Ontario Animal Health Network (OAHN) Swine Network Quarterly Veterinary Report

Novel Influenza A- H3N2 Cluster 2010.1 Update

Practitioners perceived a continuation of a lower Influenza A virus (IAV) prevalence this quarter in comparison to Q4 of 2023. There were fewer positive submissions in Q2 2024 compared to Q2 of 2023 (50). H3N2 made up a smaller proportion of positive submissions (35%) in Q2 of 2024 compared to Q2 of 2023 (62%) and 2022 (42%). This quarter also had a higher proportion of partially subtyped cases (25%) compared to previous Q2’s (6% in 2023 and 8% in 2022). Most Influenza detections this quarter were in submissions from nursery pigs, followed by grow-finish submissions. When sequenced, most submissions this quarter were in the H3N2 2010.1 cluster. It is speculated that the implementation of an updated regional influenza autogenous vaccine in January 2024, which now includes the extremely dominant H3N2 2010.1 strain, may have reduced the overall prevalence of IAV cases during Q2 of 2024.

Highly Pathogenic Avian Influenza (H5N1) in Dairy Cattle in the U.S.A.

Over 190 total cases of Highly Pathogenic Avian Influenza (HPAI) H5N1 have been reported in 13 states. Oklahoma was one of the states that was suspected to have this pathogen due to its close geographic location to Texas, New Mexico, Colorado, and Kansas. It is hard to know precisely how many other states have suspect samples that have not been tested or confirmed by the USDA to date, and it is safe to assume that the total number of cases are being underreported nationally. There was a large HPAI outbreak in an egg facility in Colorado, which resulted in the depopulation of about 1.8 million birds. The 5 individuals helping with the depopulation became ill with symptoms of HPAI previously demonstrated in humans, highlighting the zoonotic risk of this pathogen and concern for higher risk groups such as farm workers in close contact with infected poultry or dairy cattle.

The Canadian Situation: The CFIA conducted a third round of testing retail milk samples, and once again all samples in Canada came back negative. To date, there is no positive identification of HPAI H5N1 in Canadian dairy cattle. Animal Health Canada would like to remind all stakeholders that any herd or animal that currently fits CFIA’s case definition is eligible for testing and should be tested if clinical signs are present. These clinical signs include a decrease in milk production, decrease in ruminations, and decrease in feed consumption. For more information, please visit the CFIA’s guidance document for field veterinarians on their website. (Murray Gillis, Animal Health Canada)

Porcine Epidemic Diarrhea (PEDV)/ Porcine Deltacoronavirus (PDCoV)

Jessica Fox from Swine Health Ontario (SHO) provided an update on the Porcine Epidemic Diarrhea (PED) and Porcine Deltacoronavirus (PDCoV) cases in Ontario this quarter. During Q2 of 2024, there were 7 new cases of PDCoV – two sow barns, two nurseries, and three finishers. In addition, there were 13 new cases of PED reported – three sow barns, one gilt barn, five nurseries, and four finishers. Of these 20 new cases, 10 were from movement-related cases originating from known-positive sites. Jessica would like to remind practitioners that to declare sites negative on SHARC and on the SHO Map link below, vets must let her know once a site’s status has changed. In an effort to help reduce the prevalence of these cases, a working group consisting of Ontario swine vets has been created to help identify and address industry risk points.

SHO encourages members of the industry to be vigilant in the face of this outbreak and continues to support elimination as the best strategy for disease control. Practitioners are encouraged to continue to be diligent in testing for these coronaviruses in all gastrointestinal cases, as PDCoV in particular can present with extremely mild clinical signs. Timely diagnosis of these cases can help limit widespread contamination and potential spread to other sites. Practitioners are also encouraged to promote the use of SHARC by producers to stay aware of current positive sites in their proximity. Please refer any producers interested in enrollment to Jessica Fox Jessica.fox@swinehealthontario.ca. The PED and PDCoV Tracking map is available on the Swine Health Ontario website and shows current and annual cases by county. http://www.swinehealthontario.ca/Disease-Information/PED-PDCoV-Tracking-Map

Senecavirus A (SVA)- EQSP Quebec Update

Unfortunately, Senecavirus A virus (SVA) was detected again on the nursery site in St-Hyacinthe Quebec which had been declared positive on January 23, 2024, with a renewed negative status on April 12. This situation suggests that the disease was still present in the Ste-Sabine maternity ward although no clinical signs were observed there and that all the PCR tests carried out on this site also gave negative results. Serology tests were carried out on a number of animals from this site with results confirming that the disease was present.

Although no clinical signs or presence of disease have been detected in other animals from this site for several weeks, the production network concerned has quarantined several production sites following an analysis of movements since the beginning of June. In addition to the St-Hyacinthe nursery, two other nursery sites in St-Liboire and St-Pie have been quarantined. This last site was one of the two nurseries infected last winter.

Recent movements of these nurseries have led to the quarantine of 5 finishing sites. Upcoming trips in the coming weeks will involve two other finishing sites. (EQSP Statement, June 28, 2024; translated from French).

OAHN Swine Project Update- Porcine Haemagglutinating Encephalomyelitis Virus (PHEV)

Dr. Tim Blackwell from OMAFA provided a brief update on the OAHN swine project exploring PHEV incidence in Ontario. Testing has been underway for roughly three months. 29 pigs have been tested. Of these samples, there has been one positive and one inconclusive, but otherwise all other 27 samples were negative. This surveillance effort is still in its early stages, but results suggest a low prevalence, at least in the summer months. This virus does not appear to be a regular commensal in the respiratory tract of pigs. It is too early to draw any definitive conclusions, but Dr. Blackwell noted that it was found in a few severe tracheitis cases, potentially suggesting a link between the virus and clinical tracheitis. Stay tuned for more updates as data continues to be collected.

OAHN Veterinary Clinical Impression Survey Veterinary Comments

Dr. Andrea Patterson described the results of the vet clinical impression survey for Q2 2024, where there were 12 respondents. This quarter, respondents (25%) continue to perceive an increased incidence of PCV2 in the field, although this has decreased in comparison to last quarter (46%). Results from the survey confirm that PRRS is still the dominant respiratory challenge faced by practitioners in the field, but also revealed a decrease in new PRRS outbreaks in this quarter in comparison to Q2 of 2023. This difference is likely attributed to a new strain being reported in Q2 of last year, whereas that has not been the case in Q2 of 2024. Over 50% of respondents reported an increase in PED/PDCoV cases in this quarter, which would be consistent with cases reported to SHO. Practitioners also report ongoing challenges with Rotavirus and Sapovirus in herds this quarter.

Laboratory Diagnostic Reports

Animal Health Laboratory (AHL)

Dr. Josepha DeLay from Animal Health Lab provided an update on pathology cases received by the lab during Q2 2024. A total of 1297 swine cases were submitted to the AHL during this quarter. Of these, 77 cases had a pathology component (gross post-mortem and / or histopathology) and originated from commercial herds.   Five (5) additional Q2 pathology cases involved pet pigs, and two (2) provincial meat inspection cases were received.

For pathology cases, the PID inclusion rate was 83% and slightly lower than for Q1 submissions. Inclusion rates for age or commodity group (99%) and adequate clinical history (96%) remained high.  This information is very helpful in providing context for interpretation of test results by veterinary pathologists and other diagnosticians.

PEDV-positive cases increased significantly to 18 cases in 2024 Q2 (vs 7 cases in 2024 Q1), and PDCoV cases decreased to 7 cases in Q2 (vs 18 cases in Q1). PRRSV-positive case numbers have remained stable, with a total of 196 PRRSV-positive pathology and non-pathology cases in Q2 (151 diagnostic cases, 44 monitoring cases, 1 research case), similar to positive case numbers in 2024 Q1 (151 diagnostic cases, 41 monitoring cases), but higher than the 166 positive cases identified in 2023 Q2. Influenza A-positive cases in Q2 (21) were similar to those in Q1 (17) and remained decreased to approximately 50% of those in 2023 Q1 and Q2.

Interesting cases diagnosed at the AHL during 2024 Q2 are as follows:

• The frequency of testing for Brachyspira spp increased in Q2 (26 cases tested, vs 10 cases in Q1). An increased number of Brachyspira spp PCR-positive cases were identified in Q2 (12 cases, vs 4 cases in Q1), although specific detection of pathogenic species remained low. From these 12 cases, B.pilosicoli was detected in 1 case and B.murdochii (intermediate pathogenicity) was detected in 1 case. Lawsonia intracellularis-positive cases remained stable in 2024 Q2 (17 cases) compared with 2024 Q1 (15 cases), but are increased from 2023 Q2 (5 cases)
• An increase in F18-positive E.coli cases likely reflects the increased frequency of E.coli genotyping since December 2023 due to unavailability of serotyping reagents. Of the 9 F18-positive cases in Q2, 4 cases were also Stx2E-gene positive, although no cases had clinical signs described that were consistent with edema disease.
• PCV2-positive case numbers remained stable at 15 cases (vs 18 cases in Q1) but were decreased from 53 positive cases in 2023 Q2. AHL would like to remind practitioners that although these results reflect PCR-positive cases, a true PCV2 clinical diagnosis must include a PCV2 IHC positive result, as well as clinical signs of disease.
• PCV3-positive cases decreased to 16 in Q2, from 31 cases in Q1. Most of the positive cases in Q2 had low viral loads (Ct >25), with a high viral load detected in 2 cases (poor-doing neonates – Ct 18, abortion with current PPV infection – Ct 24-30).
• Porcine sapovirus was detected in 12 cases in Q2, similar to the positive case number in Q1 (16).
• Porcine astrovirus 4 was detected by PCR in lung from PRRSV-positive nursery pigs with bronchointerstitial pneumonia and mild tracheitis, but with a low viral load (Ct 30 – significance undetermined).

Gallant Custom Laboratory (CEVA) Diagnostic Reports

Anna Pietruszkiewicz and Kevin Millsap reported on 1 case submitted to Gallant Labs from Ontario in Q2 2024 in Ontario. This was an influenza case that was isolated and identified as H3N2.

Ontario Slaughter Statistics

Federal Slaughter Statistic Summary (Q1 Aggregate)

Dr. Christine Pelland reported that federal condemnation data was received for this quarter. As it was not received for the previous two quarters, this data will be compared to that of same quarter last year (Q2 2023).

Comparing by condemn/100,000 slaughtered

• Abscesses and peritonitis continue to be highest reasons for condemns, although peritonitis has stabilized since spike in Q4 2022.

When comparing Q2 2024 to previous year:

• Increase in condemns due to abscess, icterus/jaundice, and septicemia.
• Decrease in condemns due to erysipelas, moribund, nephritis, peritonitis (slight decrease).
• Stable for enteritis, neoplasm (lymphosarcoma), melanoma, pneumonia.

Comparing Q2 2024 to Q2 2023 Condemns (as a Percentage of Total Condemns)

• Increases seen in abscess (+4%), icterus/jaundice (+3.2%), septicemia (+2.5%)
  • Dr. Pelland noted that although there has been a recent significant increase in abscess incidence, when considering historical data back to 2018, this increase is consistent with what has been seen previously.
  • The incidence of icterus/jaundice this quarter is extremely notable, as it is the highest it has ever been. Since there were no data from the past two quarters, it is difficult to assess if this has trended upward gradually or if it is a sudden increase. There is no hypothesis as to why this increase has occurred.

• Decreases seen in arthritis (-2.1%), moribund (-2.1%), peritonitis (-1.9%), nephritis (-1.6%), pneumonia (-1%).

Trims

• Total number of hogs trimmed was consistent Q2 2024 vs 2023 (31,869 vs 30,794).
• Highest proportion of trims were due to “other” reasons (65.2%), and abscesses contributed 30.5% in 2024. In 2023, 63.7% of trims were due to abscess and only 27.9% “other” reasons. It is suspected that this may be due to the subjective nature of trim assessment.

Provincial Slaughter Statistic Summary

Dr. Christine Pelland commented that the provincial slaughter data from Q2 2024 had some variations compared to the previous quarter (Q1 2024). This quarter, there was an increase in abscesses, adhesions, arthritis, and inflammatory conditions. In contrast, there was a decrease in parasitic livers, pneumonia, welfare concerns, in the “other disease/condition” identifier, as well as in total overall condemnations.

Complete Carcass Condemnations

• The largest changes this quarter were increases in peritonitis, pleuritis, and overall total complete carcass condemnations. There was a slight decrease in numbers euthanized and septicemia.

Partial Portion Carcass Condemnations

• This quarter, in comparison to the previous, there was an increase in elbow/hock arthritis, hind quarter (ham) abscesses, head abscesses, rib abscesses, and stifle joint arthritis. In contrast, there was a decrease in parasitic livers, heart contamination, cystic kidneys, pneumonia (lungs), and overall total partial condemns. Dr. Pelland noted that although there were these variations compared to the previous quarter, none of these differences were extremely significant.

International Disease Topics Of Interest Summary

Dr. Al Scorgie reported on some interesting international and domestic disease surveillance reports and new research:

African Swine Fever (ASF)

Germany: German authorities announced that ASF was detected on a small backyard pig farm on July 8th in the state of Hesse. Prior to the detection of ASF on the farm in Hesse, ASF had been found from 4 cases in wild boars starting on July 2nd, in Hesse or the neighbouring state of Rhineland-Palatinate. This is significant because this means ASF has “jumped” the Rhine and is now in western Germany, within 100 kms of the border with France. Since the initial cases were detected, ASF has been detected on 4 more pig farms (2 commercial and 2 backyard), as well as 23 more cases in wild boars.  All the cases are within a 15 km distance of each other. An inner restricted zone of 3 kms as well as an outer restricted zone has been established. This area is densely populated. (Pig Progress)

Germany is deploying drones with thermal imaging cameras to monitor wild boar populations to improve surveillance and containment. This equipment will be useful in areas that are hard to access. (Pig 333, July 19 2024)

France: With increasing cases of ASF in northern Italy and ASF found in western Germany, the department of agriculture in France is stepping up warning visitors to the Paris Olympics not to bring in pork products from infected countries and not to dispose of any food in nature when taking rest stops. (Pig Progress)

Take Home Message:  People are a big factor in the international spread of ASF. In Canada, CanSpotASF is an early detection surveillance program in swine. This surveillance has been ongoing since 2020. Early detection surveillance activities are needed if ASF is detected in Canada, so this virus can be quickly contained, and impacts minimized. In July 2024, CanSpotASF launched testing in invasive wild pigs in Canada.

PED/PDCoV

SHIC-funded epidemiological study of PDCoV: PDCoV was first identified in the U.S. in 2014, one year after PEDV was first detected. A study funded by SHIC looked at data from the Morrison Swine Health Monitoring Project (MSHMP). Approximately 60% of the US breeding herd contributes data to MSHMP. Data was analyzed from January 2015 to December 2023. In that period there were 244 PDCoV breaks from 186 sites from 22 production systems in 16 different states. From year to year the incidence ranged from 0.44% (2017) to 4.28% (2023).  Not surprisingly, the cases peaked in the

winter. Of the 186 sites, 36 herds had 2 PDCoV breaks, 8 had 3 breaks, and 2 sites had more than 3 breaks. For sites that had multiple breaks the average time between breaks was 2.11 years. In terms of regions: 69.9% of the breaks were in the south, 24.7% in the Midwest, 1.6% in the West and 0.5% in the Northeast. In 2015 and 2016 most cases were in the Midwest but after 2017 more cases were in the South.

SHIC is adding PED Sequencing to it’s Disease Monitoring Report: SHIC will add PEDV PCR sequencing to its disease monitoring report. The report will include how many strains were tested and what different types of viruses were found. The strains can be classified based on specific genetic characteristics, particularly in the spike (S) protein. SHIC Associate Director Lisa Becton commented that one example of how this information could be used is looking at the detection of the non-indel strains, which are thought to be more pathogenic, compared to the indel strains which are thought to be less pathogenic. Could the difference in strains explain why some farms take longer to eliminate PED? Another use would be if a farm is using an indel (milder) strain for exposure because the farm is located in high-risk area and the clinical signs are less severe or if there is a dual infection of two strains of PEDV. This will better help understand health and biosecurity. SHIC stated that regardless of the strain, the goal of the breeding herd is to eliminate PED. (Farmscape.ca, Bruce Cochrane, July 24,2024)

PRRS

PRRS L1C.5: PRRSV L1C.5 has been detected for the first time in South Carolina. The PRRSV was found at a finishing site. (SHIC Newsletter April 2024).

MSHMP Monitoring Detects New PRRS Variant: MSHMP found an increase in a new PRRSV variant between December 2023 and January 2024. The new novel variant was classified as 1H.18. There were 61 sequences identified from 9 production systems mostly in Iowa and Minnesota with 1 isolation from Illinois. The sequences had either an RFLP of 1-8-4, 1-12-2 or 1-12-1. There have been sporadic detections of 1H.18 since 2018. An increase in cases in 2020 went undetected because the variants were misclassified. Currently there is not enough evidence to say if this is a variant of concern. The researchers did comment that grouping strains by RFLP may erroneously group genetically dissimilar PRRS viruses while segregating closely related ones. (ASSV News Archive May 29th 2024).

Researchers Identified Gene Expression Possibly Involved in Fetal Resistance to PRRS: Researchers did a trial with gilts that were infected with PRRSV at 86 days of gestation. At 21 days after infection the gilts and fetuses were euthanized. Fetuses were classified by viability and by viral load in serum and thymus. The researchers found gene expression in heart, kidney, and liver. The findings helped explain why some fetuses are compromised and others are not following maternal PRRSV infection. (Vet Microbiol. 2024, Jun 19)

PCV

PCV4 detected in the U.S.A.: PCV4 was first described in 2019 and has been found in several countries in Europe and Southeast Asia. The studies used PCR to detect PCV4. The Iowa State diagnostic lab looked at 512 clinical cases from June to September 2023.

Various tissues were tested by PCR for PCV4 including lung, feces, spleen, serum, lymphoid tissues and fetuses. PCV4 was found in 8.4% of the samples, with lymphoid tissue having the highest detection rate of 18.7%. Further research found PCV4 in the lymphocytes and macrophages in lymph nodes. PCV4 was most commonly found in nursery and finishing pigs. Often there were coinfections with PCV2, PCV3 or other endemic pathogens. The significance of PCV4 is unknown at this time. Further research and monitoring are needed. (Sci Rep 2024 Jul 5, Kroeger et al.)    

PCV2 in wild boars in Italy: There are nine different genotypes of PCV2, with PCV2a, PCV2b and PCV2d being the most widespread and clinically significant. In 2022, PCV2e was identified in multiple rural farms in Northeastern Italy. Researchers wanted to determine what strains of PCV2 were in wild pigs because often rural farms have outdoor raised pigs with risk of exposure to wild pigs. 122 wild boars from Northeastern Italy were tested. Of the 122, 81.1% were positive for PCV2 and of the positive pigs, 96% were PCV2d and 1.5% PCV2a and 2.5% PCV2b. With further phylogenetic and phylodynamic testing, researchers concluded that the viral flow of PCV2 was from domestic pigs to wild boars. (Front Microbiol 2024 Jun 17. Faustini et al.)   

APP Serotype 8 Outbreak in Quebec: Last quarter, an outbreak of APP serotype 8 was reported in Quebec. It is suspected that it originated from the sow herd based on positive serology results. Tonsillar scrapings and other diagnostic samples were negative. Multiple finishing barns within this system broke, as well as finishing barns in a different system (not originally serotype 8 positive), confirming regional spread. The herd is set to depopulate. (CSHIN 2024 Q1 report).

Finding of Sarcocystis in Feral pigs in Australia: A study was done on the presence of Sarcocystis in wild pigs and deer in the southeastern regions of Australia. Samples of diaphragm, heart and esophagus were collected. The sample size of pigs was small. On visual inspection no cysts were seen in any tissues from pigs nor deer. However, PCR testing of some samples was positive for Sarcocystis. Histology confirmed the positive findings. One concern this study identified is that visual meat inspection could miss the presence of Sarcocystis in a carcass. Another concern is the risk that wild pigs could spread Sarcocystis to domestic pigs that are raised outdoors. Studies in the U.S. found that 32% of wild pigs sampled in the southeastern U.S. were positive for Sarcocystis except wild pigs in Florida were negative. Studies in the 1980s on sows raised outside in the U.S.  found an infection rate of 3 to 18%. Sarcocystis is consider to be low risk in indoor raised pig because an intermediate host (dog, cat or human) is involved in the transmission. (Int J Food Microbiol, 2024 June, Sokoofeh et. Al)  

How can you Participate in OAHN?

Look for the 2024 Q3 veterinary clinical impression survey that will come out the first week of October via an email through the OASV listserv.

If you are a practicing vet that sees swine in Ontario, please complete this survey when the email reminders are sent out through the OASV listserv.