Swine Veterinary Report – Q1 2024

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

Novel Influenza A- H3N2 Cluster 2010.1 Update

Practitioners perceived a shift in Influenza A virus (IAV) prevalence this quarter in comparison to Q4 of 2023. 80% of respondents to the clinical impression survey reported IAV as stable, and 13% indicated a decrease in frequency of cases. This contrasts the impression reported last quarter, where 62% of responding practitioners reported an increased frequency of influenza cases. This perception is validated both by OMAFRA’s immediately notifiable disease summary, Animal Health Lab (AHL) and Gallant Laboratories (CEVA) diagnostic reports (see both below). It is speculated that the implementation of an updated regional influenza autogenous vaccine at the start of the quarter, which now includes the extremely dominant H3N2 2010.1 strain, may have reduced the overall prevalence of IAV cases during Q1 of 2024.

Figure 1. Submissions positive for influenza (not including ELISA tests) in swine by subtype and submission month, Ontario, January 2022 to March 2024. The number of IAV positive submissions seems to have stabilized in 2024 Q1. Most positive submissions in Q1 2024 (January-February) involve subtype H3N2. Figure 1 also shows counts of partial, mixed and inconclusive subtypes isolated from Ontario swine herds. (see legend above graph). Acknowledgement: Graph courtesy of Dr. Hannah Golightly- OMAFRA

Influenza A (IAV)

Dr. Hannah Golightly from OMAFRA summarized that in comparison to Q1 of 2023 and 2022, Q1 of this year has shown a decrease in the number of submissions positive for IAV. The number of influenza positive submissions this quarter is also lower in comparison to last quarter (Q4 2023). Despite a lower number of positive submissions compared to previous years, the proportion of influenza subtypes has remained consistent across Q1’s of 2022 to present, with H3N2 and H1N2 being the dominant IAV subtypes, followed closely by H1N1. When sequenced, the most prevalent strain of Influenza was the 2010.1 cluster of the H3N2 subtype, a trend consistent with the previous quarter. Most positive submissions this quarter originated from nursery pigs.

Salmonella Surveillance

Dr. Golightly provided a summary on the Salmonella positive serotypes isolated in each moth from Jan 2023-March 2024 in figure 2 (below). The number of Salmonella positive submissions this quarter was higher compared to last quarter, as well as in comparison to Q1 2023. The majority of positive submissions this quarter were isolated from enrichment, 62% of positive submissions reported GI-related clinical signs on the submission history. When comparing submissions isolated from enrichment and those not isolated from enrichment, most submissions from both groups report clinical signs. When looking at serotypes, February 2024 had an abnormally low incidence of S.Typimurium and the monophasic Typhimurium variant. By production type, the majority of Salmonella positive submissions this quarter came from nurseries, followed by grow-finish sites. All stages of production had a mix of serotypes.

Porcine Circovirus Type II (PCV2) and Type III (PCV3)

This quarter’s practitioner survey featured a separation of clinical impression of PCV2 and PCV3 cases (compared to a previously combined “porcine circovirus disease” impression). These results indicated that 47% of practitioners perceived an increase in PCV2 clinical impact compared to Q4 of 2023, and 53% of practitioners consider PCV2 common in practice. In comparison, 86% of practitioners consider PCV3 rare or never seen in practice, and 100% of respondents deemed it “stable” in comparison to last quarter.

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

Jessica Fox from Swine Health Ontario (SHO) commented on the dramatic increase in PED and PDCoV cases throughout the province this quarter. During Q1 of 2024, 19 new PDCoV cases were reported, as well as 7 new PED cases. The majority of these cases were found to be a result of contamination due to transport and/or people movements. 80% of practitioners participating in the Q1 2024 clinical impressions survey reported that PDCoV cases had increased compared to the previous quarter, and 53% reported an increase in PED cases this quarter.

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. 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

OAHN Veterinary Clinical Impression Survey Veterinary Comments

It was noted that two more practitioners responded to the clinical impressions survey in comparison to last quarter setting a new record! The network appreciates the high response rate, and practitioners’ willingness to take the time to lend their expertise. There were also a large number of comments this quarter regarding field experiences which are especially valued by the network.

Three separate practitioners noted a perceived increase in clinical erysipelas, including cases in both finishing pigs and a gilt grow-out. This was also captured within the survey, where 40% of respondents noted an increase in erysipelas this quarter. Another comment noted multiple cases of A.suis this year, typically in association with IAV or PRRS coinfection. An increase in APP was also acknowledged– one practitioner had an outbreak of APP serotype 7 this quarter, and a separate practitioner reported 3 distinct APP-positive cases in Q1 of 2024. This increase in cases is supported by the survey results, where 20% of respondents perceived an overall increase in APP this quarter. Finally, a comment was made regarding a perceived increase in overall deworming amongst herds, which this practitioner is     attributing to Conestoga now reporting all liver scores.

Laboratory Diagnostic Reports

Animal Health Laboratory (AHL)

Dr. Josepha DeLay from the AHL summarized pathology cases received during Q1 2024. A total of 1285 swine cases were submitted to the AHL during this quarter. Of these, 111 cases had a pathology component (gross post-mortem and/or histopathology) and originated from commercial herds. Three (3) additional Q1 pathology cases involved pet pigs. The PID inclusion rate remains high (91%). Inclusion rates for age or commodity group (100%) and adequate clinical history (94%) also remain high. This information is very helpful in providing context for interpretation of test results by veterinary pathologists and other diagnosticians.

PRRSV-positive pathology and non-pathology cases increased from 2023 Q4 and were similar to positive case numbers in 2023 Q1. Influenza A-positive cases were decreased 17 cases (approximately 50% of Q4 numbers), consisting of H1N1 (4 cases), H3N2 (8 cases) and H1N2 (5 cases).

Interesting cases diagnosed at the AHL during 2024 Q1 are as follows:

  • Brachyspira hampsonii was detected by PCR (Ct 37.55) in colon from 1 of 3 nursery pigs with colitis. The pigs originated from a conventional herd with a low prevalence of colitis and fallbacks. B.hampsonii was detected in Ontario for the first time in 2022 Q4 –this is the second documented case. Two herdmates had similar lesions of colitis but were negative for B.hampsonii. Three additional pigs from the current herd were subsequently tested and had similar lesions of colitis but were negative for B.hampsonii. The less pathogenic species B.innocens (Ct 25-31) and B.murdochii (Ct 21-29) were detected in colon from these additional pigs. All pigs in both groups were negative for Salmonella spp in colon by culture, and Lawsonia intracellularis was detected in some pigs by PCR, although typical lesions of proliferative enterocolitis were not present. IHC for Brachyspira spp is pending for further evaluation of potential association of these organisms with colonic lesions in this group.
  • Brachyspira pilosicoli (Ct 22) was detected by PCR in feces from 3 nursery pigs with typhlocolitis. Salmonella Typhimurium was also isolated from each pig by enrichment culture. B.pilosicoli is infrequently detected in cases submitted to the AHL (most recent previous cases in 2022 Q4).
  • Brachyspira hyodysenteriae was detected by PCR (Ct 33) in fecal samples from 2 grower pigs (originating from the same herd) with clinical bloody diarrhea. Lawsonia intracellularis was detected by PCR (Ct 36) in 1 of 2 samples. Salmonella spp was not isolated from feces. B.hyodysenteriae is infrequently detected in AHL submissions (last case in 2023 Q1).
  • Glaesserella australis was isolated from 2 cases but without lesion correlation available:(1) lung 1+ (concurrent S.suis in multiple organs) in 1 of 2 sudden death nursery pigs with no histopathology done; (2) CSF swab 3+ in a nursery pig with unknown history and brain not included for histopathology. Previously, G.australis was isolated from 3 cases in 2023.
  • Porcine sapovirus was detected in 16 of 27 cases tested in Q1, with a Ct value of ≤23 in 10/16 cases (5 cases in suckling pigs, 4 cases in nursery pigs, 1 case in unknown age group).
  • PCV2-positive case numbers decreased to 18 (vs 36 in 2023 Q4, 49 in 2023 Q1).
  • One case of congenital swine pox was identified based on gross and histologic lesions.
  • Porcine astrovirus 4 was detected by PCR in lung from a sow but was not well correlated with histologic lesions (significance undetermined).

Gallant Custom Laboratory (CEVA) Diagnostic Reports

Anna Pietruszkiewicz reported on 2 cases submitted to Gallant Labs from Ontario in Q1 2024 in Ontario. Both cases were Influenza, with 1 case of H1N1 and 1 case of H3N2 in Q1 2024.

Ontario Slaughter Statistics

Federal Slaughter Statistic Summary (Q1 Aggregate)

Dr. Christine Pelland reported that due to some technical issues the aggregate federal slaughter statistics were not available for Q1. This data will be available in the future.

Provincial Slaughter Statistic Summary

Dr. Christine Pelland commented that the provincial slaughter data from Q1 2024 was consistent with what was seen in the previous quarter (Q4 2023).

Complete Carcass Condemnations

  • The most common causes of complete carcass condemnations continue to be peritonitis and abscesses, representing 31% and 17% of all complete carcass condemnations in Q1 2024, respectively. Prevalence of these categories remained stable throughout the quarter.

Partial Portion Carcass Condemnations

  • Parasitic livers remain the predominant cause of partial condemnations at provincial slaughter plants, representing about 61% of total partial condemnations in Q1 2024.

International Disease Topics Of Interest Summary

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

Porcine Reproductive and Respiratory Virus (PRRS)

PRRSV 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).

L1C.5 (L1C variant)1-4-4: The most frequent wild type PRRSV detected in the U.S. in 2023 were: L1C.5 (L1C variant)1-4-4, L1A 1-7-4 and L1H 1-8-4.  In 2023, L1C.5 (L1C variant)1-4-4 was detected in 13 states located in the Midwest and some neighbouring states. Since the emergence of L1C.5 (L1C variant)1-4-4 in 2020, this strain has been found in 17 states. (SDRS #71, 01/02/24).

Comparison of PRRSV L1C.5 with other PRRSV Lineage 1 isolates: Researchers at Iowa State did in vivo and in vitro comparisons of PRRSV 1-4-4 L1C.5 variant with three other PRRSV 1-4-4 variants, L1C.1, L1A and L1H and a 1-7-4 L1A variant. Three-week-old pigs were used in the experiment. Pigs were either inoculated with one of the 4 strains of PRRSV or were contact pigs that were mixed with the inoculated pigs 48 hrs after inoculation. There were also some control pigs. Pigs that were inoculated with the PRRSV L1C.5 variant had more severe clinical signs, (anorexia and lethargy), higher mortality, more pigs with higher fevers, (> 40C), and higher viremia levels 2 DPI. A higher percentage of pigs that were in contact with the pigs that were inoculated with the PRRSV L1C.5 were viremic at 2 days after contact. This shows that the PRRSV L1C.5 has higher transmissibility. Researchers also found that some PRRS strains caused brain infections in inoculated and contact pigs. At this time researchers do not know why the PRRSV L1C.5 has higher transmissibility.  (Swineweb.com April 29th,2024).

Environmental Testing of PRRSV and PEDV around dead-boxes: Researchers at U. of Minnesota collected environmental samples around the dead boxes of three PRRS positive farms and one PED positive farm. One of the farms had been depopulated one week before sample collection. The farm that had depopulated had applied whitewash around the dead box. Samples were collected from outside the barn, on the equipment used to move the deadstock to the rendering box, the road near the box, the skin surface of animals in the box, around the box and the box itself. PCRs for PRRSV, PEDV, PDCoV and TGE were done on all the samples. All samples from the farm that had depopulated were negative for all viruses. For the other two farms, 10 samples from each farm were collected. Of the 20 samples, 12 were positive for PRRSV and 5 were positive for PEDV, all other viruses were negative. PRRSV positive samples were found on the skin of the dead animals, in and around the box, the bucket loader, outside of one barn and on the road near the box, (5m). Six positive PRRS samples, three from each farm were submitted for virus isolation. One isolate from the ground near one barn was found. There five positive PEDV samples, all from the PED positive site. The researchers acknowledged that isolating viable PRRSV from environmental samples can be challenging. One comment the researchers made was that finding PRRSV on the roadways could be a potential pathway for PRRSV transmission between farms. (Swine Disease Eradication Center 2024 Vol 13 Issue 4).

Alternative Sampling for PRRS in Endemic PRRSV Infected Breeding Herds: Researchers looked at different methods of detecting PRRSV in weaning pigs in endemically affected breeding herds. Three methods were evaluated: serum, family-oral-fluids (FOF) and udder wipes (UW). In the study four batches with 30 litters per batch were tested. Blood samples were collected from included litters. Samples were pooled 3:1 and 5:1. The researchers found there was good correlation between sera and FOFs, but UWs were poor at detecting PRRSV. When FOFs were pooled 3:1 there were 7 out of 9 positive samples that were misclassified as negative. When pooled 5:1 there were 8 out of 9 positive samples that were misclassified as negative. The study concluded that FOF are a good alternative to blood but need to be analyzed individually (no pooling). UW are not suitable for sampling for PRRSV. (UMN Swine News 12/08/23).

Air filtration: A study was done to evaluate the effect of different levels of biosecurity in reducing the incidence of PRRSV in a large commercial production company in the US Midwest. The study took place from 2009 to 2020. The average annual incidence of PRRS in the breeding herds was 33% with a range of 20% to 50%. A second part of the study took place over 1 year from July 2021 to June 2023. Breeding herds were classified as Next Generation Biosecurity (NGB Complete) when all biosecurity protocols and including air filtration were in place. NGB Incomplete breeding herds had implemented all next generation biosecurity protocols with the exception of air filtration.  There were 56 breeding herds that were NGB Complete and 20 breeding herds that were NGB Incomplete. The PRRS incidence risk in NGB Complete was 8.9% versus 40% in NGB Incomplete. (ASSV News 01/17/24).

ASF Albania:Albania is the 28th European country to confirm the presence of ASF, genotype 2.

ASF Taiwan: Testing of meat from China found at border inspections in Taiwan have found that 10% of the products were positive for ASF.

Overall, with stricter border inspections, Taiwan has seen a decrease in high-risk products from entering the country. The rate has fallen from 3.61 cases per 10,000 passengers to 2.85 cases per 10,000 passengers over the last 4 years. (Swine Disease Global Surveillance Report, February 06,2024).

ASF Italy: In Italy, sampling of 300 products, (many with Chinese labels), from various ethnic shops found 81,27%, contained ASF DNA. Italy has increased inspections of farms and processing plants to try to slow the spread of ASF. Numerous biosecurity violations and unregistered livestock were found. (CEZD Weekly intelligence Report, March 18th,2024).

Influenza A Virus (IAV)

HPAI H5N1 Italy: In the fall of 2021, there were outbreaks of HPAI in both wild and domestic birds in Italy. At one farm in Ostia, in the province of Rome, HPAI was detected in a flock of free ranging poultry. There were free ranging pigs on the same site. These pigs had contact with the poultry. There were no clinical signs of influenza in the pigs. Nasal swabs and blood samples were collected from the pigs. On PCR all the nasal swabs were negative for the IAV matrix. On serology, the majority of the pigs were positive on hemagglutination inhibition testing using an H5N1 strain homologous to the virus detected on the farm. The authors of the study concluded that the results show “the replicative fitness that HPAI H5N1 viruses of the clade have in mammalian species.” (Rosone F, et al, Microorganisms 2023 April).

HPAI H5N1 detected in dairy cattle in the U.S.A: On March 25, 2024, the USDA confirmed a detection of HPAI in samples collected from dairy cattle.  Since this several states have now found similar detections. There have been no detections in cattle or other livestock species in Ontario or Canada as of June 3, 2024. The initial infection was thought to be through wild bird exposure to affected dairy cattle. Pasteurization is effective to kill the virus in milk and milk products and properly cooked beef remains safe to consume. Due to the fact that pigs are known hosts for different influenza viruses and are known to act as a host for influenza virus reassortments, all efforts need to be made to prevent HPAI infection in pigs.  CSHIN, CAHSS, CPC and CASV hosted a webinar on May 30, 2024 from 12-1pm eastern time entitled “The potential for H5N1 influenza in swine: Lessons learned from the dairy industry so far” that targeted veterinarians especially veterinarians that work with swine. The webinar was recorded and can be view via this link. (Summary provided by Dr. Christa Arsenault, Lead Veterinarian OMAFRA, to the OAHN Swine Network, 2024-06-03)

UMN Studies on Influenza: Over the last 10 years the University of Minnesota has done several studies trying to understand influenza. This is a brief summary of some of those studies: 1) 2023, farm workers vaccinating and weaning 3-week-old pigs can contribute to the spread of IAV on swine farms. 2) Study by Dr. Pardo from 2011-2017 found that pigs raised by vaccinated sows were less likely to have the disease. Gilts entering the herd and who were IAV positive were more likely to have pigs positive at weaning. 3) A study of 34 breed-to-wean farms over 5 years found that the prevalence of influenza ranged from 7% to 57%, with a median of 28%. There was a cyclical pattern with peak infection rates in December and May correlated with low temperatures and low humidity.

Mycoplasma hyopneumoniae PCR: The University of Minnesota has developed a PCR test that targets the Mycoplasma hyopneumoniae gene mhp165. Other PCR tests target the DNA of Mycoplasma hyopneumoniae. The DNA is highly stable in the sample. This PCR test targets bacterial messenger RNA. The mRNA rapidly degrades after cell death.  In cells kept under standard incubation conditions RNA detection was consistent out to 20 days. If tissue was put in formaldehyde the mRNA was no longer detected after 25 mins. The new PCR test detects viable or very recently inactivated Mycoplasma hyopneumoniae. One application of this new PCR test would be in Mycoplasma hyopneumoniae eradication programs. (Swineweb.com April 29th 2024).

Wild pigs kill more people than sharks: A new study has found that wild pigs kill more people annually than sharks. The number of annual global fatalities from wild pigs is increasing. From 2014 to 2023 the average annual number of fatal shark attacks was 5.8 while for wild pigs it was 19.7. So far in 2024 there have been 7 fatal wild pig attacks. From 2000 to 2019 there have been a total of 1,532 attacks and 172 deaths from wild pigs in 29 countries.

The attacks are gruesome. Of the 172 deaths, 88% were non-hunting activities, 86% occurred in daylight, 32% were agricultural workers and almost all, (80%) were by solitary pigs. Of the fatalities, 77% died from blood loss and 55% died at the scene. The average pig in each incident weighed 110 kgs. Boars are responsible for more of the fatal attacks because boars can punch holes or slash and gouge with their tusks while sows tend to bite.

Of the fatalities, 51% were in India followed by 8% in China. The U.S. has recorded six fatalities from wild pig attacks in the last 100 years.There were probably more attacks but some were never documented. The expectation though is the attack rate will trend up as the wild pig population continues to increase. (Pork, Chris Bennet, April 18th 2024).

Actinobacillus pleuropneumoniae (APP): Swine veterinarians in Quebec have reported a regional outbreak of APP in multiple finishing herds, specifically serotype 8. These herds are reporting that cases present with sudden mortalities, with 10-15% mortality observed in affected barns at the onset of the outbreak. Due to the rapid regional spread of these cases, vets are suspicious that this serotype is spreading via aerosol.

How can you Participate in OAHN?

Look for the 2024 Q2 veterinary clinical impression survey that will come out the first week of July 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.

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