GB pig quarterly report

Disease surveillance and emerging threats

Volume 23: Q4 – October to December 2019

Highlights

African Swine Fever in South East Asia and Europe – page 4

Swine fevers ruled out in suspect report cases –page 8

Pandemic H1N1 2009 and H1N2 influenza strains circulating – page 11

Swine dysentery diagnostic trend reduces in last quarter of 2019 – page 15

Porcine circovirus 2 genotyping shows shift to PCV2d – page 16

Novel circovirus species (PCV4) identified in pigs in China – page 19

Contents

Introduction and overview ................................................................................................................ 1

New and re-emerging diseases and threats ................................................................................. 4

Unusual diagnoses or presentations ............................................................................................10

Changes in disease patterns and risk factors.............................................................................11

Horizon scanning.............................................................................................................................18

References .......................................................................................................................................20

Editor: Susanna Williamson,

APHA Bury St Edmunds Phone: + 44 (0) 1284 724499

Email: Susanna.williamson@apha.gov.uk

1

Introduction and overview

This quarterly report reviews disease trends and disease threats for the fourth quarter of

2019, October to December. It contains analyses carried out on disease data gathered

from APHA, SRUC Veterinary Services division of Scotland’s Rural College (SRUC) and

partner post mortem providers and intelligence gathered through the Pig Expert Group

networks. In addition, links to other sources of information including reports from other

parts of the APHA and Defra agencies are included. A full explanation of how data is

analysed is provided in the Annexe available on GOV.UK

https://www.gov.uk/government/publications/information-on-data-analysis.

Pig disease surveillance dashboard 2019 outputs

Diagnoses made in the fourth quarter of 2019 compared to the fourth quarter of 2018 through the GB scanning surveillance network are illustrated in Figures 1a and 1b.

Diagnoses made in the 12 months of 2019 compared to 2018 through the GB scanning surveillance network are illustrated in Figures 4a and 4b. These can be interrogated further

using the interactive pig disease surveillance dashboard which was launched in October 2017 and can be accessed from this link: http://apha.defra.gov.uk/vet-gateway/surveillance/scanning/disease-dashboards.htm

1a: 253 diagnoses in Q4-2019 1b: 226 diagnoses in Q4-2018

Figure 1: GB scanning surveillance diagnoses

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Note that diagnoses made in low numbers are not shown and that further diagnoses may

be added if records for submissions made in Q3-2019 are finalised at a later date. The

surveillance data for all diagnostic submissions to the GB scanning surveillance network in

the fourth quarter of 2019 from an enhanced pig disease surveillance dashboard are

summarised in Figure 2.

Figure 2: Summary data for 388 submission records in Q4-2019 (357 in Q4-2018)

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Figure 3: Summary data for 1,584 submission records in 2019 (1,410 in 2018)

4a: 1025 diagnoses in 2019 4b: 920 diagnoses in 2018

Figure 4: GB scanning surveillance diagnoses

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These diagnostic submissions are voluntary and subject to several sources of bias. The

profile of submissions for the fourth quarter of this year is broadly similar to that of Q4 of

2018 in that systemic, respiratory and enteric syndromes are the most commonly

submitted and diagnosed. Enteric disease was the dominant syndrome which aligns with

the most common main clinical sign reported “diarrhoea & GIT”. This is similar to the

profile of submissions in the previous quarter of 2019 and is likely, in part, to reflect current

concern about swine dysentery prompting more investigation of diarrhoea in pigs and

increased enteric diagnostic submissions. Total GB diagnostic submissions for the quarter

were higher than the totals for the same quarter for 2015 to 2018, as reported for Q3-2019,

and total annual submissions in 2019 were higher than in any year from 2015 to 2018,

influenced by increased non-carcase submissions to SAC-CVS and increased carcase

submissions to APHA. Interestingly, four of the five most common diagnoses in 2019 are

also in the top five diagnoses in 2018; namely disease due to Streptococcus suis, PRRS,

Lawsonia-associated disease and rotaviral enteritis. Brachyspira pilosicoli was also in the

five most common 2019 diagnoses which is likely to reflect increased surveillance for

swine dysentery in 2019. The geographical areas where free carcase collection is offered

for delivery to post-mortem examination sites within the APHA network were expanded in

2017 (APHA, 2017). The availability of this service is regularly publicised and there is

regular uptake of the service.

New and re-emerging diseases and threats

Please refer to the annexe on Gov.UK for more information on the data and analysis.

Summary update of African swine fever in South East Asia and Europe

Updated assessments continue to be published on African swine fever (ASF) in South

East Asia and Europe including Belgium:

https://www.gov.uk/government/collections/animal-diseases-international-monitoring.

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Figure 5: ASF cases reported in South East Asia since September 2019 (map on 13-02-19)

In South East Asia, ASF has been confirmed in China, Mongolia, Vietnam, Cambodia,

Hong Kong, North Korea, South Korea, Laos, Myanmar, Philippines, East Timor and

Indonesia (Figure 5). During Q4-2019, ASF was confirmed for the first time in domestic

pigs in Indonesia. The first Indonesian outbreaks were in North Sumatra province and

followed unofficial reports of disease and mortality since September 2019. Since these first

reports, there have been further outbreaks of ASF in domestic pigs in Indonesia, with

unofficial reports of spread to Bali. There have been further cases reported in the

Philippines, with spread to the south of the country; an administrative order has been

signed to introduce a nationwide zoning and movement plan to better control and contain

the disease.

China confirmed further ASF infection in wild boar, albeit in low numbers. Wild boar are

present across most of China, with the exception of unsuitable regions in the north and

west of the country. Further cases of ASF in wild boar were reported in South Korea where

no new outbreaks in domestic pigs have been reported recently. All wild boar cases in

South Korea have been close to the border with North Korea.

Confirmation of ASF in China, Mongolia, Vietnam, Cambodia, Hong Kong, North Korea,

South Korea, Laos, Myanmar, Philippines, East Timor, Indonesia and the wide geographic

range encompassed by these countries, demonstrates the potential for further spread into

and within the domestic pig and wild suid populations in South East Asia. Illegal

importation of pork/pork products from affected areas of Asia represents a significant

potential route of entry of ASF virus (ASFV) to the UK. With regular direct flights to the EU

and UK, there is a risk of entry of ASFV in products of animal origin from Asia in

passenger luggage emphasising the importance of raising passenger awareness and

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enhancing border vigilance. Further details are available in updates on:

https://www.gov.uk/government/publications/african-swine-fever-in-pigs-in-china.

The FAO is also providing weekly updates of the ASF situation in Asia:

http://www.fao.org/ag/againfo/programmes/en/empres/ASF/Situation_update.html

In Eastern Europe (Figure 6), significant westward spread of ASF was detected in Poland

in early November 2019 when an ASFV-positive wild boar was killed in a road accident

just 85 km from the German border. This new site of detection is around 300km from the

nearest known ASFV-infected area east near Warsaw. Large geographic jumps to new

areas like this are usually human-mediated. Fencing was implemented where the boar

was found, which has had to be expanded subsequently as further ASF-infected wild boar

carcases have been found, some nearer to Germany. Germany is on high alert and has

intensified wild boar hunting and ASFV surveillance, and fencing is being put in place. This

new area of ASF-positive wild boar is also of note as the neighbouring region of the

province has 30% of the Polish commercial pig population and lies only 70km from the

German border.

Figure 6: ASF cases reported in Europe since August 2019 (map as on 06-02-20)

Further outbreaks of ASF in commercial pig holdings have been reported in Bulgaria and

Romania. Greece reported ASF for the first time in domestic pigs on February 5 th 2020 -

the case was a small-holding with 32 pigs which were culled. Control measures including

cleansing and disinfecting, movement restrictions and tracings were implemented.

Confirmation of ASF in Greece was not surprising as ASFV has been circulating for

several months in wild boar and domestic pigs in Bulgaria close to the borders with Greece

and north Macedonia.

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Belgium has detected ASFV DNA in “bones-only” wild boar carcases in January 2020

following similar finds during the last three months of 2019. These wild boar remains were

found within the Infected Zone and the animals were estimated to have been dead for at

least three months. Belgium remains officially free of ASF in domestic pigs.

Further details are available:

https://www.gov.uk/government/publications/african-swine-fever-in-pigs-and-boars-in-europe

Information on ASF outbreaks has been disseminated to veterinary practices and Pig

Veterinary Society members. The assistance of veterinary practitioners in raising

awareness about ASF amongst their pig-keeping clients in UK is vital together with

advising them on resolving biosecurity weaknesses to reduce the risk of introduction.

The biggest risk for ASF virus entering the UK’s pig population remains pigs or wild boar

eating infected pork or pork products derived from infected pigs or wild boar. The ASF

virus can survive for months in smoked, dried and cured meats, and for years in frozen

meat. The greatest risk is from meat products brought into the UK from affected countries

as personal imports, since the commercial trade of such products is not permitted from

ASF- affected areas. Pig keepers are reminded that it is illegal to feed pigs catering,

kitchen or domestic waste or meat/meat products. Providing dedicated clothing and boots

for staff and visitors, limiting visitors to a minimum, and preventing outside vehicles or

equipment which may be contaminated from coming on to the farm, are also all valuable

procedures to reinforce. An ASF poster is available for pig keepers summarising this

information:

http://apha.defra.gov.uk/documents/surveillance/diseases/african-swine-fever-poster.pdf.

The threat of ASF to UK pigs and measures to prevent its introduction were also

emphasised at small-scale pig producer meetings organised by AHDB Pork during

October 2019. These meetings were led by APHA vets together with the British Pig

Association (BPA) and a summary was published (Williamson and others, 2020).

On-line information has been produced by Iowa State University for US pig producers as a

notifiable disease (known in the US as Foreign Animal Disease, FAD) Preparation Guide.

This shows the components of FAD preparation, steps to take on farm, and provides a

library of resources related to ASF and FADs

https://sites.google.com/iastate.edu/fadprep/home?authuser=0.

There is increasing awareness of animal feed/feed ingredients as a potential risk pathway

for introduction of ASFV to new areas. This is reflected in a recent open consultation on a

draft data section of an EFSA Scientific Opinion on the risk assessment of the ability of

products or materials to present a risk to transmit ASF virus (EFSA, 2020).

There is information on research in the US on virus transmission in feed on this webpage:

https://www.asi.k-state.edu/research-and-extension/swine/FeedSafetyResources.html.

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This includes guidance on what feed mills and ingredient suppliers might do to mitigate the

risk of pathogen contamination of animal feed or feed ingredients. The US pork industry

has also published advice on feed and feed ingredient biosecurity:

https://www.pork.org/wp-content/uploads/2019/09/RoleofFeedandIngrediantASF.v2.pdf

EFSA is also funding a collaborative initiative to obtain wild boar data from European

countries. The output page on this website has useful wild boar reference material

https://enetwild.com/reports-docs/. The FAO has recently published its “Manual on ASF in

wild boar ecology and biosecurity”. This is a comprehensive document and useful from the

perspective of knowledge about both wild boar and ASF:

http://www.fao.org/3/ca5987en/CA5987EN.pdf.

Images of the clinical signs and pathology of ASF are available; suspect cases must be

reported promptly to APHA and this is followed by an official veterinary investigation:

https://www.gov.uk/guidance/african-swine-fever and

http://apha.defra.gov.uk/documents/surveillance/diseases/african-swine-fever-images.pdf

Swine fever ruled out in suspect report cases

APHA received two reports of suspect swine fever in the fourth quarter of 2019 and official

veterinary investigations took place. Following negative test results for ASFV and Classical

Swine Fever Virus (CSFV), both cases were negated and restrictions were lifted. The first

of these cases involved a single one-year-old Kune-Kune pig which was found dead and in

which widespread haemorrhagic lesions (Figures 7a and 7b) were found by the pathologist

(University of Liverpool) at post-mortem examination. The two other pigs in the group at

the premises remained healthy. The dead pig tested negative for ruminant pestiviruses

and histopathology on a wide range of tissues including bone marrow suggested a

septicaemic/endotoxaemic episode resulting in disseminated intravascular coagulation and

a haemorrhagic diathesis. A series of sporadic cases of haemorrhagic disease in single

pigs has been described (Bidewell and others, 2013). In these cases, ruminant pestivirus

infection was the cause of disease in one pig, possible immune-mediated

thrombocytopenia caused haemorrhages in two cases and ingestion of rodenticide may

have contributed to the haemorrhagic disease in two others although concentrations were

not considered sufficiently high to be the sole cause of lesions. Investigation of further

cases such as this will help determine whether there is a previously unrecognised disease,

of undetermined aetiology, affecting individual pigs. At the outset, first consideration must

be given to the possibility of swine fever involvement which, if suspected, must be notified

promptly: https://www.gov.uk/guidance/african-swine-fever.

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a) Dark red prominent lymph nodes and b) marked epicardial haemorrhages

The second suspect swine fever case was reported to APHA by the official veterinarian at

an abattoir. Skin and kidney haemorrhages were found post-mortem in a single pig which

had been bright and alert ante-mortem; only one of two pigs sent together to the abattoir

was affected. Swine fever was ruled out by testing; diagnostic material was not available

for further investigation.

Porcine epidemic diarrhoea surveillance

Since the emergence of virulent porcine epidemic diarrhoea (PED) from mid-2013 in the

USA and elsewhere, the virulent PED virus strain has only been reported in pigs on the

European continent in the Ukraine. However, disease due to reportedly less virulent

strains (known as INDEL strains) has been diagnosed in pigs on several continents,

including countries in Europe and these continue to occur. PED due to any strain remains

notifiable in England and Scotland and suspicion of disease, or confirmation of infection,

must be reported (Defra, 2015; Scottish Government, 2016). The last diagnosis of PED

recorded in the GB diagnostic database (VIDA) was in 2002 on a farm in England. No

suspect incidents of porcine epidemic diarrhoea (PED) were reported in England or

Scotland during 2019. Enhanced surveillance for PED continues and diagnostic

submissions from cases of diarrhoea in pigs (non-suspect) submitted to APHA are

routinely tested by PCR for PEDV on a weekly basis. None have been positive for PEDV

in over 990 diagnostic submissions tested under AHDB Pork funding from June 2013 to

December 2019. Further information on PEDV is available on this link:

https://pork.ahdb.org.uk/health-welfare/health/emerging-diseases/pedv.

Figure 7: Haemorrhagic diathesis in Kune-Kune pig testing negative for swine fevers

(images kindly provided by Ann Courtenay, University of Liverpool)

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Unusual diagnoses or presentations

Abortions associated with bacterial and fungal infection

There were four cases of bacterial foetopathies, and one of fungal abortion due to

Aspergillus fumigatus infection diagnosed at SAC-CVS during Q4-2019. Risk factors for

mycotic abortion relate to exposure of the pregnant dam to fungal spores in the

environment, usually from bedding, bedding stores or feed.

Staphylococcus aureus was diagnosed as the cause of one abortion with pure growths of

this organism isolated from the stomach contents of three foetuses. Histological

examination found no evidence of placentitis, however colonies of coccoid bacteria were

observed in foetal lungs.

Foetopathy due to Streptococcus dysgalactiae subsp. equisimilis was diagnosed in

aborted foetuses from an outdoor weaner-producer unit. A seventh parity sow aborted

without showing signs of ill-health and S. dysgalactiae subsp. equisimilis was isolated in

pure growth from foetal stomach contents (FSC) of four foetuses. In the previous batch, 20

out of 112 sows had aborted but no foetuses were submitted. This organism can be

associated with suppurative conditions and septicaemia, and is a sporadic cause of

abortion in pigs. Submission of more than one litter is worthwhile when multiple sows are

affected.

Unusual pluck lesions associated with fungal disease in nursery pig

A five-week-old pig was submitted from a nursery unit to investigate dyspnoea and stertor.

The lungs had well-demarcated consolidation of both cranial and caudal lung lobes, and

pinpoint haemorrhages throughout the parenchyma (Figure 8).

Figure 8: Pluck lesions in pig with fungal tracheitis and acute alveolitis

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The associated lymph nodes were enlarged and oedematous and the apical tracheo-

bronchial lymph node was compressing the trachea. Histopathology revealed a severe

subacute ulcerative fungal tracheitis and an acute multifocal necro-haemorrhagic alveolitis

(which was porcine reproductive and respiratory syndrome virus (PRRSV) immuno-

histochemistry negative). The presence of fungal hyphae was confirmed in association with

active tracheal inflammation indicating that the fungi were clinically significant in this case.

Fungal infection is usually opportunistic and secondary to factors such as mucosal damage,

immunosuppression, or prolonged antimicrobials. No PRRSV, swine influenza virus or

bacterial pathogens were detected, although earlier influenza infection could not be ruled

out. Systemic fungaemia/toxaemia may explain the pathology seen in the lung and lymph

node which was suggestive of terminal septicaemia/toxaemia/disseminated intravascular

dissemination.

Changes in disease patterns and risk factors

Please refer to the annexe on Gov.UK for more information on the data and analysis.

Pandemic H1N1 2009 and H1N2 influenza virus strains circulate in 2019

Swine influenza diagnoses were made by PCR detection of virus in 38 of 209 (18%)

submissions tested in 2019. Where the virus strain was successfully identified, pandemic

H1N1 2009 (pH1N109) and H1N2 (including reassortant H1N2) were found in

approximately equal numbers. These strains have been predominant for several years

(Figure 9), with avian-like H1N1 occasionally identified.

Figure 9: GB swine influenza diagnoses in pigs as a percentage of diagnosable

submissions and swine influenza strains detected (rH1N2 = reassortant H1N2)

Several detections of pandemic H1N109 were only made using an adjusted PCR test

specific for this virus strain, whether of human or swine origin. It is likely that the pandemic

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H1N109 virus has evolved differently in humans and pigs since its original introduction.

This virus also retains the ability to transmit between host species, whether from pigs to

humans (zoonosis) or humans to pigs (reverse-zoonosis). Whole genome sequencing is in

progress on detected swine strains to further investigate the current situation.

Two swine influenza outbreaks were diagnosed in breeding pigs; acute respiratory disease

was evident in both outbreaks. One incident was diagnosed in replacement gilts, the other

in sows vaccinated against the pandemic H1N109 strain. The infecting strain in the

vaccinated sows was found to be reassortant H1N2 strain against which the pandemic

vaccine would not have provided protection. This illustrates the value of Defra-funded

surveillance for identifying swine influenza subtypes, as well as diagnosing outbreaks.

Detecting swine influenza virus by PCR in breeding pigs can be difficult due to the

relatively short duration of swine influenza virus excretion (approximately seven days in

individual pigs). By the time they are sampled, the sows may no longer be in the acute

stage of disease. In the above cases however, influenza virus was successfully detected

and this emphasises the value of obtaining samples as early as possible from pigs within

the first few days of showing clinical signs.

The Defra-funded swine influenza surveillance at APHA provides PCR testing at no

charge. Where acute respiratory disease suspicious of swine influenza occurs, plain nasal

swabs or tissue pools (lung, trachea, tonsil) can be submitted. Further details are given in

the link below, or cases can be discussed with an APHA Veterinary Investigation Officer:

http://apha.defra.gov.uk/documents/surveillance/diseases/swine-influenza.pdf.

Porcine reproductive and respiratory syndrome diagnoses

The annual trend for diagnoses of porcine reproductive and respiratory syndrome (PRRS)

diagnoses through the GB surveillance network is shown in Figure 10. Disease associated

with PRRSV continues to be prominent, especially in postweaned pigs, as shown in Figure

11 which summarises the surveillance data provided with 111 diagnostic submissions in

which PRRS was diagnosed in 2019. Wasting, respiratory disease and pigs found dead

remain the three most commonly reported main clinical signs. All diagnoses were due to

infection with PRRSV-1; no PRRSV-2 has been detected in submissions from GB pigs to

date.

Figure 10: Annual GB PRRS diagnoses as a percentage of diagnosable submissions

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Figure 11: Surveillance data for GB PRRS diagnoses in 2019

APHA, partner post-mortem provider and SAC-CVS surveillance, and other laboratories

testing for PRRSV outside the GB surveillance network, detect PRRSV-1 regularly, in

association with disease or in monitoring submissions and a proportion of those detected

are sequenced at APHA. As described in the last quarterly surveillance report (APHA,

2019a), this sequencing has identified PRRSV strains with vaccine-like ORF5 sequences

with at least 99% homology to each of the four live vaccines licensed for use in the UK

(Table 1). Most, but not all of these were detected in vaccinated herds. The timing of

detection of the different vaccine-like strains reflects when each of the live vaccines was

licensed for use in the UK; none were detected before the corresponding vaccine was on

the market.

To help identify potential recombinant strains of virus with a vaccine-like ORF5 sequence,

a portion of the highly variable nsp2 (non-structural protein) gene is being sequenced in

addition to ORF5. In the five examples analysed so far in a pilot study, the nsp2

sequences were all consistent with the ORF5 sequences, and were similar to those in the

same vaccine. There was thus no evidence of recombination in these five strains and,

although the possibility of recombination in other areas of the genome cannot be entirely

excluded, that is not likely.

Strains of PRRS virus have been isolated in tissue culture from diagnostic samples where

the ORF5 sequence or the clinical presentation have identified them as being of particular

interest. Full sequence data is available from four of these and there is no evidence that

any of the four are recombinant viruses. This work is continuing.

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Table 1: Vaccine-like ORF5 PRRSV detected by year – note that the numbers each year do

not reflect the prevalence of vaccine-like viruses in GB pigs as many factors affect which

pigs are sampled for surveillance biasing the sample set

Vaccine-like

ORF5 2005 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020

Vaccine 1 6 4 2 8 3 12 7 11 20 14 7 9

Vaccine 2

1

1 2

Vaccine 3

9 18

Vaccine 4

9

1

Total PRRSV

sequenced 40 21 25 51 55 86 58 88 164 108 141 127 6

Streptococcus suis 2 predominant in 2019 serotypes

Outbreaks due to Streptococcus suis represent a significant disease burden in GB pigs

(Figures 4 and 12) and remain a reason for antimicrobial use in some herds. The profile of

Streptococcus suis serotypes identified at APHA is kept under review on a quarterly basis

and in the first quarter of 2019, there was a relative increase in diagnoses of disease

associated with S. suis serotype 1, which was discussed in the Q1-2019 report (APHA,

2019b). This was not maintained during the remainder of the year and S. suis serotype 2

returned to being the predominant S. suis serotype identified.

Figure 12: Annual GB streptococcal disease (mainly S. suis) diagnoses as a percentage of

diagnosable submissions

The main S. suis serotypes causing primary disease (meningitis, septicaemia and

polyarthritis) are serotypes 1, 2, 7 and 14; Table 2 indicates the number of isolates of each

serotype in 2019. Isolates are sometimes used for autogenous vaccine production, as part

of disease control and efforts to reduce antimicrobial use. S. suis isolates serotyped at

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APHA in 2019 (Table 2) were derived from submissions to APHA (66%), SAC-CVS (29%)

and commercial laboratories (5%).

Table 2: GB S. suis isolates in 2019 from pigs – totals and by quarter (NT = non-typeable)

S. suis

serotype 1 2 3 4 5 6 7 8 9 10 14 15 16 18 19 29 31 33 NT Total

Q1 2019 17 15 3 5 7 3 6 5 2 63

Q2 2019 9 11 1 1 1 1 4 1 1 3 1 2 36

Q3 2019 6 14 5 1 1 1 1 1 30

Q4 2019 3 14 4 1 1 3 1 2 2 1 1 1 34

TOTAL

2019 35 54 8 7 2 1 19 4 8 3 10 1 2 1 1 1 1 1 4 163

Swine dysentery diagnostic trend reduces in last quarter of 2019

The trend in swine dysentery diagnoses in GB has been upward from 2017 to 2019

(Figure 13), however, the quarterly data shows a significant reduction in the last quarter of

2019 (Figure 14) with just one diagnosis recorded through the GB surveillance network in

North Yorkshire in October 2019. This is encouraging, though too early to know if this

represents better control in the longer term.

Figure 13: Annual GB swine dysentery diagnoses as a percentage of diagnosable

submissions

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Figure 14: Seasonality of GB swine dysentery diagnoses to Q4-2019

Molecular analysis of B. hyodysenteriae isolates from 2017 to 2019 shows that they group

into nine sequence types (STs), the majority (91.8%) being ST52, 88, 229, 242 or 251.

ST52 was detected in six GB regions and was most commonly detected in smaller pig

herds. The other four main STs were detected in two or three regions. Antimicrobial

sensitivity testing (minimum inhibitory concentrations) continues to be undertaken on B.

hyodysenteriae isolates at APHA at no charge under the “Monitoring of Antimicrobial

Resistance in Bacteria from Animals and their Environment Project”. Although some had

raised Minimum Inhibitory Concentration (MIC) values to tiamulin, none were clinically

resistant (MIC >4µg/ml) in 2019. A comprehensive overview of the use of whole genome

sequencing to investigate swine dysentery outbreaks was given by Rod Card, APHA, at

the autumn 2019 Pig Veterinary Society meeting.

Pig industry initiatives to assist swine dysentery control remain active and include raising

awareness and providing advice through AHDB Pork (http://pork.ahdb.org.uk/health-

welfare/health/swine-dysentery/; http://pork.ahdb.org.uk/media/272132/swine-dysentery-

for-producers.pdf); the Significant Diseases Charter

https://pork.ahdb.org.uk/health-welfare/health/significant-diseases-charter/ and the

#MuckFreeTruck campaign https://twitter.com/hashtag/muckfreetruck?src=hash.

Swine dysentery was highlighted at the small-scale pig producer meetings organised by

AHDB Pork during October 2019 (Williamson and others, 2020) and guidance for small-

scale pig herds is being discussed by the BPA, Pig Veterinary Society and AHDB Pork.

There will be an opportunity to gain and exchange knowledge on spirochaetal infections,

including swine dysentery, at the “Ninth conference on Spirochaetal infections in animals

and humans” to be held at the Pentlands Science Park, Edinburgh on 1-2 October 2020.

Porcine circovirus 2 genotyping shows shift to PCV2d

Porcine circovirus disease (PCVD) diagnoses in GB pigs have reduced to a low level since

porcine circovirus 2 (PCV2) vaccines became available (Figure 15). PCVD is occasionally

diagnosed, usually in either unvaccinated herds or in groups of pigs where a problem was

identified with the vaccination regime.

A genotyping study to characterise PCV2 associated with confirmed PCVD cases in

England and Wales from 2011 to January 2016 was published (Grierson and others, 2017)

and described the first detection and emergence of PCV2d with the majority identified as

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PCV2b. Surveillance of PCV2 genotype associated with confirmed PCVD cases in

England and Wales has continued. PCV2 ORF2 was successfully sequenced from 20

PCVD cases from 2016 to 2019 and phylogenetic analysis shows that the virus in four

cases clusters within genotype PCV2b. The remaining cases have sequences which

cluster with reference PCV2d strains, specifically within group PCV2d-2 (Xiao and others,

2015). The sequences will be added to Genbank.

These results indicate that for cases diagnosed at APHA, the genotypic shift from PCV2b

to PCV2d in England and Wales has progressed as reported elsewhere in the global pig

population, with PCV2d-2 becoming predominant. The significance of this shift is

uncertain; PCV2a-based vaccines have been shown to be effective against PCV2d

challenge under experimental conditions (Opriessnig and others, 2014). The clinical and

pathological details, and PCV2 genotype of PCVD cases diagnosed at APHA will continue

to be monitored.

Antimicrobial resistance surveillance

The Veterinary Medicines Directorate UK Veterinary Antibiotic Resistance and Sales

Surveillance Report (UK-VARSS) for 2018 was published 2018 (VMD, 2019). This

includes information on antimicrobial sensitivity test results for bacterial pathogens of

relevance to pig health, isolated from carcases or other diagnostic samples submitted by

private veterinary practices to APHA from pigs in England and Wales.

A report summarising data on Livestock-associated Methicillin-resistant Staphylococcus

aureus (LA-MRSA) from animals and animal products in the UK was published (Anjum and

others, 2019). LA-MRSA is not a significant disease issue in pigs, however, two of the pig

isolates were from scanning surveillance (diagnostic) submissions to APHA and were

involved in skin disease in young pigs (Hall, 2015; APHA, 2017). Guidance for those

working with livestock to reduce the risk of LA-MRSA infection is available.

Figure 15: Annual GB PCV2 disease diagnoses as a percentage of diagnosable

submissions

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Horizon scanning

Classical swine fever in Japan

In September 2018, Japan reported Classical swine fever (CSF) in domestic swine for the

first time since 1992, in Gifu prefecture, and a wild boar case was detected a week later.

Since then, CSF cases in Japan have been regularly reported to OIE, with the majority of

cases being in wild boar in Gifu and Aichi prefectures, and some cases in neighbouring

prefectures. CSF has continued to circulate in these areas, and has spread to seven new

prefectures. In early January 2020, CSF was reported in domestic swine on the island of

Okinawa; this is the first detection of CSF there since 1986 (Figure 16). Okinawa is a

separate island of Japan approximately 1500km south of the main area that was affected

by CSF. Since October 2019, vaccination of domestic pigs has been permitted in certain

prefectures on the main island. Vaccination of wild boar with an oral (bait) vaccine is

ongoing.

Japan is not approved for export of fresh or frozen pig meat to the EU. The overall risk of

CSF introduction to the UK remains very low (no change) and the situation continues to be

monitored. Further details are available at:

https://www.gov.uk/government/publications/classical-swine-fever-in-pigs-in-japan.

Figure 16: CSF cases reported in Japan since August 2019 (map prepared on 05-02-19)

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Novel circovirus species (PCV4) identified in pigs in China

Three circovirus species have been previously identified in pigs within the genus

Circovirus: non-pathogenic Porcine circovirus 1 (PCV1), pathogenic Porcine circovirus 2

(PCV2), and recently identified Porcine circovirus 3 (PCV3). No zoonotic concern is

reported relating to porcine circoviruses 1-3. However in April 2019, a new circovirus

(tentatively designated as PCV4) was identified in several pigs with severe clinical disease

in Hunan Province, China (Zhang and others, 2019). PCV4 was detected on two farms in

pigs aged seven and 12-weeks-old which were showing respiratory and enteric signs, and

(in a few pigs) porcine dermatitis and nephropathy syndrome-like skin lesions. PCV4 was

detected together with PRRSV and PCV2 and disease in the pigs could not be attributed

specifically to PCV4. PCV4 shows highest genomic identity to mink circovirus (66.9%) and

has lower genetic homology of 43.2%-51.5% to the other pig PCV genomes. A real-time

PCR was developed to investigate the prevalence of PCV4 in random clinical samples

from Hunan province, China. The PCV4 prevalence was highest in nasal swabs at 28.5%

(6/21) followed by serum samples at 13.4% (11/82). It has not yet been possible to isolate

the virus. The clinical significance of PCV4 is uncertain at this stage and this finding, and

any future reports will be kept under review for more information on this virus, or

associated disease.

Senecavirus A – potential live attenuated vaccine development

Senecavirus A (SVA) is an emerging virus in the family Picornaviridae, which can cause

vesicular disease (VD) clinically indistinguishable from foot-and-mouth disease (FMD) in

pigs. Outbreaks of VD associated with SVA infection have been reported in the Americas

and several Asian counties. No vaccines are currently available for SVA, however Sharma

and others (2020) published results for a live attenuated vaccine candidate which

protected pigs against heterologous SVA challenge in an experimental setting. When SVA

emerged in Brazil in 2014-15 (Leme and others, 2015), it rapidly became widespread

across the country. The main impact in both Brazil and the US related to the close

resemblance of SVA-associated VD to notifiable vesicular diseases (particularly FMD).

Incidents are reported to the Animal Health authorities and the investigations usually

require testing to rule out notifiable vesicular diseases. This is both costly and disruptive to

the AH authorities and the pig industry. There was also concern that SVA outbreaks could

lead to complacency with respect to reporting vesicular disease as suspect notifiable

disease. The possibility of a future vaccine is a promising development for countries where

VD due to SVA becomes established. No SVA-associated VD has been detected in UK

pigs to date and the message to UK pig keepers is that all disease incidents with vesicular

lesions must be reported promptly as suspect notifiable disease for investigation

https://www.gov.uk/guidance/foot-and-mouth-disease.

Porcine Astrovirus type 3 detected in US polioencephalomyelitis cases

Porcine astrovirus 3 (PoAstV3) has been described in pigs with nervous disease and

lesions of polioencephalomyelitis in the United States (Arruda and others, 2017). A recent

publication by the same group describes a retrospective study for PoAstV3 on cases of

undiagnosed nervous disease with lesions consistent with a viral encephalomyelitis.

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PoAstV3 was detected by RT-qPCR and in-situ hybridisation in the central nervous system

(CNS) in 13 of 50 (26%) such cases. PoAstV3 was detected from 2010, the earliest year

from which material was tested. PoAstV3 was detected in samples from adult females

most frequently, and also in finisher and nursery pigs. Clinical signs reported included

lateral recumbency, paresis, and ataxia. This paper supports PoAstV3 as a potential cause

of viral polioencephalomyelitis in pigs although significant gaps remain in knowledge about

this virus.

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