yemen covi d19 labo rato ry t e s t i n g str ategy

Y e m e nC O V I D 1 9 L a b o r a t o r y T e s t i n g S t r a t e g y

Contents

Purpose of this strategy...............................................................................................................3

Who gets tested.....................................................................................................................................7

Laboratory testing procedures for covid-19.............................................................8

Laboratory indicators data and surveillance.....................................................1 0

Annex 1: COVID-19 Laboratory requisition form......................................................1 1

2

Final _ 6.7.2020 _ Laboratory Testing Strategy for COVID-19, YEMEN

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Purpose of this strategy

The objective of COVID-19 testing is to identify individuals with COVID-19 infec-tion, isolate and manage laboratory con-firmed cases, and undertake rapid con-tact tracing for exposed in-dividuals to reduce the transmission and spread. The strategy will allow those having a higher risk of poorer outcomes from COVID-19 infection be rapidly identified and prioritized for accessing health care services. Laboratory data will also be used to supplement epidemiological da-ta for a comprehensive COVID-19 surveil-lance system. This strategy should be read together with other detailed WHO technical guidance on COVID-19 labora-tory and diagnosis .Case Definition: COVID-19 case defini-tions are as per WHO guidelines and are also outlined in the Yemen Covid-19 Surveillance Strategy.

Situation overview

Six laboratory facilities in Yemen are cur-rently able to test for COVID-19, four are in the south and two are in the north. By end June 2020 the laboratories in the north were fully functional and had re-ceived supplies to conduct up to 40,000 tests. In the South, 10,500 PCR diagnos-tic kits have been provided by WHO, however other necessary supplies like RNA isolation kit and PCR plastics (tubes/caps) provided so far are only enough to conduct 4500 tests. More PCR diagnostic kits and essential consuma-bles are expected to be delivered in the coming weeks.

Human Resources The table 1 shows the total number of laboratory staff (Laboratory techni-cians/technologist) working in the each of the laboratories and the number that has been trained so far.

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Table 1: Trained laboratory staff capacity in Yemen

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P C R M a c h i n e sExcept Sanaa CPHL, all other testing laborato-ries have one PCR thermocycler for performing the molecular detection of COVID-19. Sanaa CPHL have two functional PCR thermocyclers. With one PCR machine, a single laboratory can perform two testing runs per day with each run analyzing at least 90 samples from suspected cases. Hence, in total a single laboratory with all the necessary requirements can perform testing for 180 samples a day. The six testing laboratories in Yemen have capacity to perform 1080 samples every day within normal working hours without overwhelming the laboratory system. Currently, the combined throughput of the 6 testing CPHLs average about 200 samples a day which is below the available capacity.An extra 11 PCR machines are expected into the country courtesy of HSA donation (5 machines), and WHO procurement (6 machines). A new machine for Hodeidah Central Public Health Lab (CPHL) has been delivered and is ready for installation. These new PCR machines provided together with all the necessary accessories re-quired for a complete PCR test will be essential in expanding access to COVID-19 testing and in improving the testing output of the existing laboratories. All laboratories currently perform manual ex-traction of RNA using commercial kits. There is no laboratory testing COVID-19 with automated RNA extraction machine at the moment. This factor needs to be considered when planning ex-pansion of testing output as the RNA extraction step is a labour-intensive step especially when dealing with large number samples. It is important to note that the two administra-

tions in the South and North have two different approaches in terms of expanding access to laboratory testing for COVID-19. While the Southern part of the Yemen adopted a decentralized testing strategy where testing is availed in every governorates, the MOPHP in North favours centralized testing for reason of having better control on quality procedures as only the Sanaa Central labs have trained laboratory person-nel who are proficient in performing real time RT-PCR assays. Emphasis will therefore be made regarding putting in place a robust laboratory sample transport system, and results feedback system to cover all gover-norates. The envisaged mechanism can be supported ether by partners or by revitalized polio surveillance structures.

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Enhancing or improving testing capacity:Some of the activities planned to enhance testing capacity are as follows (details in Annex 3);

• Establish 3 more PCR testing laboratories in Ibb, Hodeida, Saada.

• Deploy point of care PCR Diagnostic machines (GeneXpert) in Socotra, Al-Maharah, Marib

• Ensure availability of testing kits, routine supplies, and consumables.

• Train more laboratory staff • Ensure compliance to SOPs and testing algorithms through frequent supportive supervision. The map below shows the existing and planned PCR labs as well as locations of the point of care diag-nostic PCRs (GeneXpert) in the country.

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WHO recommends that all suspected or probable cases who meet the standard case definition be tested for COVID-19. This strategy therefore recommends the following individuals to get tested:• All suspected cases as per established COVID-19 suspect case definition • All probable cases as per established COVIFD-19 probable case definition• All SARI/Pneumonia cases (requiring admission)• Testing of contacts (in home or facility quarantine) who develop symptoms• Close household caregivers (even if asymptomatic) of confirmed pneumonia/COVID-19 • Exposed health care workers or Laboratory workers who has handled a covid-19 patients or laboratory specimens without PPE

It is anticipated that testing capacity will remain constrained for a consider-able length of time due to shortage of test kits or other operational issues; therefore, prioritization of testing will be conducted due to limitations in testing, and also in view of increasing community transmission of COV-ID-19. Groups or individuals prioritized highly for testing are as follows:

1. Suspect or probable cases amongst vulnerable populations, detainees, refugees, IDPs, migrants, residences

2. SARI/pneumonia patients admitted in hospital

3. Health care workers, RRTs, contact tracers, community volunteers, po-tentially exposed, both in health facilities and at community levels, and who develop symptoms

4. Mothers seeking urgent maternity care, emergency cases, children under five with wasting, with symptoms when detected at triage at ‘non-COVID’ health facilities.

5. Travellers at POEs (air and land border crossings) who develop symp-toms

6. Close household caregivers of confirmed cases, and who develop symp-toms

7. Individuals at risk of developing severe disease due to age, presence of comorbidities, or other risk factors.

Who gets tested:

High priority for testing

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Laboratory testing procedures for covid-19a) Testing algorithm

Testing for COVID-19 virus is a two-step process, involving first a screening assay for both SARS virus and COVID-19 virus, and secondly, a con-firmatory assay for COVID-19 virus only;

1. Screening with E gene assay to detect both SARS virus, MERSCOC and SARS-COV2

2. Confirmation with RdRP gene assay to detect SARS-COV2.

The above procedure was applied in Yemen in the beginning of the outbreak, whereby samples positive on the screening assay were then ana-lysed with a confirmatory assay that is specific to SARS-COV2. However, it became apparent that conducting the screening and the confirma-tory assays in an area with high positivity rates was both labour and resources (tubes, tips, caps, gloves) intensive. As results, laboratory test-ing strategy was reviewed to perform only the screening assay, which is more sensitive assay. Samples are now analysed using only one assay and with final results of a patient are based on the outcome of the screening assay. This simplified testing strategy is widely practiced by countries in the regions and has been shown to be offer a similar diagnostic accuracy when compared with two-step diagnostic assays. In the meantime, pro-curement has been initiated at the country level for multiplex assays that combine the detection of 2-3 genes in a single reaction tubes hence saving on time and consumables and delivery of these kits is expected in the coming weeks.

b) BiosafetyLaboratories undertaking testing for COVID-19 virus should adhere strictly to appropriate biosafe-ty practices. This include conducting risk assess-ment before handling clinical samples, identifying procedures that are likely to produce risks and putting in place measures to eliminate or reduce such risks. Diagnosis of COVID-19 by a Real Time PCR test requires (Biosafety Level 2) laboratory. All laboratories conducting tests for COVID-19 in Yemen are BSL 2 and each one of them has at least one class 2 biosafety cabinet where sampling processing is conducted. Laboratory staff have also been trained on bio-safety due sample processing and were provided with all updated guidelines on biosafety as regards to COVID-19 samples han-dling from WHO.

c) Sample collectionAt minimum, respiratory material should be col-lected with strict adherence to infection preven-tion and control procedures as follows:

• Upper respiratory specimens: nasopharyngeal and oropharyngeal swab or wash in ambulatory patients, and/or

• Lower respiratory specimens: sputum (if pro-duced) and/or endotracheal aspirate or bron-choalveolar lavage in patients with more severe respiratory disease.

All specimens delivered to the testing laboratory should be accompanied by a completed labora-tory test request form (Annex 1)

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d) Sample packaging and transport

Specimens for virus detection should reach the laboratory as soon as possible after collec-tion. Correct handling of specimens during transportation is essential, ensuring that collected swabs are packaged properly using the triple package systems and delivered to the testing laboratory. Specimens that can be delivered promptly to the laboratory can be stored and shipped at 2-8°C. When there is likely to be a delay in specimens reaching the laboratory, the use of viral transport medium is strongly recommended. Once, in the labora-tory, lab staff will document the patient details and give the sample a unique identification number. The samples are analyzed according to the existing SOPs and results are released in the same day. To reach governorates located outside testing laboratories, plans are on-going to procure courier services to enable sample referral system. It is anticipated that samples from suspected cases in a defined district/governo-rate will be collected through the RRT system, pre-stationed at a central location (usually governorate hospital lab), and be picked-up by the appointed courier service provider. The frequency of collection will depend on the sample volume but a daily collection and delivery to one of the CPHL testing site within a period of not more than 72 hours from time of collection is expected.

It is required that all COVID-19 laborato-ries are to participate in WHO SARS-CoV-2 External Quality Assurance Program (EQAP). Currently two laboratories – Sanaa and Aden are participating in WHO SARS-CoV-2 EQAP EQAP organized by Centre for Health Protection (CHP) of the Department of Health, Hong Kong. EQAP samples have been received in Yemen and the two participating labs will submit their analysis to organizers.

A total of 28 laboratory technicians have been trained on PCR technique and biosafety as pertains to handling specimen from sus-pected COVID-19 patient. Second round of training is planned to be conducted in the third quarter of 2020.

Training on sample collection, packaging and transport will also be provided to staff at tri-age EHS (NON-COVID HFs), RRTs, and to all other HCWs who will be involved in the collection and transport of samples.

Private and other Laboratories

Testing facilities run by partners and NGO, as well as private for-profit laboratories will be required to align their testing kits and proce-dures according to WHO/MOH/CPHL guid-ance, participate in EQAP and training, and they should also regularly share COVID-19 test data with MOH.

EQAP and Training

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Daily indicators

All laboratories with the capacity to test for SARS-CoV-22 should report daily: • Total persons tested for SARS-CoV-2 • Total number of persons testing positive for SARS-CoV-2 (and any testing inconclusive)• Total number of tests performed for SARS-CoV-2 per type of testing method.

Weekly indicators

To assess access to testing facilities and the ad-equacy of testing per region, the following indica-tors should be measured on weekly basis. 1. Number of COVID-19 PCR tests conducted per 1000 people for every governorate

2. COVID-19 PCR test Percent Positivity (total positive/total test) for every governorateHospital laboratories should also report to the central level, on a regular basis (e.g. weekly), the complete information on tested patients (e.g. age, sex/gender, residence, date of symptom onset, and any other data collected) to permit more in-depth analysis of testing patterns.

A sample of laboratory test request form is at-tached for reference (Annex 1). Arabic version is available. Lab line list - a uniform lab line list has been developed and a sample format is attached (Annex 2). Most labs use this format except Mu-kalla CPHL.

Laboratory data will be integrated with national COVID-19 epi data for surveillance purposes. Lab Line lists will be submitted daily to surveil-lance and information management teams at WHO and MOH who will use the same to update their dashboards and produce other information products, and calculate required indices such as COVID-19 population testing rates per Governo-rate, and test positivity rates (TPR) per Governo-rate.

Laboratory indicators data and surveillance

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Annex 1: COVID-19 Laboratory requisition form

Annex 1: COVID-19 Laboratory requisition form COVID-19 Surveillance Laboratory Requisition and Report form

Unique Sample Lab ID no.

Ministry of Population and Public Health National Central Public Health Laboratory – Aden

Lab Request and Reporting Form Date of collection: __________ Date of disease onset: __________

Patient information Name: Age: Sex:

Unique Case ID no.: Phone Number:

Type of sample: tick where appropriate

Oral/Nasopharyngeal swab Sputum Bronchoalveolar lavage Tracheal Aspirate

Reason for testing (tick where appropriate)

Travel to country with confirmed cases Contact with confirmed/probable case Has typical clinical symptoms Others: _____________________________

Demographic information Governorate: District:

Location: Village:

Clinical Symptoms (Tick where appropriate)

Fever Cough Respiratory Distress Sore throat Other symptoms, specify: ______________________________________

Laboratory Report Realtime PCR Results TTaarrggeett ggeennee –– SSAARRSS-- CCooVV22 (to be reported as Negative or Positive)

1. Screening Test – EE--GGeennee Lot Number: _____________________

2. Confirmatory tests RdRP/oorrff11bb Lot Number: _____________________

3. Other, specify: ______________ Lot Number: _____________________

Conclusion:

Positive results: indicates that an individual is infected with SARS-COV2 (causative agent for COVID-19)

Negative result: may mean the patient is not infected with the virus causing COVID-19, or that the patient has been tested too early, and may test positive later. In that case, the patient may need to be re-tested if the patient continues to show symptoms or deteriorates clinically. Negative results should also be based on eval-uation of date of disease onset, and consideration of optimal sample type.

Name of laboratory technologist: __________________________________________

Date: ______________ Signature:

Report reviewed by: __________________________________________

Date: ______________ Signature:

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Annex 2: COVID-19 Sample Line List

Patient Current Address Clinical Symptom

Unique Sample

Lab ID no.

Unique Case ID

no. Patient Name Phone

number

Age in

Years Sex Type of sample

Reason for

screening Governorate District Subdistrict

Name of the area Fever

Sore throat Cough

Respiratory Distress

Date of onset

Date of collection

Date of Result

Realtime PCR Screening

Results

Confirmatory Test CoV RdRP

(specific to COVID-19)

Conclusive Results for

SARS-COV 2

Name of laboratory

technologist Comments Yes/No Yes/No Yes/No Yes/No DD/MM/YYYY DD/MM/YYYY DD/MM/YYYY Positive/Negative Positive/Negative Positive/Negative

Annex 3: Yemen Laboratory workplan for COVID-19

Main ObjectiveActivities Target

Governorates

Primary Responsible

Officer

Co-responsible

staff

Source of

funding

Estimated funds (USD)

Provide training for laboratory staff on technical procedures, biosafety, good lab practices (GLP), and reporting techniques for all testing laboratories.

A Aseemah, Aden, Taiz, Hodeida, Hadramaut, Ibb, Saada

Dr. Saeed Al-Shaibani

Ismail M Bashir

WB

48,000

Procurement of additional NPS swabs/VTMs, PCR testing kits, RNA isolation kits, tubes/tips and routine consumables required to perform a PCR tests.

All governorates Dr. Saeed Al-Shaibani

Ismail M Bashir

WB1.100,000

Procurement of additional lab equipments to expand testing for selected laboratories

All governorates Dr. Saeed Al-Shaibani

Ismail M Bashir

WB850,000

Development guidelines and SOPs for collecting clinical samples and performing testing for suspected cases. Provide arabic translated versions to all testing laboratories



Ismail M Bashir WB

50,000

For governorates without lab capacity for testing COVID-19, Support the transportation of samples from THE health facil ities to the nearest testing laboratories.

All governoratesDr. Saeed Al-

Shaibani Ismail M

Bashir WB100,000

Support all testing laboratories to participate in external quality assessment schemes organized at the regional level (EMRO).



Ismail M Bashir WB

30,000

Provide quarterly supportive supervision and facil ity assessment to assess compliance to SOPs, biosafety guidelines, GLPs and



Ismail M Bashir

WB

25,000

Organize targeted testing of populations through campaign of mass testing for COVID-19 All governorates


Ismail M Bashir

300,000

Ensure that national laboratories identified for providing testing for COVID-

19 have the appropriate capacity and readiness to provide timely and quality

laboratory reports.

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yemen covi d19 labo rato ry t e s t i n g str ategy

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