been notified. All parties who were

contacts of these cases have been contacted. Contact tracing and testing is underway

for these families.

Case investigation Auckland Community Cluster

13. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

IN CONFIDENCE – NOT FOR DISTRIBUTION

1.

2.

s 9(2)(a)

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7

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing10 14. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

15.

16. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

17. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

18.

10 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

IN CONFIDENCE – NOT FOR DISTRIBUTION

8

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202011

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing12 19. Since the 11 August, 4044 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 4025 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest.

Table 7: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 24 September 2020

21/09/2020 22/09/2020 23/09/2020 24/09/2020

Cumulative number of close

contacts identified1 3989 4003 4014 4044

Cumulative number of close

contacts successfully contacted 3978 3992 4006 4025

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 11 11 8 19

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

11 ESR email 1608 14 September 2020

12 COVID-19 NCCS Analytics and Reporting 0857 24 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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9

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage13 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

23 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

13 Response Analyst – Digital Channels, 1625 23 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

09

05/

09

08/

09

11/

09

14/

09

17/

09

20/

09

23/

09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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10

Testing14 Table 8: Testing by functional groups, as at 0900 24 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers15 Table 9: Number of laboratory tests processed nationally as at 0900 24 September 2020

Testing supply update16

20. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

14 ÉCLAIR/MoH Public Health Intelligence, 1000 24 September 2020

15 Daily Lab Report, 0905 24 September 2020

16 Testing supply email, 0939 21 September 2020

Reason for test 23 September 17–23 September

GPs and other primary health 2543 15802

CBACs and pop-ups 2555 19515

Border workers - air crew 41 248

Border workers - airport staff 215 1295

Border workers - maritime crew 0 43

Border workers – Port of Tauranga staff 0 354

Border workers – Remaining Port staff 26 223

Border workers - MIF 233 1192

Border workers - MIQ 39 344

Travellers - Staying at MIF 490 2013

Travellers - Staying at MIQ 0 177

Total 6142 41206*

Time period Number of laboratory tests

23 September 6142

Last 7 days (17 Sep to 23 Sep) 41,062*

Total 930,779

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11

Healthline updates17 21. On 23 September there were 2,236 contacts in Healthline. Of those calls, 1068 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 696 contacts (higher than forecast).

22. The main themes on 22 September were:

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested. Increased level of people checking testing centre locations.

o Some questions on pre-departure testing requirements.

o Questions relating to the changes to alert levels.

Logistics

Health Workforce18

23. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

24. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

25. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity19 Table 10: Number and occupancy of hospital beds by type as at 0800 24 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 325 217 (66.8%)

Ventilators 296 60 (20.3%)

Ward beds 6822 5553 (81.4%)

17 National Telehealth Service Coronavirus Update, 0918 24 September 2020

18 Health Workforce Directorate, 0945 14 September 2020

19 COVID-19 Hospital Summary, 0905 24 September 2020

12

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Appendix 1: Case summary Table 11: All new community cases reported between 0900 23 September and 0900 24 September. Source: ESR EpiSurv Extract 0900 24 September 2020

Cumulative

Number

Date tested

positive Onset date Case status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation Source of transmission

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13

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification12 Table 12: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

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Table 13:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 23 September

Table 14: Metro Auckland Summary Total of Testing for 22 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

23/09/2020 780 187 543 173 34 0 1717

Table 15: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09 23/09*

MIQ Staff 2132 659 1488 912 1086 908 118 246 187

Guests 2972 3767 3600 3406 3424 3843 599 600 543

Border Airport 2129 933 1349 1158 853 951 112 121 173

Port 1588 678 161 392 153 320 49 16 34

Crew 0 0 0 0 0 0 0 0 0

*23/09 day still in progress

Table 16: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09

20/09

21/09 22/09 23/09*

Airport Oaks 1148 515 366 265 181 152 18 25 23

Botany CTC 1151 948 905 749 681 802 99 93 74

Health New Lynn 2603 1258 1703 732 889 621 102 66 65

Mangere Town

Centre

1748 1684 1599 860 660 487 70

45 55

Otara CTC 3221 1712 1429 930 699 938 65 61 61

St Lukes 1368 1045 1414 797 666 830 158 101 104

Takanini Urgent

Care

1886 1216 1153 684 440 487 65

61 40

Whanau House 2502 1371 1442 928 1613 870 129 126 88

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16

Whanau Ora -

Central

1957 964 1583 937 783 470 75

64 58

Whanau Ora -

North

1442 669 637 982 947 907 113

119 96

Whanau Ora -

South

2945 1250 718 677 620 470 66

62 26

Takanini Pop Up N/A N/A N/A N/A N/A N/A 17 25 22

Mangere Pop Up N/A N/A N/A N/A N/A N/A N/A 12 17

Glen Eden Pop Up N/A N/A N/A N/A N/A N/A N/A N/A 20

Waipuna

Targeted Site

143 549 376 219 251 220 28

34 29

Henderson

Targeted Site

N/A N/A N/A N/A 631 93 1

2 2

Total 26,148 16,781 21,215 13,002 10,475 8,832 1,020 896 780

*23/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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17

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 17: Number of people tested for COVID-19 from 12 August to 23 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3777 7595 10,504 22,286 462 44,624

Bay of Plenty 2873 380 657 7340 72 11,322

Canterbury 1779 713 2081 15,212 268 20,053

Capital and Coast 1663 1399 1665 10,772 254 15,753

Counties Manukau 8255 21,856 10,392 14,165 486 55,154

Hawkes Bay 1557 339 258 3976 67 6197

Hutt Valley 911 604 657 3606 52 5830

Lakes 2483 316 497 3507 110 6913

MidCentral 1182 285 444 4699 105 6715

Nelson Marlborough 670 258 317 4900 72 6217

Northland 3315 229 304 4584 59 8491

South Canterbury 158 46 93 1895 16 2208

Southern 1241 429 895 11,442 110 14,117

Tairāwhiti 964 61 70 896 23 2014

Taranaki 751 75 197 3018 67 4108

Waikato 4784 1061 1750 11,338 285 19,218

Wairarapa 263 48 52 1320 11 1694

Waitematā 5272 5764 9360 28,625 403 49,424

West Coast 50 10 13 372 8 453

Whanganui 683 85 77 1590 18 2453

Unknown 1566 774 866 4897 2570 10673

Total 44,197 42,327 41,149 160,441 5518 293,632

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Table 18: Rate per 1000 people tested for COVID-19 from 12 August to 23 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 86.8 135.4 56.1 85.3 81.4

Bay of Plenty 48 85.5 33.5 46.7 46.9

Canterbury 33.9 50.3 34.2 34.1 35

Capital and Coast 45.5 63.1 33.2 50.6 49

Counties Manukau 92.7 182 68.8 67.7 96.8

Hawkes Bay 36 52.8 28.2 36.8 37.1

Hutt Valley 35 51.7 35 38.3 38.7

Lakes 64.5 123.7 51.1 58.5 62.4

MidCentral 32.5 51.4 28.6 38 37.1

Nelson Marlborough 41.8 104.4 42.7 38.9 41

Northland 54.5 60.9 36.8 42.1 46.7

South Canterbury 29.8 94.2 39.3 36.7 36.9

Southern 37 62.3 34.7 42.8 42.3

Tairāwhiti 38.9 54.6 60 40.5 41

Taranaki 32.2 53.9 31.6 33.6 34

Waikato 49.6 79.6 39.7 42.1 45.4

Wairarapa 33 57.7 41.7 37 37

Waitematā 84.2 129.3 65.1 74.9 78

West Coast 12.9 39.6 14.1 13.8 14.1

Whanganui 39.3 55.9 26.3 36.9 37.8

Total 56.8 132.3 53.7 51.8 59.2

1

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SITREP 063

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 25 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

1

IMPORTED MIQ CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

153

132

COMMUNITY CASES

ACTIVE

31 TOTAL CASES SINCE 11 AUG

187

29 TOTAL IMPORTED MIQ CASES

161

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 60

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

6,465

LABORATORY TESTS

LAST SEVEN DAYS

40,167

LABORATORY TESTS

TOTAL

937,244

CASES DECEASED

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 25 September 20201

Case status Active Recovered Deceased Total

Confirmed 60* (-5) 1393 (+7) 20 1473 (+2)

Probable 0 351 5 356

Total 60* (-5) 1744 (+7) 25 1829 (+2)

*2 newly identified cases, 5 cases classified as recovered.

New cases in New Zealand since 0900 24 September 2020, as at 0900 25 September2

Imported in MIQ facilities

1. One new case has been detected at the border. In total 161 cases have been detected

at the border since the establishment of MIQ facilities.

o The case arrived on 19 September from Moscow via Istanbul and Kuala Lumpur. They

tested positive on day 3 in an Auckland MIQ facility and have since moved to Jet Park

Auckland.

Community

2. One new community case has been reported.

o The case is a contact of a confirmed case, associated with the MREF Bereavement

sub-cluster. The case was in Jet Park as a close contact of this known case. The case

left Jet Park on 18 September to complete a 14 day isolation period at home (the

clock was re-started on leaving Jet Park). The case has been monitored daily. The

case tested positive on day five. The case has now returned to Jet Park. Community

risk is assessed as low.3

Total community cases by DHB since 11 August

Table 2: Community cases by DHB and case status as at 0900 25 September 20204

1 EpiSurv Database, 0900 25 September 2020

2 EpiSurv Database, 0900 25 September 2020

3 NRHCC Intelligence lead phone call 1035 25 September

4 EpiSurv Database, 0900 25 September 2020

Case Status Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 56 (+1) 50 1 186 (+1)

Probable 1 0 0 0 1

Total 80 56 (+1) 50 1 187 (+1)

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Total community cases by outbreak since 11 August5 Table 3: Community cases by Outbreak as at 0900 25 September 20206

Community cases and household contacts at Jet Park

3. As at 0800 25 September there are 35 people isolating in Jet Park from the community.

15 are confirmed cases, the remaining 20 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.7

Cases in hospital

4. Three cases in hospital with COVID-19 as at 0800 25 September.8

Table 4: Number of cases in hospital with COVID-19 by DHB as at 0800 25 September 2020

Pop up testing9

5. Testing services around New Zealand have been strengthened in relation to the

Christchurch returnees cluster. See table 9 for more details.

6. The following CTCs have been stood up:

o Lakes DHB: 2 x Rotorua, 1 x Taupo

o Canterbury DHB: 3 x Christchurch

o Awaiting information from Bay of Plenty and Capital & Coast DHBs.

5 EpiSurv Database, 0900 25 September 2020

6 EpiSurv Database, 0900 25 September 2020

7 NRHCC Morning Report, 0859 25 September 2020

8 NRHCC Morning Report, 0859 25 September 2020

9 Testing Strategy email 1024 25 September 2020

Outbreak New cases (last 24 hrs) Total cases

Auckland August 1 179

Christchurch Returnees 0 6

Rydges Hotel (MIF) 0 1

Under Investigation 0 1

Total 1 187

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 1 0

Counties Manukau Middlemore 1 0

Total - 3 0

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Health system response

Overall approach

7. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification – An expert panel has been established to consider cases with

high CT counts to determine their status and develop a protocol for reporting,

management, and investigation of potentially historic infections.

Current outbreak investigation priorities10

o Ongoing management of healthcare worker from Jet Park.

o Ongoing management of Auckland August outbreak.

o Ongoing source investigation and contact tracing of Christchurch Returnees outbreak.

Settings of interest11

8. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

9. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

Case investigation Christchurch Returnee Outbreak

10. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September. The test returned positive on 18 September. The case and

their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September. The

case’s genome sequence is consistent with two confirmed cases from the same flight to

New Zealand.12 Source of infection is still under investigation.

11. Another passenger from the same chartered flight returned a positive test with a high

CT value on 21 September. They were retested and returned a negative result on 22

10NRHCC Morning Report, 0845 24 September 2020

11 NRHCC Morning Report, 0845 24 September 2020

12 WGS Interim Report, 0313 21 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

5

September. They are classified as under investigation until it is determined if it is an

historic case and if they were already reported as a case in India.

12. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

The family has

been in isolation since 20 September. Contact tracing has been underway for this family

since 20 September, and whole genome sequencing for the three cases is underway.

The family visited Tāupo from 18 to 20 September and met parties from across the

country. They also had dinner with a family of outside of the Tāupo trip.

13. 34 close contacts have been identified in total to date. As at 1700 24 September, 31

contacts are isolating. Relevant PHUs have been notified. All parties who were

contacts of these cases have been contacted. Contact tracing and testing is underway

for these families. All PHUs with responsibility for close contacts have reported good

compliance with isolation requirements.13

14. 12 contacts from the charter flight on 11 September from Christchurch to Auckland

who subsequently went to Taranaki have all been swabbed 4 times and will come out

of isolation on 26 September.14

Case investigation Auckland August Outbreak

15. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

13 PHU MOH phone call, 1000 25 September

14 Canterbury DHB report, 24 September

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IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing15 16. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

17.

18. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

19. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

20.

15 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

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Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202016

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing17 21. Since the 11 August, 4044 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 4025 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 25 September 2020

22/09/2020 23/09/2020 24/09/2020 25/09/2020

Cumulative number of close

contacts identified1 4003 4014 4044 4053

Cumulative number of close

contacts successfully contacted 3992 4006 4025 4050

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 11 8 19 3

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

16 ESR email 1608 14 September 2020

17 COVID-19 NCCS Analytics and Reporting 0857 24 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

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10

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage18 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

24 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

18 Response Analyst – Digital Channels, 1614 24 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

09

05/

09

08/

09

11/

09

14/

09

17/

09

20/

09

23/

09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing19 Table 7: Testing by functional groups, as at 0900 25 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers20 Table 8: Number of laboratory tests processed nationally as at 0900 25 September 2020

Testing supply update21

22. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

19 ÉCLAIR/MoH Public Health Intelligence, 1000 25 September 2020

20 Daily Lab Report, 0958 25 September 2020

21 Testing supply email, 0939 21 September 2020

Reason for test 24 September 18–24 September

GPs and other primary health 3147 15,293

CBACs and pop-ups 2661 19,241

Border workers - air crew 33 300

Border workers - airport staff 159 1268

Border workers - maritime crew 0 58

Border workers – Port of Tauranga staff 0 325

Border workers – Remaining Port staff 13 209

Border workers - MIF 140 1111

Border workers - MIQ 40 322

Travellers - Staying at MIF 274 2122

Travellers - Staying at MIQ 0 174

Total 6467 40,423*

Time period Number of laboratory tests

24 September 6465

Last 7 days (18 Sep to 24 Sep) 40,167*

Total 937,244

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Community Testing Centres for the Christchurch returnee cluster22 Table 9: Number of CTCs available in relation to the Christchurch Returnee Outbreak as at 1000 25

September 2020

Lakes DHB Rotorua 2 Vaughan Rd • 9am – 4pm –

Thursday (24/9) -

Sunday (27/9)

Rotorua Pukatua st (note

change of

venue)

• 11am-4pm –

Monday (28/9)

• 9am-4pm – Tuesday

– Friday (29/9-2/10)

Taupo 79 Miro Street • 1pm – 4pm –

Thursday (24/9)

• 9am-4pm – Friday

(25/9) – Friday

(2/10)

Canterbury DHB Christchurch Orchard Road CBAC

(near Airport)

• Open 9am- 4pm 7

days a week

Christchurch Whanau Ora

Community Clinic

CBAC

(Wainoni)

• Open 9am- 4pm 7

days a week

Capital and

Coast DHB

On standby depending outcome of testing

Bay of Plenty

DHB

Healthline updates23 23. On 24 September there were 2,578 contacts in Healthline. Of those calls, 1203 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 696 contacts (higher than forecast).

24. The main themes on 22 September were:

o A large number of calls relating to the exposure events outlined in the media

yesterday. Registration of casual and close contacts is ongoing.

22 Testing Strategy Lead MoH, 1025 25 September

23 National Telehealth Service Coronavirus Update, 0938 25 September 2020

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o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested. Increased level of people checking testing centre locations.

o Some questions on pre-departure testing requirements.

o Questions relating to the changes to alert levels.

Logistics

Health Workforce24

25. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

26. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

27. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity25 Table 10: Number and occupancy of hospital beds by type as at 0800 25 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 330 210 (63.6%)

Ventilators 298 38 (12.8%)

Ward beds 6933 5806 (83.7%)

24 Health Workforce Directorate, 0945 14 September 2020

25 COVID-19 Hospital Summary, 0917 25 September 2020

14

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Appendix 1: Case summary Table 11: All new community cases reported between 0900 24 September and 0900 25 September. Source: ESR EpiSurv Extract 0900 25 September 2020

s 9(2)(a)

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Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification17 Table 12: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

16

Table 13:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 24 September

Table 14: Metro Auckland Summary Total of Testing for 24 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

24/09/2020 754 184 447 122 59 20 1586

Table 15: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09 23/09 24/09*

MIQ Staff 2132 659 1488 912 1086 908 136 246 187 184

Guests 2972 3767 3600 3406 3424 3843 599 600 543 447

Border Airport 2129 933 1349 1158 853 951 112 121 173 122

Port 1588 678 161 392 153 320 49 16 34 59

Crew 0 0 0 0 0 0 0 0 0 20

*24/09 day still in progress

Table 16: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09

13/09

14/09 –

20/09

21/09 22/

09

23/09 24/09

*

Airport Oaks 1148 515 366 265 181 152 18 25 23 15

Botany CTC 1151 948 905 749 681 802 99 93 74 74

Health New

Lynn 2603 1258 1703 732 889 621 102 66 73 61

Mangere Town

Centre 1748 1684 1599 860 660 487 70 45 55 44

Otara CTC 3221 1712 1429 930 699 938 65 61 67 53

St Lukes 1368 1045 1414 797 666 830 158 101 104 105

Takanini Urgent

Care 1886 1216 1153 684 440 487 65 61 40 50

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18

Whanau House 2502 1371 1442 928 1613 870 129 126 88 80

Whanau Ora -

Central 1957 964 1583 937 783 470 75 64 71 45

Whanau Ora -

North 1442 669 637 982 947 907 113 119 112 90

Whanau Ora -

South 2945 1250 718 677 620 470 66 62 29 51

Takanini Pop Up N/A N/A N/A N/A N/A N/A 17 25 22 5

Glen Eden Pop

Up N/A N/A N/A N/A N/A N/A N/A N/A 20 25

Henderson Pop

Up N/A N/A N/A N/A N/A N/A N/A N/A 11 13

Beach haven

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A 14

Waipuna

Targeted Site 143 549 376 219 251 220 28 34 30 27

Henderson

Targeted Site N/A N/A N/A N/A 631 93 1 2 2 2

Total 26,148 16,781 21,215 13,002 10,475 8,832 1,020 896 843 754

*24/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

IN CONFIDENCE – NOT FOR DISTRIBUTION

19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 17: Number of people tested for COVID-19 from 12 August to 24 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3826 7655 10,679 22,631 481 45,272

Bay of Plenty 2895 386 667 7441 74 11,463

Canterbury 1781 715 2084 15,223 270 20,073

Capital and Coast 1687 1421 1708 10,962 259 16,037

Counties Manukau 8377 22,063 10,586 14,384 486 55,896

Hawkes Bay 1559 339 258 3976 70 6202

Hutt Valley 926 609 671 3656 53 5915

Lakes 2502 317 502 3551 112 6984

MidCentral 1193 285 452 4771 106 6807

Nelson Marlborough 674 260 324 4983 74 6315

Northland 3360 230 306 4637 59 8592

South Canterbury 158 46 94 1913 30 2241

Southern 1257 433 903 11,583 110 14,286

Tairāwhiti 968 62 70 902 23 2025

Taranaki 758 77 203 3052 68 4158

Waikato 4833 1068 1787 11,468 289 19,445

Wairarapa 266 49 53 1337 12 1717

Waitematā 5341 5812 9511 29,099 410 50,173

West Coast 50 10 13 373 8 454

Whanganui 685 85 78 1599 18 2465

Unknown 1585 772 858 4938 2570 10,723

Total 44,681 42,694 41,807 162,480 5582 297,244

20

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Table 18: Rate per 1000 people tested for COVID-19 from 12 August to 24 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 88 136.5 57.1 86.6 82.6

Bay of Plenty 48.4 86.8 34 47.3 47.5

Canterbury 34 50.4 34.3 34.1 35

Capital and Coast 46.2 64.1 34 51.5 49.9

Counties Manukau 94.1 183.7 70 68.7 98.1

Hawkes Bay 36 52.8 28.2 36.8 37.2

Hutt Valley 35.5 52.1 35.8 38.8 39.2

Lakes 65 124.1 51.6 59.2 63.1

MidCentral 32.8 51.4 29.2 38.6 37.6

Nelson Marlborough 42 105.2 43.7 39.6 41.6

Northland 55.2 61.2 37 42.5 47.2

South Canterbury 29.8 94.2 39.7 37 37.5

Southern 37.5 62.9 35 43.3 42.8

Tairāwhiti 39.1 55.5 60 40.8 41.2

Taranaki 32.5 55.3 32.6 33.9 34.4

Waikato 50.1 80.1 40.5 42.6 46

Wairarapa 33.3 58.9 42.5 37.5 37.5

Waitematā 85.3 130.3 66.1 76.1 79.2

West Coast 12.9 39.6 14.1 13.8 14.2

Whanganui 39.4 55.9 26.6 37.2 38

Total 57.5 133.5 54.6 52.5 59.9

1

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SITREP 064

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 26 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

153

132

COMMUNITY CASES

ACTIVE

31 TOTAL CASES SINCE 11 AUG

187

30 TOTAL IMPORTED MIQ CASES

162

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 61

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

5,952

LABORATORY TESTS

LAST SEVEN DAYS

37,760

LABORATORY TESTS

TOTAL

943,196

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 26 September 20201

Case status Active Recovered Deceased Total

Confirmed 61* (+1) 1394 (+1) 20 1475 (+2)

Probable 0 351 5 356

Total 61* (+1) 1745 (+1) 25 1831 (+2)

*2 newly identified cases, 1 case classified as recovered.

New cases in New Zealand since 0900 25 September 2020, as at 0900 26 September2

Imported in MIQ facilities

1. One new case has been detected at the border. In total 162 cases have been detected

at the border since the establishment of MIQ facilities.

o The case arrived on 21 September from Russia via United Arab Emirates. They tested

positive on day 3 in an Auckland MIQ facility and have moved to Jet Park Auckland.

Community

2. No new community cases have been reported.

Historic cases

3. One case has been reported.

o The case has been under investigation since 22 September. The case was tested because

they were a passenger on the charter flight from Christchurch to Auckland associated

with the Christchurch Returnees cluster. They returned a positive test with a high CT

value on 21 September. They were retested and returned a negative result on 22

September. ARPHS and Ministry of Health have determined this case is historic based

on the testing history and a positive serology result. The case is reported in the total

New Zealand case numbers. As this case is historic they are not included in the

Christchurch Returnees cluster.

Total community cases by DHB since 11 August

Table 2: Community cases by DHB and case status as at 0900 26 September 20203

1 EpiSurv Database, 0900 25 September 2020

2 EpiSurv Database, 0900 25 September 2020

3 EpiSurv Database, 0900 25 September 2020

Case Status Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 56 50 1 186

Probable 1 0 0 0 1

Total 80 56 50 1 187

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3

Total community cases by outbreak since 11 August4 Table 3: Community cases by Outbreak as at 0900 26 September 20205

Community cases and household contacts at Jet Park

4. As at 0800 26 September there are 32 people isolating in Jet Park from the community.

15 are confirmed cases, the remaining 17 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.6

Cases in hospital

5. Two cases in hospital with COVID-19 as at 0800 26 September.7

Table 4: Number of cases in hospital with COVID-19 by DHB as at 0800 26 September 2020

Pop up testing8

6. Testing services around New Zealand have been strengthened in relation to the

Christchurch returnees cluster. See table 9 for more details.

7. The following CTCs have been stood up:

o Lakes DHB: 2 x Rotorua, 1 x Taupo

o Canterbury DHB: 2 x Christchurch

4 EpiSurv Database, 0900 25 September 2020

5 EpiSurv Database, 0900 25 September 2020

6 NRHCC Morning Report, 0859 25 September 2020

7 NRHCC Morning Report, 0859 25 September 2020

8 Testing Strategy email 1024 25 September 2020

Outbreak New cases (last 24 hrs) Total cases

Auckland August 0 179

Christchurch Returnees 0 6

Rydges Hotel (MIF) 0 1

Under Investigation 0 1

Total 0 187

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 1 0

Waitematā North Shore 0 0

Counties Manukau Middlemore 1 0

Total - 2 0

s 9(2)(a)

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4

Health system response

Overall approach

8. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification – An expert panel has been established to consider cases with

high CT counts to determine their status and develop a protocol for reporting,

management, and investigation of potentially historic infections.

Current outbreak investigation priorities9

o Ongoing management of healthcare worker from Jet Park.

o Ongoing management of Auckland August outbreak.

o Ongoing source investigation and contact tracing of Christchurch Returnees outbreak.

Settings of interest10

9. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

10. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

Case investigation Christchurch Returnee Outbreak

11. The case reported in SitRep on 25 September is a contact of a confirmed case and

associated with the Mt Roskill Evangelical Church Bereavement sub-cluster. The case

was in Jet Park as a close contact of this known case. The case is and left Jet Park

on 18 September to complete a 14 day isolation period at home (the

isolation clock was re-started on leaving Jet Park). The case has been monitored daily,

and tested positive on day five. Community risk is assessed as low.11

9NRHCC Morning Report, 0845 24 September 2020

10 NRHCC Morning Report, 0845 24 September 2020

11 NRHCC Intelligence lead phone call 1035 25 September

12 MoH PHU 1000 phone call 26 September

s 9(2)(a)

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5

12. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September and returned a positive result on 18 September. The case

and their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September. The

case’s genome sequence is consistent with two confirmed cases from the same flight to

New Zealand.13 Source of infection is still under investigation.

13. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

The family has

been in isolation since 20 September. Contact tracing has been underway for this family

since 20 September. Genome sequencing has been performed and the three cases are

all part of the B.1.36 cluster. Source investigation continues14. The family visited Tāupo

from 18 to 20 September and met parties from across the country. They also had

dinner with a family of outside of the Tāupo trip. All parties who were

contacts of these cases have been tested and are self-isolating. Contact tracing is

underway for these families. All PHUs with responsibility for close contacts have

reported good compliance with isolation requirements.15. Scoping of possible exposure

settings and contact tracing is still ongoing.

14. 42 close contacts have been identified in total to date. As at 0915 26 September, 42 of

these contacts have been tested and are isolating, and 34 have returned a negative

result16. Relevant PHUs have been notified.

15. All passengers on the Christchurch to Auckland charter flight have been tested, except

one. Of those tested, one result is pending and the rest are negative.

Case investigation Auckland August Outbreak

16. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

13 WGS Interim Report, 0313 21 September 2020

14 End of day update, Chief Advisor public health, 25 September 1700.

15 PHU MOH phone call, 1000 25 September

16 26 September: NICTS report 0915

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a) s 9(2)(a)

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ESR and wider testing17 17. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

18.

19. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

20. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

21.

17 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

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9

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202018

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing19 22. Since the 11 August, 4177 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 4170 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 26 September 2020

23/09/2020 24/09/2020 25/09/2020 26/09/2020

Cumulative number of close

contacts identified1 4014 4044 4053 4177

Cumulative number of close

contacts successfully contacted 4006 4025 4050 4170

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 8 19 3 7

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

18 ESR email 1608 14 September 2020

19 COVID-19 NCCS Analytics and Reporting 0937 26 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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10

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage20 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

25 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20 Response Analyst – Digital Channels, 1616 25 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

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09

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09

14/

09

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09

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ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Testing21 Table 7: Testing by functional groups, as at 0900 25 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers22 Table 8: Number of laboratory tests processed nationally as at 0900 26 September 2020

Testing supply update23

23. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

21 ÉCLAIR/MoH Public Health Intelligence, 1000 25 September 2020

22 Daily Lab Report, 0844 26 September 2020

23 Testing supply email, 0939 21 September 2020

Reason for test 24 September 18–24 September

GPs and other primary health 3147 15,293

CBACs and pop-ups 2661 19,241

Border workers - air crew 33 300

Border workers - airport staff 159 1268

Border workers - maritime crew 0 58

Border workers – Port of Tauranga staff 0 325

Border workers – Remaining Port staff 13 209

Border workers - MIF 140 1111

Border workers - MIQ 40 322

Travellers - Staying at MIF 274 2122

Travellers - Staying at MIQ 0 174

Total 6467 40,423*

Time period Number of laboratory tests

25 September 5952

Last 7 days (19 Sep to 25 Sep) 37,760*

Total 943,196

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12

Community Testing Centres for the Christchurch returnee cluster24 Table 9: Number of CTCs available in relation to the Christchurch Returnee Outbreak as at 1000 25

September 2020

Lakes DHB Rotorua 2 Vaughan Rd • 9am – 4pm –

Thursday (24/9) -

Sunday (27/9)

Rotorua Pukatua st (note

change of

venue)

• 11am-4pm –

Monday (28/9)

• 9am-4pm – Tuesday

– Friday (29/9-2/10)

Taupo 79 Miro Street • 1pm – 4pm –

Thursday (24/9)

• 9am-4pm – Friday

(25/9) – Friday

(2/10)

Canterbury DHB Christchurch Orchard Road CBAC

(near Airport)

• Open 9am- 4pm 7

days a week

Christchurch Whanau Ora

Community Clinic

CBAC

(Wainoni)

• Open 9am- 4pm 7

days a week

Capital and

Coast DHB

On standby depending outcome of testing

Bay of Plenty

DHB

Healthline updates25 24. On 25 September there were 2,307 contacts in Healthline. Of those calls, 977 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 560 contacts (lower than forecast).

25. The main themes on 25 September were:

o Questions relating to what it means to take your alert level with you from Auckland.

o A large number of calls relating to the exposure events outlined in the media

yesterday. Registration of casual and close contacts is ongoing.

24 Testing Strategy Lead MoH, 1025 25 September

25 National Telehealth Service Coronavirus Update, 0939 26 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

13

o Most of the general public Service Users were calling because they are symptomatic

and wanted to be tested. Increased level of people checking testing centre locations.

o Questions relating to the changes to alert levels.

Logistics

Health Workforce26

26. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

27. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

28. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity27 Table 10: Number and occupancy of hospital beds by type as at 0800 26 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 327 213 (65.1%)

Ventilators 295 42 (14.2%)

Ward beds 6868 5528 (80.5%)

26 Health Workforce Directorate, 0945 14 September 2020

27 COVID-19 Hospital Summary, 0924 26 September 2020

14

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Appendix 1: Case summary Table 11: All new community cases reported between 0900 25 September and 0900 26 September. Source: ESR EpiSurv Extract 0900 26 September 2020

Cumulative

Number

Date tested

positive Onset date Case status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation

Source of

transmission

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15

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification19 Table 12: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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16

Table 13:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 25 September

Table 14: Metro Auckland Summary Total of Testing for 25 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

25/09/2020 732 104 525 102 39 0 1502

Table 15: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09 23/09 24/09 25/09

*

MIQ Staff 2132 659 1488 912 1086 908 136 246 187 184 104

Guests 2972 3767 3600 3406 3424 3843 599 600 543 447 525

Border Airport 2129 933 1349 1158 853 951 112 121 173 167 102

Port 1588 678 161 392 153 320 49 16 34 59 39

Crew 0 0 0 0 0 0 0 0 0 21 0

*25/09 day still in progress

Table 16: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08

30/08

31/08

06/09

07/09

13/09

14/09

20/09

21/09 22/

09

23/0

9

24/0

9

25/0

9*

Airport Oaks 1148 515 366 265 181 152 18 25 23 15 14

Botany CTC 1151 948 905 749 681 802 99 93 74 74 79

Health New

Lynn 2603 1258 1703 732 889 621 102 66 73 61

66

Mangere Town

Centre 1748 1684 1599 860 660 487 70 45 55 44

31

Otara CTC 3221 1712 1429 930 699 938 65 61 67 65 52

St Lukes 1368 1045 1414 797 666 830 158 101 104 105 128

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18

Takanini

Urgent Care 1886 1216 1153 684 440 487 65 61 40 50

50

Whanau

House 2502 1371 1442 928 1613 870 129 126 88 80

71

Whanau Ora -

Central 1957 964 1583 937 783 470 75 64 71 65

63

Whanau Ora -

North 1442 669 637 982 947 907 113 119 112 105

66

Whanau Ora -

South 2945 1250 718 677 620 470 66 62 29 55

54

Takanini Pop

Up N/A N/A N/A N/A N/A N/A 17 25 22 5

11

Glen Eden Pop

Up N/A N/A N/A N/A N/A N/A N/A N/A 20 25

11

Henderson

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A 11 13

No

data

Beach haven

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A 14

19

Waipuna

Targeted Site 143 549 376 219 251 220 28 34 30 28

15

Henderson

Targeted Site N/A N/A N/A N/A 631 93 1 2 2 3

2

Total 26,148 16,781 21,356 13,002 10,475 8,832 1,020 896 843 768 732

*25/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 17: Number of people tested for COVID-19 from 12 August to 24 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3826 7655 10,679 22,631 481 45,272

Bay of Plenty 2895 386 667 7441 74 11,463

Canterbury 1781 715 2084 15,223 270 20,073

Capital and Coast 1687 1421 1708 10,962 259 16,037

Counties Manukau 8377 22,063 10,586 14,384 486 55,896

Hawkes Bay 1559 339 258 3976 70 6202

Hutt Valley 926 609 671 3656 53 5915

Lakes 2502 317 502 3551 112 6984

MidCentral 1193 285 452 4771 106 6807

Nelson Marlborough 674 260 324 4983 74 6315

Northland 3360 230 306 4637 59 8592

South Canterbury 158 46 94 1913 30 2241

Southern 1257 433 903 11,583 110 14,286

Tairāwhiti 968 62 70 902 23 2025

Taranaki 758 77 203 3052 68 4158

Waikato 4833 1068 1787 11,468 289 19,445

Wairarapa 266 49 53 1337 12 1717

Waitematā 5341 5812 9511 29,099 410 50,173

West Coast 50 10 13 373 8 454

Whanganui 685 85 78 1599 18 2465

Unknown 1585 772 858 4938 2570 10,723

Total 44,681 42,694 41,807 162,480 5582 297,244

20

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Table 18: Rate per 1000 people tested for COVID-19 from 12 August to 24 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 88 136.5 57.1 86.6 82.6

Bay of Plenty 48.4 86.8 34 47.3 47.5

Canterbury 34 50.4 34.3 34.1 35

Capital and Coast 46.2 64.1 34 51.5 49.9

Counties Manukau 94.1 183.7 70 68.7 98.1

Hawkes Bay 36 52.8 28.2 36.8 37.2

Hutt Valley 35.5 52.1 35.8 38.8 39.2

Lakes 65 124.1 51.6 59.2 63.1

MidCentral 32.8 51.4 29.2 38.6 37.6

Nelson Marlborough 42 105.2 43.7 39.6 41.6

Northland 55.2 61.2 37 42.5 47.2

South Canterbury 29.8 94.2 39.7 37 37.5

Southern 37.5 62.9 35 43.3 42.8

Tairāwhiti 39.1 55.5 60 40.8 41.2

Taranaki 32.5 55.3 32.6 33.9 34.4

Waikato 50.1 80.1 40.5 42.6 46

Wairarapa 33.3 58.9 42.5 37.5 37.5

Waitematā 85.3 130.3 66.1 76.1 79.2

West Coast 12.9 39.6 14.1 13.8 14.2

Whanganui 39.4 55.9 26.6 37.2 38

Total 57.5 133.5 54.6 52.5 59.9

1

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SITREP 065

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 27 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

157

132

COMMUNITY CASES

ACTIVE

27 TOTAL CASES SINCE 11 AUG

187

32 TOTAL IMPORTED MIQ CASES

164

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 59

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

5,746

LABORATORY TESTS

LAST SEVEN DAYS

38,089

LABORATORY TESTS

TOTAL

948,942

CASES DECEASED

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 27 September 20201

Case status Active Recovered Deceased Total

Confirmed 59* (-2) 1398 (+4) 20 1477 (+2)

Probable 0 351 5 356

Total 59* (-2) 1749 (+4) 25 1833 (+2)

*2 newly identified cases, 4 cases classified as recovered.

New cases in New Zealand since 0900 26 September 2020, as at 0900 27 September2

Imported in MIQ facilities

1. Two new case has been detected at the border. In total 164 cases have been detected

at the border since the establishment of MIQ facilities.

o The case arrived on 23 September from Philippines via Taiwan. They tested positive

on day 3 in an Auckland MIQ facility and have moved to Jet Park Auckland.

o The case arrived on 21 September from Germany via United Arab Emirates and

Malaysia. They tested positive on day 3 in an Auckland MIQ facility and have moved

to Jet Park Auckland.

Community

2. No new community cases have been reported.

Historic cases

3. No new historic cases have been reported.

Total community cases by DHB since 11 August

Table 2: Community cases by DHB and case status as at 0900 27 September 20203

1 EpiSurv Database, 0900 27 September 2020

2 EpiSurv Database, 0900 27 September 2020

3 EpiSurv Database, 0900 27 September 2020

Case Status Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 56 50 1 186

Probable 1 0 0 0 1

Total 80 56 50 1 187

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3

Total community cases by outbreak since 11 August4 Table 3: Community cases by Outbreak as at 0900 27 September 20205

Community cases and household contacts at Jet Park

4. As at 0800 27 September there are 22 people isolating in Jet Park from the community.

10 are confirmed cases, the remaining 12 are household contacts. This number will

fluctuate as people finish their isolation and depart from the facility.6

Cases in hospital

5. One case in hospital with COVID-19 as at 0800 27 September.7

Table 4: Number of cases in hospital with COVID-19 by DHB as at 0800 27 September 2020

Pop up testing8

6. Testing services around New Zealand have been strengthened in relation to the

Christchurch returnees cluster. See table 9 for more details.

7. The following CTCs have been stood up:

o Lakes DHB: 2 x Rotorua, 1 x Taupo

o Canterbury DHB: 2 x Christchurch

4 EpiSurv Database, 0900 27 September 2020

5 EpiSurv Database, 0900 27 September 2020

6 NRHCC Morning Report, 0859 25 September 2020

7 NRHCC Morning Report, 0859 25 September 2020

8 Testing Strategy email 1024 25 September 2020

Outbreak New cases (last 24 hrs) Total cases

Auckland August 0 179

Christchurch Returnees 0 6

Rydges Hotel (MIF) 0 1

Under Investigation 0 1

Total 0 187

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Waitematā North Shore 0 0

Counties Manukau Middlemore 1 0

Total - 1 0

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4

Health system response

Overall approach

8. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification – An expert panel has been established to consider cases with

high CT counts to determine their status and develop a protocol for reporting,

management, and investigation of potentially historic infections.

Current outbreak investigation priorities9

o Ongoing management of healthcare worker from Jet Park.

o Ongoing management of Auckland August outbreak.

o Ongoing source investigation and contact tracing of Christchurch Returnees outbreak.

Settings of interest10

9. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

10. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

Case investigation Christchurch Returnee Outbreak –

11. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September and returned a positive result on 18 September. The case

and their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September.

Source of infection is still under

investigation.

9NRHCC Morning Report, 0845 24 September 2020

10 NRHCC Morning Report, 0845 24 September 2020

11 ESR email update 09.24 27 September 2020

s 9(2)(a)

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5

12. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

The family has

been in isolation since 20 September. Genome sequencing has been performed, all

three cases are part of the B.1.36 lineage and are closely matched to other cases epi-

linked to 12 Source investigation continues13. The family visited Tāupo

from 18 to 20 September and met parties from across the country. They also had

dinner with a family of outside of the Tāupo trip. All parties who were

contacts of these cases have been tested and are self-isolating. All PHUs with

responsibility for close contacts have reported good compliance with isolation

requirements.14. Contact Tracing and testing results can be seen in Table 5.

13. All passengers on the Christchurch to Auckland charter flight have been tested, except

one. Of those tested no results are pending and the rest are negative.

Case investigation Auckland August Outbreak -

14. The case reported in SitRep on 25 September is a contact of a confirmed case and

associated with the Mt Roskill Evangelical Church Bereavement sub-cluster. The case

was in Jet Park as a close contact of this known case. and left Jet Park

on 18 September to complete a 14 day isolation period at home (the

isolation clock was re-started on leaving Jet Park). The case has been monitored daily

and tested positive on day five. Community risk is assessed as low.15

15. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

12 ESR email update 09.24 27 September 2020

13 End of day update, Chief Advisor public health, 25 September 1700.

14 PHU MOH phone call, 1000 25 September

15 NRHCC Intelligence lead phone call 1035 25 September

16 MoH PHU 1000 phone call 26 September

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)s 9(2)(a)

s 9(2)(a) s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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6

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ESR and wider testing17 16. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

17.

18. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

19. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

20.

17 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

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9

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202018

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing19 21. Since the 11 August, 4072 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 4069 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest. Please note that the

total number and number successfully contacted has decreased due to close contact

records being marked as casual contacts or invalid records in the system

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 27 September 2020

24/09/2020 25/09/2020 26/09/2020 27/09/2020

Cumulative number of close

contacts identified1 4044 4053 4177 4072

Cumulative number of close

contacts successfully contacted 4025 4050 4170 4069

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 19 3 7 3

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

18 ESR email 1608 14 September 2020

19 COVID-19 NCCS Analytics and Reporting 0933 27 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

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10

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage20 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

25 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

20 Response Analyst – Digital Channels, 1616 25 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/0

523

/05

26/0

529

/05

01/0

604

/06

07/0

610

/06

13/0

616

/06

19/0

622

/06

25/0

628

/06

01/0

704

/07

07/0

710

/07

13/0

716

/07

19/0

722

/07

25/0

728

/07

31/0

703

/08

06/0

809

/08

12/0

815

/08

18/0

821

/08

24/0

827

/08

30/0

802

/09

05/0

908

/09

11/0

914

/09

17/0

920

/09

23/0

9

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

regi

stra

tio

ns

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing21 Table 7: Testing by functional groups, as at 0900 27 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers22 Table 8: Number of laboratory tests processed nationally as at 0900 27 September 2020

Testing supply update23

22. There are good levels of testing supplies available, with 299,747 tests currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

21 ÉCLAIR/MoH Public Health Intelligence, 1000 27 September 2020

22 Daily Lab Report, 0905 27 September 2020

23 Testing supply email, 0939 21 September 2020

Reason for test 26 September 20–26 September

GPs and other primary health 3611 17,185

CBACs and pop-ups 1158 15,098

Border workers - air crew 18 268

Border workers - airport staff 217 1108

Border workers - maritime crew 0 70

Border workers – Port of Tauranga staff 1 10

Border workers – Remaining Port staff 24 270

Border workers - MIF 52 975

Border workers - MIQ 31 331

Travellers - Staying at MIF 103 2128

Travellers - Staying at MIQ 4 170

Total 5219* 37,613*

Time period Number of laboratory tests

26 September 5746*

Last 7 days (20 Sep to 26 Sep) 38,089*

Total 948,942

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12

Community Testing Centres for the Christchurch returnee cluster24 Table 9: Number of CTCs available in relation to the Christchurch Returnee Outbreak as at 1000 25

September 2020

Lakes DHB Rotorua 2 Vaughan Rd • 9am – 4pm –

Thursday (24/9) -

Sunday (27/9)

Rotorua Pukatua st (note

change of

venue)

• 11am-4pm –

Monday (28/9)

• 9am-4pm – Tuesday

– Friday (29/9-2/10)

Taupo 79 Miro Street • 9am-4pm – Friday

(25/9) – Friday

(2/10)

Canterbury DHB Christchurch Orchard Road CBAC

(near Airport)

• Open 9am- 4pm 7

days a week

Christchurch Whanau Ora

Community Clinic

CBAC

(Wainoni)

• Open 9am- 4pm 7

days a week

Capital and

Coast DHB

On standby depending outcome of testing

Bay of Plenty

DHB

Healthline updates25 23. On 26 September there were 2,241 contacts in Healthline. Of those calls, 1,039 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 538 contacts (lower than forecast).

24. The main themes on 25 September were:

o A large number of calls relating to the exposure events outlined in the media

including Fuller ferries this morning.

o We are continuing to see a higher than normal acuity (of non covid related health

issues) through Healthline and some of this is geographically focussed – i.e. the wider

Auckland region.

24 Testing Strategy Lead MoH, 1632 25 September

25 National Telehealth Service Coronavirus Update, 0928 27 September 2020

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13

o Most service users were calling because they are symptomatic and wanted to get a

test. Increased level of users checking testing centre locations relating to the special

sites created at the end of last week.

o Questions relating to what it means to be from Auckland and travel to a region at

Alert Level One for the school holidays.

Logistics

Health Workforce26

25. Health Workforce continue to work with employers who have expressed a need for

assistance with identifying people who are willing to work within the health system and

to provide some relief from COVID-19 related staffing issues.

26. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. Following on from the

didactic component, will be practical training and assessment, which will continue to be

provided by the relevant DHB.

27. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity27 Table 10: Number and occupancy of hospital beds by type as at 0800 27 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 182 117 (64.3%)

Ventilators 145 30 (20.7%)

Ward beds 3169 2315 (73.1%)

26 Health Workforce Directorate, 0945 14 September 2020

27 COVID-19 Hospital Summary, 0914 27 September 2020

14

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Appendix 1: Case summary Table 11: All new community cases reported between 0900 26 September and 0900 27 September. Source: ESR EpiSurv Extract 0900 27 September 2020

Cumulative

Number

Date tested

positive Onset date Case status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation

Source of

transmission

IN CONFIDENCE – NOT FOR DISTRIBUTION

15

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification19 Table 12: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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16

Table 13:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 25 September

Please note this report is not run on the weekends Table 14: Metro Auckland Summary Total of Testing for 25 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

25/09/2020 732 104 525 102 39 0 1502

Table 15: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09 23/09 24/09 25/09

*

MIQ Staff 2132 659 1488 912 1086 908 136 246 187 184 104

Guests 2972 3767 3600 3406 3424 3843 599 600 543 447 525

Border Airport 2129 933 1349 1158 853 951 112 121 173 167 102

Port 1588 678 161 392 153 320 49 16 34 59 39

Crew 0 0 0 0 0 0 0 0 0 21 0

*25/09 day still in progress

Table 16: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08

30/08

31/08

06/09

07/09

13/09

14/09

20/09

21/09 22/

09

23/0

9

24/0

9

25/0

9*

Airport Oaks 1148 515 366 265 181 152 18 25 23 15 14

Botany CTC 1151 948 905 749 681 802 99 93 74 74 79

Health New

Lynn 2603 1258 1703 732 889 621 102 66 73 61

66

Mangere Town

Centre 1748 1684 1599 860 660 487 70 45 55 44

31

Otara CTC 3221 1712 1429 930 699 938 65 61 67 65 52

St Lukes 1368 1045 1414 797 666 830 158 101 104 105 128

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18

Takanini

Urgent Care 1886 1216 1153 684 440 487 65 61 40 50

50

Whanau

House 2502 1371 1442 928 1613 870 129 126 88 80

71

Whanau Ora -

Central 1957 964 1583 937 783 470 75 64 71 65

63

Whanau Ora -

North 1442 669 637 982 947 907 113 119 112 105

66

Whanau Ora -

South 2945 1250 718 677 620 470 66 62 29 55

54

Takanini Pop

Up N/A N/A N/A N/A N/A N/A 17 25 22 5

11

Glen Eden Pop

Up N/A N/A N/A N/A N/A N/A N/A N/A 20 25

11

Henderson

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A 11 13

No

data

Beach haven

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A 14

19

Waipuna

Targeted Site 143 549 376 219 251 220 28 34 30 28

15

Henderson

Targeted Site N/A N/A N/A N/A 631 93 1 2 2 3

2

Total 26,148 16,781 21,356 13,002 10,475 8,832 1,020 896 843 768 732

*25/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 17: Number of people tested for COVID-19 from 12 August to 26 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3889 7728 10,964 23,135 505 46,221

Bay of Plenty 2947 393 685 7575 76 11,676

Canterbury 1810 725 2137 15,505 271 20,448

Capital and Coast 1726 1441 1760 11,266 271 16,464

Counties Manukau 8510 22,283 10,835 14,651 496 56,775

Hawkes Bay 1596 342 263 4064 73 6338

Hutt Valley 952 619 688 3753 53 6065

Lakes 2566 319 521 3680 116 7202

MidCentral 1205 293 461 4852 112 6923

Nelson Marlborough 692 264 333 5117 71 6477

Northland 3409 232 316 4737 60 8754

South Canterbury 160 46 95 1947 31 2279

Southern 1299 444 936 11,832 114 14,625

Tairāwhiti 993 63 72 922 23 2073

Taranaki 774 80 203 3111 72 4240

Waikato 4926 1096 1839 11,800 294 19,955

Wairarapa 271 52 55 1379 13 1770

Waitematā 5423 5860 9749 29,660 424 51,116

West Coast 50 10 13 379 8 460

Whanganui 690 85 81 1620 19 2495

Unknown 1621 779 889 5037 2666 10,992

Total 45,509 43,154 42,895 166,023 5768 303,349

20

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Table 18: Rate per 1000 people tested for COVID-19 from 12 August to 26 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 89.4 137.8 58.6 88.5 84.3

Bay of Plenty 49.3 88.4 35 48.1 48.4

Canterbury 34.5 51.1 35.2 34.8 35.7

Capital and Coast 47.3 65 35.1 53 51.2

Counties Manukau 95.6 185.6 71.7 70 99.7

Hawkes Bay 36.9 53.3 28.7 37.6 38

Hutt Valley 36.5 53 36.7 39.8 40.2

Lakes 66.7 124.9 53.6 61.4 65

MidCentral 33.1 52.8 29.7 39.2 38.2

Nelson Marlborough 43.1 106.8 44.9 40.7 42.7

Northland 56 61.7 38.2 43.5 48.1

South Canterbury 30.1 94.2 40.1 37.7 38.1

Southern 38.7 64.5 36.3 44.2 43.8

Tairāwhiti 40.1 56.4 61.7 41.7 42.2

Taranaki 33.2 57.4 32.6 34.6 35.1

Waikato 51.1 82.2 41.7 43.8 47.2

Wairarapa 34 62.5 44.1 38.7 38.7

Waitematā 86.7 131.4 67.8 77.6 80.7

West Coast 12.9 39.6 14.1 14 14.4

Whanganui 39.7 55.9 27.7 37.6 38.5

Total 58.5 134.9 56 53.6 61.2

1

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SITREP 066

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 28 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ CASES

NEW LAST 24 hrs

0

COMMUNITY CASES

TOTAL RECOVERED

157

136

COMMUNITY CASES

ACTIVE

27 TOTAL CASES SINCE 11 AUG

187

28 TOTAL IMPORTED MIQ CASES

164

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 55

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

3,539

LABORATORY TESTS

LAST SEVEN DAYS

37,533

LABORATORY TESTS

TOTAL

951,954

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 28 September 20201

Case status Active Recovered Deceased Total

Confirmed 55* (-4) 1402 (+4) 20 1477

Probable 0 351 5 356

Total 55* (-4) 1753 (+4) 25 1833

*0 newly identified cases, 4 cases classified as recovered.

New cases in New Zealand since 0900 27 September 2020, as at 0900 28 September2

Imported in MIQ facilities

1. No new cases have been detected at the border. In total 164 cases have been detected

at the border since the establishment of MIQ facilities.

Community

2. No new community cases have been reported.

Historic cases

3. No new historic cases have been reported.

Total community cases by DHB since 11 August

Table 2: Community cases by DHB and case status as at 0900 28 September 20203

1 EpiSurv Database, 0900 27 September 2020

2 EpiSurv Database, 0900 28 September 2020

3 EpiSurv Database, 0900 28 September 2020

Case Status Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 56 50 1 186

Probable 1 0 0 0 1

Total 80 56 50 1 187

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3

Total community cases by outbreak since 11 August4 Table 3: Community cases by Outbreak as at 0900 28 September 20205

Community cases and household contacts at Jet Park

4. As at 0800 28 September there are 18 people isolating in Jet Park from the community.

9 are confirmed cases, the remaining 9 are household contacts. This number will

decrease as people finish their isolation and depart from the facility.6

Cases in hospital

5. One case in hospital with COVID-19 as at 0800 28 September.7

Table 4: Number of cases in hospital with COVID-19 by DHB as at 0800 28 September 2020

4 EpiSurv Database, 0900 28 September 2020

5 EpiSurv Database, 0900 28 September 2020

6 NRHCC Morning Report, 0900 28 September 2020

7 NRHCC Morning Report, 0900 28 September 2020

Outbreak New cases (last 24 hrs) Total cases

Auckland August 0 179

Christchurch Returnees 0 6

Rydges Hotel (MIF) 0 1

Under Investigation 0 1

Total 0 187

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Waitematā North Shore 0 0

Counties Manukau Middlemore 1 0

Total - 1 0

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4

Health system response

Overall approach

6. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification –has been established to consider cases with high CT counts will

be investigated by an expert panel to determine their status and develop a protocol

for reporting, management, and investigation of potentially historic infections.

Current outbreak investigation priorities8

o Ongoing management of healthcare worker from Jet Park.

o Ongoing management of Auckland August outbreak.

o Ongoing source investigation and contact tracing of Christchurch Returnees outbreak.

Settings of interest9

7. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

8. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

Case investigation Christchurch Returnee Outbreak –

9. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September and returned a positive result on 18 September. The case

and their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September.

Genomically, the three cases are part of the B.1.36 lineage and sequencing is consistent

with three confirmed cases from the same flight to New Zealand, all of whom tested

positive while in an MIQ facility in Christchurch.10 Source of infection is still under

investigation.

8NRHCC Morning Report, 0845 24 September 2020

9 NRHCC Morning Report, 0845 24 September 2020

10 ESR email update 09.24 27 September 2020

s 9(2)(a)

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5

10. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

The family has

been in isolation since 20 September. Genomes have been sequenced and all three

cases are part of the B.1.36 lineage and are closely matched to other cases epi-linked to

the Christchurch Returnees outbreak.11 Source investigation continues12. The family

visited Tāupo from 18 to 20 September and met parties from across the country.

They also had dinner with a family of outside of the Tāupo trip. All parties

who were contacts of these cases have been tested and are self-isolating. All PHUs with

responsibility for close contacts have reported good compliance with isolation

requirements.13. Contact Tracing and testing results can be seen in Table 5.

11. All passengers on the Christchurch to Auckland charter flight have been tested, except

one. Of those tested no results are pending and the rest are negative.

Case investigation Auckland August Outbreak -

12. The case reported in SitRep on 25 September is a contact of a confirmed case and

associated with the Mt Roskill Evangelical Church Bereavement sub-cluster. The case

was in Jet Park as a close contact of this known case. and left Jet Park

on 18 September to complete a 14 day isolation period at home (the

isolation clock was re-started on leaving Jet Park). The case has been monitored daily

and tested positive on day five. Community risk is assessed as low.14

13. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

11 ESR email update 09.24 27 September 2020

12 End of day update, Chief Advisor public health, 25 September 1700.

13 PHU MOH phone call, 1000 25 September

14 NRHCC Intelligence lead phone call 1035 25 September

15 MoH PHU 1000 phone call 26 September

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s 9(2)(a)

s 9(2)(a) s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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s 9(2)(a)

s 9(2)(a)

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6

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IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing16 14. A further 10 community cases are genomically linked with the Auckland cluster. These

cases are from the following known subclusters; Church 1 (1 cases), Church 3 (5 cases),

Americold HH (2 cases), MREF Bereavement (C-0018) (2 cases). A total of 153 cases

(86%) from the community cluster have now been sequenced, of which 134 (76%)

yielded a high quality genome.

15.

16. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

17. No direct links have been found between the community outbreak genome

sequencing, and the 65 full genomes (49 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

18.

16 ESR Whole Genome Sequencing Report 02 September 2020, Email 0946 16 September 2020

s 9(2)(g)(i)

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9

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202017

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing18 19. Since the 11 August, 4075 community close contacts have been identified and recorded

in the National Contact Tracing Solution, 4072 of these have been contacted and are

self-isolating, and we are in the process of contacting the rest.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 28 September 2020

25/09/2020 26/09/2020 27/09/2020 28/09/2020

Cumulative number of close

contacts identified1 4053 4177 4072 4075

Cumulative number of close

contacts successfully contacted 4050 4170 4069 4072

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 3 7 3 3

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

17 ESR email 1608 14 September 2020

18 COVID-19 NCCS Analytics and Reporting 0917 28 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

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10

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage19 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

25 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

19 Response Analyst – Digital Channels, 1616 25 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/0

523

/05

26/0

529

/05

01/0

604

/06

07/0

610

/06

13/0

616

/06

19/0

622

/06

25/0

628

/06

01/0

704

/07

07/0

710

/07

13/0

716

/07

19/0

722

/07

25/0

728

/07

31/0

703

/08

06/0

809

/08

12/0

815

/08

18/0

821

/08

24/0

827

/08

30/0

802

/09

05/0

908

/09

11/0

914

/09

17/0

920

/09

23/0

9

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

regi

stra

tio

ns

Day and month

Cumulative App registrations Daily scans and manual entries

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11

Testing20 Table 7: Testing by functional groups, as at 0900 28 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers21 Table 8: Number of laboratory tests processed nationally as at 0900 28 September 2020

Testing supply update22

20. There are good levels of supplies available, with 278,208 tests available currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

20 ÉCLAIR/MoH Public Health Intelligence, 1000 27 September 2020

21 Daily Lab Report, 0844 28 September 2020

22 Testing supply email, 0920 28 September 2020

Reason for test 27 September 21–27 September

GPs and other primary health 2207 17,869

CBACs and pop-ups 619 14,302

Border workers - air crew 14 258

Border workers - airport staff 174 1208

Border workers - maritime crew 23 93

Border workers – Port of Tauranga staff 2 11

Border workers – Remaining Port staff 15 282

Border workers - MIF 184 1019

Border workers - MIQ 45 313

Travellers - Staying at MIF 256 2212

Travellers - Staying at MIQ 0 169

Total 3539 37,736*

Time period Number of laboratory tests

27 September 3,539

Last 7 days (21 Sep to 27 Sep) 37,533*

Total 951,954

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12

Community Testing Centres for the Christchurch returnee cluster23 Table 9: Number of CTCs available in relation to the Christchurch Returnee Outbreak as at 1000 25

September 2020

Lakes DHB Rotorua 2 Vaughan Rd • 9am – 4pm –

Thursday (24/9) -

Sunday (27/9)

Rotorua Pukatua st (note

change of

venue)

• 11am-4pm –

Monday (28/9)

• 9am-4pm – Tuesday

– Friday (29/9-2/10)

Taupo 79 Miro Street • 9am-4pm – Friday

(25/9) – Friday

(2/10)

Canterbury DHB Christchurch Orchard Road CBAC

(near Airport)

• Open 9am- 4pm 7

days a week

Christchurch Whanau Ora

Community Clinic

CBAC

(Wainoni)

• Open 9am- 4pm 7

days a week

Capital and

Coast DHB

On standby depending outcome of testing

Bay of Plenty

DHB

Healthline updates24 21. On 27 September there were 1,994 contacts in Healthline. Of those calls, 1,068 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 574 contacts (lower than forecast).

22. The main themes on 26/27 September were:

o Ongoing calls relating to the exposure events.

o Healthline are continuing to see a higher than normal acuity (of non covid related

health issues) through Healthline and some of this is geographically focussed – i.e.

the wider Auckland region.

23 Testing Strategy Lead MoH, 1632 25 September

24 National Telehealth Service Coronavirus Update, 0923 28 September 2020

IN CONFIDENCE – NOT FOR DISTRIBUTION

13

o Increased level of people checking testing centre locations relating to the special

sites created at the end of last week.

o Most service users were calling because they are symptomatic and wanted to get a

test.

o Questions relating to what it means to be from Auckland and travel to a region at

Alert Level One for the school holidays.

Logistics

Health Workforce25

23. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. It is anticipated this package

will be released in the week of 12 October 2020.

24. Surge workforce requests continue to be monitored and responded to, with 3779

people listed on the surge as “available”.

25. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity26 Table 10: Number and occupancy of hospital beds by type as at 0800 28 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 307 196 (63.8%)

Ventilators 272 42 (15.4%)

Ward beds 6775 5292 (78.1%)

25 Health Workforce Directorate, 0853 28 September 2020

26 COVID-19 Hospital Summary, 0913 28 September 2020

14

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Appendix 1: Case summary Table 11: All new community cases reported between 0900 27 September and 0900 28 September. Source: ESR EpiSurv Extract 0900 28 September 2020

Cumulative

Number

Date tested

positive Onset date Case status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation

Source of

transmission

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15

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification18 Table 12: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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16

Table 13:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 25 September

Please note this report is not run on the weekends Table 14: Metro Auckland Summary Total of Testing for 25 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

25/09/2020 732 104 525 102 39 0 1502

Table 15: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 22/09 23/09 24/09 25/09

*

MIQ Staff 2132 659 1488 912 1086 908 136 246 187 184 104

Guests 2972 3767 3600 3406 3424 3843 599 600 543 447 525

Border Airport 2129 933 1349 1158 853 951 112 121 173 167 102

Port 1588 678 161 392 153 320 49 16 34 59 39

Crew 0 0 0 0 0 0 0 0 0 21 0

*25/09 day still in progress

Table 16: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08

30/08

31/08

06/09

07/09

13/09

14/09

20/09

21/09 22/

09

23/0

9

24/0

9

25/0

9*

Airport Oaks 1148 515 366 265 181 152 18 25 23 15 14

Botany CTC 1151 948 905 749 681 802 99 93 74 74 79

Health New

Lynn 2603 1258 1703 732 889 621 102 66 73 61

66

Mangere Town

Centre 1748 1684 1599 860 660 487 70 45 55 44

31

Otara CTC 3221 1712 1429 930 699 938 65 61 67 65 52

St Lukes 1368 1045 1414 797 666 830 158 101 104 105 128

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18

Takanini

Urgent Care 1886 1216 1153 684 440 487 65 61 40 50

50

Whanau

House 2502 1371 1442 928 1613 870 129 126 88 80

71

Whanau Ora -

Central 1957 964 1583 937 783 470 75 64 71 65

63

Whanau Ora -

North 1442 669 637 982 947 907 113 119 112 105

66

Whanau Ora -

South 2945 1250 718 677 620 470 66 62 29 55

54

Takanini Pop

Up N/A N/A N/A N/A N/A N/A 17 25 22 5

11

Glen Eden Pop

Up N/A N/A N/A N/A N/A N/A N/A N/A 20 25

11

Henderson

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A 11 13

No

data

Beach haven

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A 14

19

Waipuna

Targeted Site 143 549 376 219 251 220 28 34 30 28

15

Henderson

Targeted Site N/A N/A N/A N/A 631 93 1 2 2 3

2

Total 26,148 16,781 21,356 13,002 10,475 8,832 1,020 896 843 768 732

*25/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 17: Number of people tested for COVID-19 from 12 August to 27 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3900 7755 11,047 23,251 519 46,472

Bay of Plenty 2970 398 718 7636 76 11,798

Canterbury 1841 731 2191 15,816 278 20,857

Capital and Coast 1731 1445 1764 11,323 276 16,539

Counties Manukau 8530 22,335 10,900 14,718 499 56,982

Hawkes Bay 1624 351 266 4131 74 6446

Hutt Valley 954 619 688 3769 56 6086

Lakes 2568 319 523 3692 119 7221

MidCentral 1210 293 462 4862 114 6941

Nelson Marlborough 692 264 333 5127 72 6488

Northland 3416 232 316 4753 60 8777

South Canterbury 160 46 95 1950 31 2282

Southern 1299 445 941 11,857 116 14,658

Tairāwhiti 993 63 72 924 23 2075

Taranaki 778 81 205 3156 73 4293

Waikato 4950 1100 1850 11,872 296 20,068

Wairarapa 272 52 57 1389 13 1783

Waitematā 5449 5907 9829 29,797 438 51,420

West Coast 50 11 13 387 8 469

Whanganui 691 85 81 1623 19 2499

Unknown 1630 784 896 5108 2774 11,192

Total 45,708 43,316 43,247 167,142 5934 305,347

20

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Table 18: Rate per 1000 people tested for COVID-19 from 12 August to 27 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 89.7 138.3 59 88.9 84.8

Bay of Plenty 49.7 89.5 36.6 48.5 48.9

Canterbury 35.1 51.5 36.1 35.4 36.4

Capital and Coast 47.4 65.2 35.1 53.2 51.4

Counties Manukau 95.8 186 72.1 70.3 100.1

Hawkes Bay 37.5 54.7 29 38.2 38.6

Hutt Valley 36.6 53 36.7 40 40.4

Lakes 66.7 124.9 53.8 61.6 65.2

MidCentral 33.3 52.8 29.8 39.3 38.3

Nelson Marlborough 43.1 106.8 44.9 40.7 42.7

Northland 56.1 61.7 38.2 43.6 48.3

South Canterbury 30.1 94.2 40.1 37.7 38.1

Southern 38.7 64.6 36.5 44.3 43.9

Tairāwhiti 40.1 56.4 61.7 41.8 42.2

Taranaki 33.3 58.2 32.9 35.1 35.5

Waikato 51.3 82.5 41.9 44.1 47.4

Wairarapa 34.1 62.5 45.7 38.9 39

Waitematā 87.1 132.5 68.4 77.9 81.2

West Coast 12.9 43.5 14.1 14.3 14.6

Whanganui 39.8 55.9 27.7 37.7 38.5

Total 58.8 135.4 56.4 54 61.6

1

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SITREP 067

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 29 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ CASES

NEW LAST 24 hrs

2

COMMUNITY CASES

TOTAL RECOVERED

158

137

COMMUNITY CASES

ACTIVE

26 TOTAL CASES SINCE 11 AUG

187

29 TOTAL IMPORTED MIQ CASES

166

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 55

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

3,636

LABORATORY TESTS

LAST SEVEN DAYS

37,891

LABORATORY TESTS

TOTAL

955,590

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 29 September 20201

Case status Active Recovered Deceased Total

Confirmed 55* 1404 (+2) 20 1479 (+2)

Probable 0 351 5 356

Total 55* 1755 (+2) 25 1835 (+2)

*2 newly identified cases, 2 cases classified as recovered.

New cases in New Zealand since 0900 28 September 2020, as at 0900 29 September2

Imported in MIQ facilities

1. Two new cases have been detected at the border. In total 166 cases have been

detected at the border since the establishment of MIQ facilities.

o One case arrived on 23 September from Pakistan via UAE. Managed isolation in

Waikato transferred to Auckland Jet Park facility.

o One case arrived on 23 September from Ukraine via UAE. Managed isolation in

Waikato transferred to Auckland Jet Park facility.

Community

2. No new community cases have been reported. It has been four days since the last

community case was reported.

Historic cases

3. No new historic cases have been reported.

Total community cases by DHB since 11 August

Table 2: Community cases by DHB and case status as at 0900 29 September 20203

1 EpiSurv Database, 0900 29 September 2020

2 EpiSurv Database, 0900 29 September 2020

3 EpiSurv Database, 0900 29 September 2020

Case Status Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 56 50 1 186

Probable 1 0 0 0 1

Total 80 56 50 1 187

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3

Total community cases by outbreak since 11 August4

Table 3: Community cases by Outbreak as at 0900 29 September 20205

Community cases and household contacts at Jet Park

4. As at 0800 29 September there are 18 people isolating in Jet Park from the community.

9 are confirmed cases, the remaining 9 are household contacts. This number will

decrease as people finish their isolation and depart from the facility.6

Cases in hospital

5. One case in hospital with COVID-19 as at 0800 29 September.7

Table 4: Number of cases in hospital with COVID-19 by DHB as at 0800 29 September 2020

4 EpiSurv Database, 0900 29 September 2020

5 EpiSurv Database, 0900 29 September 2020

6 NRHCC Morning Report, 0900 29 September 2020

7 NRHCC Morning Report, 0900 29 September 2020

Outbreak New cases (last 24

hrs)

Total cases Active cases

remaining

Auckland August 0 179 20

Christchurch Returnees 0 6 6

Rydges Hotel (MIF) 0 1 0

Under Investigation (

0 1 0

Total 0 187 26

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Waitematā North Shore 0 0

Counties Manukau Middlemore 1 0

Total - 1 0

s 9(2)(a)

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4

Health system response

Overall approach

6. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification –has been established to consider cases with high CT counts will

be investigated by an expert panel to determine their status and develop a protocol

for reporting, management, and investigation of potentially historic infections.

Current outbreak investigation priorities8

o Follow up of Christchurch Returnees cases and settings of interest.

o Ongoing management of Auckland August outbreak.

Settings of interest9

7. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

8. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

9. No new settings of interest have been identified.

Case investigation Christchurch Returnee Outbreak –

10. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September and returned a positive result on 18 September. The case

and their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September.

Source of infection is still under

investigation.

8NRHCC Morning Report, 0900 29 September 2020

9 NRHCC Morning Report, 0845 24 September 2020

10 ESR email update 09.24 27 September 2020

s 9(2)(a)

s 9(2)(g)(i)

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5

11. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

The family has

been in isolation since 20 September. Genomes have been sequenced and all three

cases are part of the B.1.36 lineage and are closely matched to other cases epi-linked to

the Christchurch Returnees outbreak.11 Source investigation continues12. The family

visited Tāupo from 18 to 20 September and met parties from across the country.

They also had dinner with a family of outside of the Tāupo trip. All parties

who were contacts of these cases have been tested and are self-isolating. All PHUs with

responsibility for close contacts have reported good compliance with isolation

requirements.13. Contact Tracing and testing results can be seen in Table 5.

12. All passengers on the Christchurch to Auckland charter flight have been tested, except

one. Of those tested no results are pending and the rest are negative.

Case investigation Auckland August Outbreak -

13. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing:

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

11 ESR email update 09.24 27 September 2020

12 End of day update, Chief Advisor public health, 25 September 1700.

13 PHU MOH phone call, 1000 25 September

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a) s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

6

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7

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8

IN CONFIDENCE – NOT FOR DISTRIBUTION

ESR and wider testing14 14. A total of 172 cases (96%) from the Auckland community cluster have now been

sequenced, of which 143 (80%) yielded a high quality genome. The remaining cases did

not have sufficient genetic material to be sequenced reliably. All cases are part of the

same B1.1.1 lineage and genomic cluster and the subsequent mutations observed are

consistent with the epidemiological sub-groupings.

15.

16. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

17. No direct links have been found between the community outbreak genome

sequencing, and the 71 full genomes (52 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

18. Genome sequencing on cases from the Christchurch returnees cluster

has also been completed, all cases are part of the B1.36 lineage.

19.

14 ESR Whole Genome Sequencing Report, Email 0927 29 September 2020

s 9(2)(g)(i)

s 9(2)(g)(i)

s 9(2)(a)

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9

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202015

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing16 20. Since the 11 August, 4079 community close contacts have been identified and recorded

in the National Contact Tracing Solution, all of these have been contacted and are self-

isolating.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 29 September 2020

26/09/2020 27/09/2020 28/09/2020 29/09/2020

Cumulative number of close

contacts identified1 4177 4072 4075 4079

Cumulative number of close

contacts successfully contacted 4170 4069 4072 4079

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 7 3 3 0

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

15 ESR email 1608 14 September 2020

16 COVID-19 NCCS Analytics and Reporting 0819 29 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

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10

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

28 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

17 Response Analyst – Digital Channels, 1625 28 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

20/

05

23/

05

26/

05

29/

05

01/

06

04/

06

07/

06

10/

06

13/

06

16/

06

19/

06

22/

06

25/

06

28/

06

01/

07

04/

07

07/

07

10/

07

13/

07

16/

07

19/

07

22/

07

25/

07

28/

07

31/

07

03/

08

06/

08

09/

08

12/

08

15/

08

18/

08

21/

08

24/

08

27/

08

30/

08

02/

09

05/

09

08/

09

11/

09

14/

09

17/

09

20/

09

23/

09

26/

09

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

re

gist

rati

on

s

Day and month

Cumulative App registrations Daily scans and manual entries

IN CONFIDENCE – NOT FOR DISTRIBUTION

11

Testing18 Table 7: Testing by functional groups, as at 0900 28 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 8: Number of laboratory tests processed nationally as at 0900 29 September 2020

Testing supply update20

21. There are good levels of supplies available, with 278,208 tests available currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 27 September 2020

19 Daily Lab Report, 0826 29 September 2020

20 Testing supply email, 0920 28 September 2020

Reason for test 27 September 21–27 September

GPs and other primary health 2207 17,869

CBACs and pop-ups 619 14,302

Border workers - air crew 14 258

Border workers - airport staff 174 1208

Border workers - maritime crew 23 93

Border workers – Port of Tauranga staff 2 11

Border workers – Remaining Port staff 15 282

Border workers - MIF 184 1019

Border workers - MIQ 45 313

Travellers - Staying at MIF 256 2212

Travellers - Staying at MIQ 0 169

Total 3539 37,736*

Time period Number of laboratory tests

28 September 3,636

Last 7 days (22 Sep to 28 Sep) 37,891*

Total 955,590

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12

Community Testing Centres for the Christchurch returnee cluster21 Table 9: Number of CTCs available in relation to the Christchurch Returnee Outbreak as at 1000 25

September 2020

Lakes DHB Rotorua 2 Vaughan Rd • 9am – 4pm – Thursday

(24/9) -Sunday (27/9)

Rotorua Pukatua st (note change

of venue)

• 11am-4pm – Monday (28/9)

• 9am-4pm – Tuesday –

Friday (29/9-2/10)

Taupo 79 Miro Street • 9am-4pm – Friday (25/9) –

Friday (2/10)

Canterbury DHB Christchurch Orchard Road CBAC

(near Airport)

• Open 9am- 4pm 7 days a

week

Christchurch Whanau Ora Community

Clinic CBAC

(Wainoni)

• Open 9am- 4pm 7 days a

week

Capital and

Coast DHB

On standby depending outcome of testing

Bay of Plenty

DHB

Healthline updates22 22. On 28 September there were 2,053 contacts in Healthline. Of those calls, 968 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 641 contacts (in line forecast).

23. The main themes on 27/28 September were:

o Ongoing calls relating to the exposure events.

o Healthline are continuing to see a higher than normal acuity (of non covid related

health issues) through Healthline and some of this is geographically focussed – i.e.

the wider Auckland region.

o Increased level of people checking testing centre locations relating to the special

sites created at the end of last week.

o Questions relating to travel between alert levels.

o Most service users were calling because they are symptomatic and wanted to get a

test.

21 Testing Strategy Lead MoH, 1632 25 September

22 National Telehealth Service Coronavirus Update, 0923 28 September 2020

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13

Logistics

Health Workforce23

24. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. It is anticipated this package

will be released in the week of 12 October 2020.

25. Surge workforce requests continue to be monitored and responded to, with 3779

people listed on the surge as “available”.

26. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity24 Table 10: Number and occupancy of hospital beds by type as at 0800 29 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 339 212 (62.5%)

Ventilators 297 48 (16.2%)

Ward beds 7193 5865 (81.5%)

23 Health Workforce Directorate, 0853 28 September 2020

24 COVID-19 Hospital Summary, 0918 29 September 2020

14

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Appendix 1: Case summary Table 11: All new community cases reported between 0900 28 September and 0900 29 September. Source: ESR EpiSurv Extract 0900 29 September 2020

Cumulative

Number

Date tested

positive Onset date Case status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation

Source of

transmission

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15

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification16 Table 12: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Table 13:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 28 September

Table 14: Metro Auckland Summary Total of Testing for 28 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

26/09/2020 550 105 536 80 11 0 1282

27/09/2020 558 145 569 88 No Testing 0 1360

28/09/2020 685 89 454 129 76 0 1433

Table 15: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09

27/09

26/09 27/09 28/09*

MIQ Staff 2132 659 1488 912 1086 908 1136 105 145 89

Guests 2972 3767 3600 3406 3424 3843 3819 536 569 454

Border Airport 2129 933 1349 1158 853 951 843 80 88 129

Port 1588 678 161 392 153 320 208 11 0 76

Crew 0 0 0 0 0 0 21 0 0 0

*28/09 day still in progress

Table 16: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 –

27/09

26/09 27/09 28/09

*

Airport Oaks 1148 515 366 265 181 152 118 8 15 21

Botany CTC 1151 948 905 749 681 802 526 65 42 63

Health New

Lynn 2603 1258 1703 732 889 621 451 38 45 44

Mangere

Town Centre 1748 1684 1599 860 660 487 300 29 26 45

Otara CTC 3221 1712 1429 930 699 938 428 59 41 47

St Lukes 1368 1045 1414 797 666 830 793 73 124 85

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Takanini

Urgent Care 1886 1216 1153 684 440 487 313 17 30 44

Whanau

House 2502 1371 1442 928 1613 870 594 66 34 74

Whanau Ora

- Central 1957 964 1583 937 783 470 465 52 71 42

Whanau Ora

- North 1442 669 637 982 947 907 633 59 55 85

Whanau Ora

- South 2945 1250 718 677 620 470 310 18 19 36

Papakura

Pop Up N/A N/A N/A N/A N/A N/A N/A N/A N/A 13

Te Atatu Pop

Up N/A N/A N/A N/A N/A N/A N/A N/A N/A 48

West

Harbour Pop

Up

N/A N/A N/A N/A N/A N/A N/A N/A N/A 9

Mangere Pop

Up N/A N/A N/A N/A N/A N/A 66 16 16 N/A

Beach Haven

Pop Up N/A N/A N/A N/A N/A N/A 38 5 N/A N/A

Manukau

Pop Up N/A N/A N/A N/A N/A N/A 29 29 N/A N/A

Waipuna

Targeted Site 143 549 376 219 251 220 186 15 36 28

Henderson

Targeted Site N/A N/A N/A N/A 631 93 15 1 4 1

Total 26,148 16,781 21,356 13,002 10,475 8,832 5436 550 558 685

*28/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

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19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 17: Number of people tested for COVID-19 from 12 August to 27 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3900 7755 11,047 23,251 519 46,472

Bay of Plenty 2970 398 718 7636 76 11,798

Canterbury 1841 731 2191 15,816 278 20,857

Capital and Coast 1731 1445 1764 11,323 276 16,539

Counties Manukau 8530 22,335 10,900 14,718 499 56,982

Hawkes Bay 1624 351 266 4131 74 6446

Hutt Valley 954 619 688 3769 56 6086

Lakes 2568 319 523 3692 119 7221

MidCentral 1210 293 462 4862 114 6941

Nelson Marlborough 692 264 333 5127 72 6488

Northland 3416 232 316 4753 60 8777

South Canterbury 160 46 95 1950 31 2282

Southern 1299 445 941 11,857 116 14,658

Tairāwhiti 993 63 72 924 23 2075

Taranaki 778 81 205 3156 73 4293

Waikato 4950 1100 1850 11,872 296 20,068

Wairarapa 272 52 57 1389 13 1783

Waitematā 5449 5907 9829 29,797 438 51,420

West Coast 50 11 13 387 8 469

Whanganui 691 85 81 1623 19 2499

Unknown 1630 784 896 5108 2774 11,192

Total 45,708 43,316 43,247 167,142 5934 305,347

20

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Table 18: Rate per 1000 people tested for COVID-19 from 12 August to 27 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 89.7 138.3 59 88.9 84.8

Bay of Plenty 49.7 89.5 36.6 48.5 48.9

Canterbury 35.1 51.5 36.1 35.4 36.4

Capital and Coast 47.4 65.2 35.1 53.2 51.4

Counties Manukau 95.8 186 72.1 70.3 100.1

Hawkes Bay 37.5 54.7 29 38.2 38.6

Hutt Valley 36.6 53 36.7 40 40.4

Lakes 66.7 124.9 53.8 61.6 65.2

MidCentral 33.3 52.8 29.8 39.3 38.3

Nelson Marlborough 43.1 106.8 44.9 40.7 42.7

Northland 56.1 61.7 38.2 43.6 48.3

South Canterbury 30.1 94.2 40.1 37.7 38.1

Southern 38.7 64.6 36.5 44.3 43.9

Tairāwhiti 40.1 56.4 61.7 41.8 42.2

Taranaki 33.3 58.2 32.9 35.1 35.5

Waikato 51.3 82.5 41.9 44.1 47.4

Wairarapa 34.1 62.5 45.7 38.9 39

Waitematā 87.1 132.5 68.4 77.9 81.2

West Coast 12.9 43.5 14.1 14.3 14.6

Whanganui 39.8 55.9 27.7 37.7 38.5

Total 58.8 135.4 56.4 54 61.6

1

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SITREP 068

Coronavirus disease 2019 (COVID-19)

Issued: 1030 hours 30 September 2020

Information current at: 1000 hours

This report provides a daily update on the COVID-19 health system response. New information is denoted by red text.

Please use the single point of contact email [email protected] for help/support. Your email will be

logged and promptly passed to the appropriate team.

This document is classified IN CONFIDENCE and not for further distribution.

Need to know

COMMUNITY CASES

NEW LAST 24 hrs

0

IMPORTED MIQ CASES

NEW LAST 24 hrs

1

COMMUNITY CASES

TOTAL RECOVERED

170

137

COMMUNITY CASES

ACTIVE

14 TOTAL CASES SINCE 11 AUG

187

30 TOTAL IMPORTED MIQ CASES

167

TOTAL ACTIVE CASES IN NZ (COMMUNITY & MIQ): 44

IMPORTED MIQ CASES

TOTAL RECOVERED

IMPORTED MIQ CASES

ACTIVE

LABORATORY TESTS

LAST 24 hrs

4,969

LABORATORY TESTS

LAST SEVEN DAYS

35,922

LABORATORY TESTS

TOTAL

960,559

CASES DECEASED

3

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2

Total COVID-19 cases

Table 1: Total number of COVID-19 cases as at 0900 30 September 20201

Case status Active Recovered Deceased Total

Confirmed 44* (-11) 1416 (+12) 20 1480 (+1)

Probable 0 351 5 356

Total 44* (-11) 1767 (+12) 25 1836 (+1)

*1 newly identified case, 12 cases classified as recovered.

New cases in New Zealand since 0900 29 September 2020, as at 0900 30 September2

Imported in MIQ facilities

1. One new case has been detected at the border. In total 167 cases have been detected

at the border since the establishment of MIQ facilities.

o One case arrived on 25 September from France via Singapore. Managed isolation in

Auckland transferred to Auckland Jet Park facility.

Community

2. No new community cases have been reported. It has been five days since the last

community case was reported.

Historic cases

3. No new historic cases have been reported.

Total community cases by DHB since 11 August

Table 2: Community cases by DHB and case status as at 0900 30 September 20203

1 EpiSurv Database, 0900 30 September 2020

2 EpiSurv Database, 0900 30 September 2020

3 EpiSurv Database, 0900 30 September 2020

Case Status Counties Manukau Waitematā Auckland Waikato Total

Confirmed 79 56 50 1 186

Probable 1 0 0 0 1

Total 80 56 50 1 187

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Total community cases by outbreak since 11 August4

Table 3: Community cases by Outbreak as at 0900 30 September 20205

Community cases and household contacts at Jet Park

4. As at 0800 30 September there are 17 people isolating in Jet Park from the community.

nine are confirmed cases, the remaining eight are household contacts. This number will

decrease as people finish their isolation and depart from the facility.6

Cases in hospital

5. One case in hospital with COVID-19 as at 0800 30 September.7

Table 4: Number of cases in hospital with COVID-19 by DHB as at 0800 30 September 2020

4 EpiSurv Database, 0900 30 September 2020

5 EpiSurv Database, 0900 30 September 2020

6 NRHCC Morning Report, 0900 30 September 2020

7 NRHCC Morning Report, 0900 30 September 2020

Outbreak New cases (last 24

hrs)

Total cases Active cases

remaining

Auckland August 0 179 8

Christchurch Returnees 0 6 6

Rydges Hotel (MIF) 0 1 0

Under Investigation

0 1 0

Total 0 187 14

DHB Hospital Number in a general ward Number in ICU/HDU

Auckland Auckland City 0 0

Waitematā North Shore 0 0

Counties Manukau Middlemore 1 0

Total - 1 0

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4

Health system response

Overall approach

6. Our investigation has two main focus areas that run in parallel:

o Source attribution – a focus on investigating the case with the earliest symptom

onset date to gather details actions of movements 14 days prior. This will help to

understand the possible source of the new outbreak.

o Containment – rigorous case investigation, identification of close contacts and

isolation and testing to ensure that chain of transmission is broken.

o Case classification –has been established to consider cases with high CT counts will

be investigated by an expert panel to determine their status and develop a protocol

for reporting, management, and investigation of potentially historic infections.

Current outbreak investigation priorities8

o Follow up of Christchurch Returnees cases and settings of interest.

o Ongoing management of Auckland August outbreak.

Settings of interest9

7. Christchurch to Auckland Charter flight and related Christchurch MIF cases.

8. Settings of interest for the Christchurch Returnees outbreak include

o A supermarket and two retail stores in Auckland.

o Several locations outside of Auckland, which have been identified and are being

followed up by the relevant PHUs.

9. No new settings of interest have been identified.

Case investigation Christchurch Returnee Outbreak –

10. A case reported on 19 September is a returnee who arrived in New Zealand on 27

August and completed managed isolation in Christchurch. The case tested negative on

day 3 and day 12. They left managed isolation on 11 September and returned home to

Auckland on a charter flight from Christchurch. They were tested after developing

symptoms on 16 September and returned a positive result on 18 September. The case

and their two household contacts (both reported as confirmed cases on 19 September)

were transferred to the Auckland Jet Park quarantine facility on 18 September.

Genomically, the three cases are part of the B.1.36 lineage and sequencing is consistent

with three confirmed cases from the same flight to New Zealand, all of whom tested

positive while in an MIQ facility in Christchurch.10 Source of infection is still under

investigation.

8NRHCC Morning Report, 0900 30 September 2020

9 NRHCC Morning Report, 0845 24 September 2020

10 ESR email update 0924 27 September 2020

s 9(2)(a)

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5

11. Three cases from the same family unit tested positive on 22 September. Two cases were

tested because they were passengers on the chartered flight

and the third case is a household contact

The family has

been in isolation since 20 September. Genomes have been sequenced and all three

cases are part of the B.1.36 lineage and are closely matched to other cases epi-linked to

the Christchurch Returnees outbreak.11 Source investigation continues12. The family

visited Tāupo from 18 to 20 September and met parties from across the country.

They also had dinner with a family of outside of the Tāupo trip. All parties

who were contacts of these cases have been tested and are self-isolating. All PHUs with

responsibility for close contacts have reported good compliance with isolation

requirements.13. Contact Tracing and testing results can be seen in Table 5.

12. All passengers on the Christchurch to Auckland charter flight have been tested, except

one. Of those tested no results are pending and the rest are negative.

Case investigation Auckland August Outbreak -

13. Source investigation for an epidemiological link to the main cluster for four cases who

have been genomically linked to the main cluster is ongoing. Updates on the

investigation will be included in tomorrow’s SitRep (01 Oct):

o The

o GP

o The second Mount Albert Grammar student

o The Botany case

11 ESR email update 0924 27 September 2020

12 End of day update, Chief Advisor public health, 25 September 1700.

13 PHU MOH phone call, 1000 25 September

s 9(2)(a)

s 9(2)(a)

s 9(2)(a)

s 9(2)(a) s 9(2)(a)

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ESR and wider testing14 14. A total of 172 cases (96%) from the Auckland community cluster have now been

sequenced, of which 143 (80%) yielded a high quality genome. The remaining cases did

not have sufficient genetic material to be sequenced reliably. All cases are part of the

same B1.1.1 lineage and genomic cluster and the subsequent mutations observed are

consistent with the epidemiological sub-groupings.

15.

16. Ongoing analysis of the whole genome sequencing results is being used to show how

COVID-19 has been transmitted through the community cluster and to further inform

its management.

17. No direct links have been found between the community outbreak genome

sequencing, and the 71 full genomes (52 high quality) currently available from cases

detected in border arrivals in managed isolation facilities (MIFs). There has been one

case in a health worker at a managed isolation facility. WGS results indicate that this

case is genomically linked to the Auckland community cluster and clustered closely with

three community cases in the managed isolation facility (as discussed in para 8).

18. Genome sequencing on cases from the Christchurch returnees cluster

has also been completed, all cases are part of the B1.36 lineage.

19.

14 ESR Whole Genome Sequencing Report, Email 0927 29 September 2020

s 9(2)(g)(i)

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10

Figure 1: Number of cases that have been whole genome sequenced and are genomically clustered

with the Auckland August cluster by sub-cluster as at 14 September 202015

Source: ESR *A sample may not have been received by ESR, may not have been sequenced yet or a sequencing result could not be

obtained from the sample received.

Contact tracing16 20. Since the 11 August, 4073 community close contacts have been identified and recorded

in the National Contact Tracing Solution, all of these have been contacted and are self-

isolating.

Table 6: Close contact tracing recorded in the National Contact Tracing Solution since 11 August as at

0830 30 September 2020

27/09/2020 28/09/2020 29/09/2020 30/09/2020

Cumulative number of close

contacts identified1 4072 4075 4079 4073

Cumulative number of close

contacts successfully contacted 4069 4072 4079 4073

Number of close contacts

referred to "finding services"2 0 0 0 0

Number of close contacts

awaiting contact 3 3 0 0

1. Contacts loaded into the National Contact Tracing Solution, and managed by either the National Investigation and Tracing

Unit or the Public Health Units. Contacts from MIQ and overseas cases are not included in this report.

2. "Finding services" refers to the mechanism the National Close Contact Service uses to find valid contact details for close

contacts we do not have the correct contact details for. These services utilise internal Ministry of Health databases along with

Police, Customs and Airlines where relevant.

15 ESR email 1608 14 September 2020

16 COVID-19 NCCS Analytics and Reporting 0819 30 September 2020

0 5 10 15 20 25 30 35

Americold

Americold HH

Auckland Bus

Botany

Church 1

Church 2

Church 3

Finance Now

Finance Now HH

Household 1

Household 2

Household 3

MREF-Bereavement

GP

NZ Courier Post

Pending

Warehouse

Number of cases

Sequenced and genomically clustered Sequence not available*

s 9(2)(a)

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11

3. The total number and number successfully contacted can decrease due to duplicates and invalid records being removed from

the system.

COVID-19 Tracer App usage17 Figure 2: COVID-19 Tracer App cumulative registered users and daily scans/manual entries as at 1615

29 September 2020

1. The number of scans and manual entries on any given date is subject to change for up to 31 days. This is because there can be

a delay before anonymised analytic information is received (e.g. device not connected to internet when scan carried out).

2. The number of App registrations and QR codes for any given date is subject to change for up to 1 day. This is because due to

reporting timeframes these numbers may be extracted before the 12pm cut-off for the reporting period.

3. The ability to scan without being logged into the App was introduced on 09 September, delaying the data transfer to the

Ministry of Health until the individual re-logs into the App. This possibly results in under-reporting of daily scans reflected in

the data.

17 Response Analyst – Digital Channels, 1625 29 September 2020

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

28/0

7

31/0

7

03/0

8

06/0

8

09/0

8

12/0

8

15/0

8

18/0

8

21/0

8

24/0

8

27/0

8

30/0

8

02/0

9

05/0

9

08/0

9

11/0

9

14/0

9

17/0

9

20/0

9

23/0

9

26/0

9

29/0

9

Dai

ly s

can

s an

d m

anu

al e

ntr

ies

Cu

mu

lati

ve A

pp

regi

stra

tio

ns

Day and month

Cumulative App registrations Daily scans and manual entries

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12

Testing18 Table 7: Testing by functional groups, as at 0900 30 September 2020

*Numbers have been sourced from different data extracts in comparison to Table 7.

Laboratory testing numbers19 Table 8: Number of laboratory tests processed nationally as at 0900 30 September 2020

Testing supply update20

21. There are good levels of supplies available, with 278,208 tests available currently in the

labs. The Ministry of Health is continuing to work with major suppliers in order to meet

ongoing need.

18 ÉCLAIR/MoH Public Health Intelligence, 1000 30 September 2020

19 Daily Lab Report, 0934 30 September 2020

20 Testing supply email, 0920 28 September 2020

Reason for test 29 September 23–29 September

GPs and other primary health 2207 16578

CBACs and pop-ups 2041 14162

Border workers - air crew 20 255

Border workers - airport staff 63 1267

Border workers - maritime crew 0 49

Border workers – Port of Tauranga staff 14 22

Border workers – Remaining Port staff 25 278

Border workers - MIF 254 1149

Border workers - MIQ 25 304

Travellers - Staying at MIF 257 2001

Travellers - Staying at MIQ 65 72

Total 4,971* 36,137*

Time period Number of laboratory tests

29 September 4,969*

Last 7 days (23 Sept to 29 Sept) 35,922*

Total 960,559

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13

Healthline updates21 22. On 29 September there were 1,857 contacts in Healthline. Of those calls, 668 were to

the COVID-19 Info line. Demand on 1737 Need to talk? and other mental health services

was 567 contacts (in line forecast).

23. The main themes on 27/28 September were:

o Ongoing calls relating to the exposure events.

o Healthline are continuing to see a higher than normal acuity (of non-COVID related

health issues) through Healthline and some of this is geographically focussed – i.e.

the wider Auckland region.

o Questions relating to travel between alert levels.

o Most service users were calling because they are symptomatic and wanted to get a

test.

Logistics

Health Workforce22

24. Upskilling of alternative workforces for testing continues to progress. Health Workforce

are currently engaged with Careerforce and DHBs to create a testing workforce training

and education package. This will be utilised by DHBs across the country, to increase the

pool of people who are able to perform COVID-19 testing. It is anticipated this package

will be released in the week of 12 October 2020.

25. Surge workforce requests continue to be monitored and responded to, with 3779

people listed on the surge as “available”.

26. Health Workforce are monitoring staffing needs in MIFs facilities and are providing

support where possible.

Hospital capacity23 Table 9: Number and occupancy of hospital beds by type as at 0800 30 September 2020

Type Number of units Number (%) occupied/in use

ICU and HDU beds 339 229 (67.6%)

Ventilators 298 44 (14.8%)

Ward beds 7201 5982 (83.1%)

21 National Telehealth Service Coronavirus Update, 0938 30 September 2020

22 Health Workforce Directorate, 0853 28 September 2020

23 COVID-19 Hospital Summary, 0918 30 September 2020

14

IN CONFIDENCE – NOT FOR DISTRIBUTION

Appendix 1: Case summary Table 10: All new community cases reported between 0900 29 September and 0900 30 September. Source: ESR EpiSurv Extract 0900 30 September 2020

Cumulative

Number

Date tested

positive Onset date Case status DHB Sex Age Ethnicity

Symptoms

[Yes/No] Hospitalised Occupation

Source of

transmission

IN CONFIDENCE – NOT FOR DISTRIBUTION

15

Appendix 2: COVID-19 Provisional Disease Indicators, by date

of case notification16 Table 11: NCTS data for cases in the community - Please note, National Investigation and Tracing Centre are working through data quality issues, so

will not be reporting the metrics this morning.

Indicator (as per Table

9832) Refined Indicator description Target 13 Sept ** 14 Sept

** 15 Sept ** 16 Sept ** 17 Sept **

18 Sept **

19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine 80% within 96 hours - - - - - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine 80% within 96 hours - - - - - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine 80% within 72 hours - 100% - - - - -

4 – (C001) Time from first symptom to test sample taken for positive cases 80% within 48 hours - - - - - 100% -

5 – (L001) Time from test sample taken to notification of positive result 80% within 24 hours - 0% - - - 100% 100%

6 – (P002) Time from case notification to isolation / quarantine of contact 80% within 48 hours - 100% - - - 84% -

7 – (P001) Time from notification to case interview 80% within 24 hours - 100% - - - 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined 80% within 24 hours - 100% - - - 83% 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - - - 84% -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing <20% - 0% - - - 7% 0%

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

IN CONFIDENCE – NOT FOR DISTRIBUTION

16

Table 12:NCTS data for cases in the community Managed Isolation and Quarantine, International, and Unknown

Indicator (as per Table 9832) Refined Indicator description Target 13 Sept ** 14 Sept 15 Sept ** 16 Sept 17 Sept ** 18 Sept ** 19 Sept **

1 - (S001) Time from exposure to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

2 – (S002) Time from case first symptom to contact isolation / quarantine

80% within 96 hours - 100% - 38% - - -

3 – (S003) Time from test sample taken to close contact isolation / quarantine

80% within 72 hours - 100% - 100% 100% - -

4 – (C001) Time from first symptom to test sample taken for positive cases

80% within 48 hours - 33% - 50% - - -

5 – (L001) Time from test sample taken to notification of positive result

80% within 24 hours - 0% - 71% 0% 100% 50%

6 – (P002) Time from case notification to isolation / quarantine of contact

80% within 48 hours - 100% - 100% 100% - -

7 – (P001) Time from notification to case interview 80% within 24 hours - 75% - 58% 100% 100% 100%

8 – (P003) Time from close contact identification to isolated / quarantined

80% within 24 hours - 100% - 100% 100% - 100%

10 – (P004) Proportion of contacts traced in 48 hours 80% within 48 hours - 100% - 100% 100% - -

C – (S005) Proportion of close contacts with confirmed or suspected COVID-19 at the time of tracing

<20%

- 0% - 0% 0% - 0%

Note:

• * The numerator and denominator are provided in some instances to provide context for low percentages.

• **Data is not available for metrics where there is no data that meets the definition, or where the time/days to reach target has not fully elapsed

• The value of P002 can drop due to the addition of new close contacts to exposure events after the 48-hour period since case notification had elapsed. This can happen for a number of reasons, including a case recalling further details following the original case

interview.

• These metrics report all cases during the specified period, including those in Managed Isolation and Quarantine, and do not include casual contacts.

• There are three additional indicators under development requiring both technical and clinical input to define data requirements. These are due to be completed by end October 2020.

17

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Appendix 3: NRHCC Testing Report

Novel Coronavirus (COVID-19)

Issued: 1700 29 September

Table 13: Metro Auckland Summary Total of Testing for 29 September 2020

Community MIQ

staff

MIQ

guests

Airport Maritime port Ship’s

Crew

TOTAL

29/09/2020 617 133 625 124 PM Testing 0 1499

Table 14: Estimated tests taken since 12 August 2020, based on manual site reports at 5pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 –

27/09

28/09 29/09*

MIQ Staff 2132 659 1488 912 1086 908 1136 122 133

Guests 2972 3767 3600 3406 3424 3843 3819 454 625

Border Airport 2129 933 1349 1158 853 951 843 129 124

Port 1588 678 161 392 153 320 208 76 PM

Testing

Crew 0 0 0 0 0 0 21 0 0

*29/09 day still in progress

Table 15: Estimated tests taken at Metro Auckland CTCs, since 12 August 2020, based on manual site reports at 4pm

Site 12/08-

16/08

17/08-

23/08

24/08 –

30/08

31/08 –

06/09

07/09 –

13/09

14/09 –

20/09

21/09 –

27/09

28/09 29/09*

Airport Oaks 1148 515 366 265 181 152 118 21 8

Botany CTC 1151 948 905 749 681 802 526 63 59

Health New

Lynn 2603 1258 1703 732 889 621 451 44 49

Mangere

Town Centre 1748 1684 1599 860 660 487 300 45 34

Otara CTC 3221 1712 1429 930 699 938 428 64 44

St Lukes 1368 1045 1414 797 666 830 793 85 72

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Takanini

Urgent Care 1886 1216 1153 684 440 487 313 44 29

Whanau

House 2502 1371 1442 928 1613 870 594 74 62

Whanau Ora -

Central 1957 964 1583 937 783 470 465 50 49

Whanau Ora -

North 1442 669 637 982 947 907 633 89 54

Whanau Ora -

South 2945 1250 718 677 620 470 310 40 33

Papakura Pop

Up N/A N/A N/A N/A N/A N/A N/A 13 21

Te Atatu Pop

Up N/A N/A N/A N/A N/A N/A N/A 48 39

West Harbour

Pop Up N/A N/A N/A N/A N/A N/A N/A 9 8

Otara Pop Up N/A N/A N/A N/A N/A N/A 38 N/A 27

Waipuna

Targeted Site 143 549 376 219 251 220 186 28 28

Henderson

Targeted Site N/A N/A N/A N/A 631 93 15 1 1

Total 26,148 16,781 21,356 13,002 10,475 8,832 5436 718 617

*29/09 day still in progress; N/A = not open as a CTC; Previous sites that are no longer open are not included

in this report

CTCs and mobile testing site locations

Please see https://www.arphs.health.nz/public-health-topics/covid-19/where-to-get-tested for the most up-

to-date information on CTCs and mobile testing sites in the Auckland region.

IN CONFIDENCE – NOT FOR DISTRIBUTION

19

Appendix 4: Testing by DHB and ethnicity The tables that follow are the number of people tested. The numbers in the laboratory testing

section are the number of laboratory tests processed.

Table 16: Number of people tested for COVID-19 from 12 August to 29 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Unknown Total

Auckland 3945 7828 11,220 23,647 542 47,182

Bay of Plenty 3003 402 734 7736 84 11,959

Canterbury 1851 739 2213 15,971 277 21,051

Capital and Coast 1771 1471 1795 11,507 291 16,835

Counties Manukau 8641 22,538 11,072 14,978 521 57,750

Hawkes Bay 1644 352 274 4179 85 6534

Hutt Valley 971 699 704 3832 57 6263

Lakes 2607 323 528 3755 124 7337

MidCentral 1238 299 476 4991 120 7124

Nelson Marlborough 704 271 339 5212 75 6601

Northland 3438 236 318 4823 64 8879

South Canterbury 162 47 95 1957 31 2292

Southern 1319 457 960 12,053 126 14,915

Tairāwhiti 1004 63 73 943 23 2106

Taranaki 783 82 206 3183 75 4329

Waikato 5012 1112 1877 12,048 304 20,353

Wairarapa 278 52 57 1414 14 1815

Waitematā 5525 5981 9958 30,269 454 52,187

West Coast 50 11 13 387 8 469

Whanganui 701 85 83 1662 20 2551

Unknown 1667 789 908 5208 2938 11,510

Total 46,314 43,837 43,903 169,756 6233 310,043

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IN CONFIDENCE – NOT FOR DISTRIBUTION

Table 17: Rate per 1000 people tested for COVID-19 from 12 August to 29 September

Prioritised ethnicity MPAO

DHB of domicile Māori Pacific Asian Other Total

Auckland 90.7 139.6 59.9 90.5 86.1

Bay of Plenty 50.2 90.4 37.5 49.2 49.6

Canterbury 35.3 52.1 36.4 35.8 36.7

Capital and Coast 48.5 66.3 35.8 54.1 52.3

Counties Manukau 97.1 187.7 73.3 71.6 101.4

Hawkes Bay 38 54.8 29.9 38.7 39.2

Hutt Valley 37.3 59.9 37.5 40.7 41.5

Lakes 67.8 126.4 54.3 62.6 66.3

MidCentral 34 53.9 30.7 40.3 39.3

Nelson Marlborough 43.9 109.7 45.7 41.4 43.5

Northland 56.5 62.8 38.4 44.2 48.8

South Canterbury 30.5 96.3 40.1 37.9 38.3

Southern 39.3 66.4 37.2 45.1 44.7

Tairāwhiti 40.5 56.4 62.5 42.7 42.8

Taranaki 33.5 58.9 33.1 35.4 35.8

Waikato 52 83.4 42.5 44.8 48.1

Wairarapa 34.9 62.5 45.7 39.6 39.7

Waitematā 88.3 134.1 69.3 79.2 82.4

West Coast 12.9 43.5 14.1 14.3 14.6

Whanganui 40.4 55.9 28.3 38.6 39.3

Total 59.6 137.1 57.3 54.8 62.5