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

H5N1 Highly Pathogenic Avian Influenza (HPAI) Detected in a Smallholder swine farm in Oregon U.S.A.

On Nov 6, 2024, the USDA and APHIS provided updates with further information on the detection of HPAI H5N1 in a backyard (smallholder) farm operation in Crook County, Oregon, U.S.A. This case was first announced on October 30, 2024, and was the first known case of H5N1 HPAI Influenza detected in a pig. Later that week, the USDA National Veterinary Services Laboratories (NVSL) communicated that a second pig on this same farm had also tested positive for HPAI H5N1. Sequencing from the positive pig samples were incomplete due to the low virus levels, but sequencing from clinically infected poultry on this same premises indicated infection from the D1.2 genotype of H5N1. This is a different genotype then the one currently spreading in dairy cattle in the U.S.A. known as B3.13.
Genomic sequencing of samples from migratory birds in the area showed very similar sequences, which increases the probability the pigs and poultry on this farm became infected after contact with infected migratory birds, not dairy cattle or other livestock. This farm is a non-commercial operation, and the animals were not intended for the commercial food supply. There is no concern about the safety of the nation’s pork supply because of this finding. (SHIC Webinar, Nov 20, 2024)

Update on H5N1 Highly Pathogenic Avian Influenza In U.S.A Dairy Cattle and in U.S. and Canadian poultry flocks

As of Dec 6, 2024, the USDA reported influenza H5N1 HPAI in a total of 722 outbreaks in 16 states in livestock, with 272 of these outbreaks occurring in the last 30 days. The majority of these cases continue to be reported from the state of California. It is important to note that cases reported are an underestimate. Many U.S. states have not been conducting surveillance, though on Dec 6th, the USDA announced a new Federal Order requiring that raw (unpasteurized) milk samples nationwide be collected and shared with the USDA for testing to facilitate comprehensive H5N1 surveillance of the nation’s milk supply and dairy herds.  The first round of testing under the Federal Order is scheduled to begin the week of Dec 16, 2024.  The majority of the 58 human cases reported by the CDC have also come from California, particularly those who work with infected animals. As of Dec 9, 2024, in Canada, the CFIA is reporting 77 infected poultry premises (some with Low Pathogenic Avian Influenza (LPAI) and the USDA is reporting that 7.21 M birds have been affected in the last 30 days in the U.S.A.  Outbreaks have concentrated in the south-west particularly around California, in the mid-north and the general south. Many of these outbreaks have involved turkey operations. In Canada, BC has reported the majority of the HPAI in poultry detections with 67 flocks, Alberta 4, Saskatchewan 1, Manitoba 1, Quebec 4. (Murray Gilles, AHC)

Influenza A (IAV)- H3N2 clade 2010.1 detected for the first time in Quebec swine

In Q3 of 2024, there appears to be an increasing trend in IAV cases over the course of the quarter. This increase seems to be driven by H3N2 detections. However, despite this trend, the overall number of positive IAV cases this quarter is comparable to Q3 of 2023. The majority of IAV detections this quarter were from grow-finish pigs, followed by nursery pigs. Most isolations this quarter were H3N2 cluster 2010.1, with its prevalence increasing over the course of the quarter. The majority of H1N1 detections this quarter were of the pandemic cluster, with four total detections originating from four different premises, two of which had the same owner.

Unfortunately, on Nov 19, 2024, RAIZO (the swine surveillance network in Quebec) released a statement that the first case of H3N2 clade 2010.1 Influenza was detected in a swine herd in Eastern Quebec.  There have been no identified epidemiological links to Ontario with this detection. Quebec is the only other province to have detected H3N2 clade 2010.1 outside of Ontario to date. Ontario first detected this clade in April 2022.  All other provinces have been on the lookout for this virus since Ontario first detected it.

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

Jessica Fox from SHO provided an update on coronavirus cases in Ontario for Q3 of 2024. This quarter there were 8 new cases of PED– three nursery sites and five finisher sites. Five of these eight cases were determined to originate from pig movement, with three resulting from suspected transport contamination. This quarter there were also two new cases of PDCOV, both at finisher sites. One case is suspected to be a result of transport contamination, whereas the other is unknown.

Of the 66 reported cases since Jan 2024, 40 are considered closed and several more should be cleared soon. So far, no cases have been reported in Q4, though with the start of cold weather, Jessica Fox would like to encourage everyone to stay vigilant with biosecurity to help keep cases under control.

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

Salmonella

Salmonella positive submissions have been steady throughout 2024. The majority of the detections this quarter were isolated from enrichment (IFE). The distribution of reported clinical signs has been consistent over all three quarters this year, with most submissions consistently having gastrointestinal clinical signs reported. In terms of isolated serotypes, the monophasic Typhimurium variant was the most commonly isolated serotype. This was the case for both cultured and IFE submissions. The majority of Salmonella positive submissions continue to be predominantly from samples taken from nursery pigs.

OAHN Veterinary Clinical Impression Survey Veterinary Comments

In Q3, 20-30% of vets responding to the survey reported an increase in Glassers, Strep, and Porcine Circovirus Type-2 (PCV2). This is a 10-15% increase compared to Q3 of last year (2023). Responding swine veterinarians suspect that this increase is likely attributable to PRRS infections, and potentially some vaccine related issues as well. Notably, an increase in PCV2 incidence has trended upwards for the last two quarters. Many responding veterinarians have reported increased PCV2 challenges, specifically in regard to PCV2 type D. Additionally, 23% of responding swine veterinarians reported seeing an increase in the number of new breeding herds breaking with PRRS, which coincides with the above-mentioned challenges with secondary infections typically in conjunction with PRRS-positive herds.

Vets also noted an increase in ascarids (38% reported an increased incidence); this increase is notable, as last quarter all vets indicated that infection rates were stable. Almost half of the vets responding to the survey reported a decrease in PED cases, and about one third of respondents felt there was a decrease in PDCoV infections. 23% perceived an increase in Salmonella cases during this quarter, which is a continuation of the upward trend appreciated in Q2 2024. An increase in greasy pig was also reported this quarter (21% of vets indicated increased incidence), which is consistent with Q3 of last year. This can likely be attributed to seasonal environmental changes, and perhaps also to an increase in PRRS and IAV infections.

Laboratory Diagnostic Reports

Animal Health Laboratory (AHL)

Dr. Josepha DeLay and Dr. Tim Pasma from Animal Health Lab provided an update on pathology cases received by the lab during this quarter. A total of 1,368 swine cases were received during 2024 Q3. Of these, 90 cases had a pathology component.  A good or adequate clinical history was included for all (100%) of this quarter’s pathology cases. Age group was included for 99% of cases, and the PID inclusion rate was 93%, all of which are excellent for this quarter.

Cases and pathogens of interest during 2024 Q3 are as follows:

• Influenza case numbers were increased in 2024 Q3 among both pathology and non-pathology cases compared to Q2 and Q1, although positive case numbers were similar to those during the same quarter in the previous year (2023 Q3).
• Overall, identification of other infectious agents and disease conditions remained relatively stable during 2024 Q3. PRRSV-positive diagnostic cases decreased during Q3 (120 cases, vs 151 cases in Q3). PCV2 subtyping results for 2024 have been added to the report this quarter, with predominance of PCV2d overall but identification of PCV2a as well in Q1 and Q2.
• Congenital tremors due to atypical porcine pestivirus was identified in 1 herd, targeting gilt litters and involving most piglets in affected litters. As expected, disease incidence tapered off over the span of a few weeks, and the situation has returned to normal in the herd.
• As expected, more routine use of genotyping for enterotoxigenic E.coli (ETEC) continues to identify a wider range of subtypes than previously seen using agglutination serotyping alone. Edema disease due to F18 / STX2e-positive was confirmed in 1 herd with compatible clinical signs.
• PCV3 was detected by PCR with a high viral load (Ct18-20) in 1 herd with increased stillbirths. No additional diagnostic testing was requested for the case.
• Porcine sapovirus (PSaV) was detected with a high viral load (Ct 18-21) in 8 of 16 PSaV-positive cases. Of the 8 cases, 3 cases involved suckling piglets, 1 case was from nursery pigs, and age was unknown for the 4 remaining cases.
• The increased frequency of testing for Brachyspira spp reported in Q2 (26 cases) has decreased in Q3 to 10 cases. Pathogenic species of Brachyspira spp were not detected during Q3.

Gallant Custom Laboratory (CEVA) Diagnostic Reports

Anna Pietruszkiewicz and Kevin Millsap reported on 1 case submitted to Gallant Labs from Ontario in Q3 2024 in Ontario. This was an influenza case that was isolated and identified as a coinfection of two subtypes H1N1 and H1N2. 

Ontario Slaughter Statistics

Federal Slaughter Statistic Summary (Q1 Aggregate)

Dr. Christine Pelland noted that in Q3 of 2024 there were more hogs slaughtered and overall, less condemnations in comparison to Q2 of this year. There was also a decrease in trims as a result of abscesses, which is a positive change to note. An increase in condemnations due to “other” reasons was also appreciated this quarter.

Provincial Slaughter Statistic Summary

Dr. Christine Pelland commented that there were more hogs slaughtered in Q3 of 2024 compared to the other quarters this year. As a result, numerically there were a higher number of condemns; however, proportionally, the percentage did not differ dramatically compared to previous quarters. The majority of these condemns were due to parasitic livers. There was also a decrease this quarter in inflammatory conditions. An increase in “other” as a reason for condemnation was also appreciated, as it had a 9% prevalence this quarter compared to a 7.3% prevalence last quarter. As mentioned above, this was also the case at the federal level. Dr. Pelland plans on investigating this further.

CanSpotASF Surveillance Update 

Dr. Christa Arseneault updated the network on this quarter’s CanSpotASF testing. In Ontario during Q3 of 2024, 13 federal abattoir and 13 provincial abattoir tests were conducted. Ontario also had 26 laboratory tests completed under CanSpotASF in Q3 of 2024, which surpassed all other Canadian regions. This quarter saw the introduction of invasive wild pig testing into the CanSpotASF program, which tests any wild pigs depopulated and will submit for testing inclusion into CanSpotASF. In Ontario, one invasive wild pig depopulated was tested this quarter. Quebec reported that they tested 14 invasive wild pigs depopulated this quarter and the western provinces reported testing 25. It is important to note that CanSpotASF testing numbers for invasive wild pigs is not directly proportional or an indicator in the invasive wild pig populations within reporting provinces or regions. It is also important to note that since CanSpotASF launched, there have been no positive test results or false positives for ASF.

OAHN Project Update- Porcine Hemagglutinating and Encephalomyelitis Virus (PHEV)

Dr. Josepha DeLay provided an update on the porcine hemagglutinating and encephalomyelitis virus (PHEV) project currently underway. This organism has been identified in tracheobronchitis cases, so this project aims to understand its prevalence in lung and tracheal samples in Ontario swine. This project started in April of 2024. As of November 8, 2024, 82 cases have been tested. Of these cases, 5 were PCR positive, indicating low prevalence so far. Most of these positive cases have been in nursery or grow-finish pigs. These PCR-positive cases have been sent to Iowa State’s lab for further in situ hybridization to see virus localization in the lesion.

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)

Sri Lanka: Sri Lanka reported its first cases of ASF. Initially, ASF was found in the Western Province and now has been detected in 3 other provinces. ASF was found on commercial swine farms. There were reports that initially the high mortality was attributed to PRRS but further testing detected ASF. Residents in affected provinces have reported increased mortality in invasive wild pigs as well. (CEZD Weekly Intelligence Report October 21st ,2024)

Vietnam: In 2023 a new variant of ASF emerged in Vietnam. This new variant was a recombinant of a genotype ASF I and ASF II. The new variant was highly pathogenic. Vietnam currently has two licensed vaccines against ASF. Testing was done to see if the vaccines could protect pigs against this new strain. Neither vaccine was protective. Vaccinated pigs exposed to the new strain either died or developed signs of chronic ASF. (Vaccines 2024, 12(10) Nguyen Van Diep et al.)

Italy: The EU has raised concerns over Italy’s effort to control ASF. The EU Commission’s Veterinary Emergency Team, (EUVET) visited the Lombardy and Emilia-Romagna regions in early July to evaluate the effectiveness of ASF control measures in northern Italy. The team looked at risk reduction strategies, hunting practices, surveillance, biosecurity protocols and fencing. The team released a report that highlighted concerns that the current measures are not keeping pace with the epidemic. If a new plan for the control and eradication of ASF is not implemented, it is likely ASF will continue to spread east and south. In the summer Italy had 24 farms infected with ASF. Over 41,000 pigs were culled. Since ASF was first detected in Italy in January 2022 estimates are that producers have lost $45 million in direct losses and $84 million in indirect losses. (Swineweb August 12th 2024, SHIC Swine Disease Global Surveillance Report September 03rd – September 30th 2024)

Sweden: The EU has recognized Sweden as being free from ASF. The country reported its first case of ASF on September 06th, 2023 in an invasive wild pig. Authorities identified 70 more infected wild pigs and euthanized 116 more wild boars in the region. Since September 2023 there have been no more cases of ASF. No domestic pigs were infected with ASF. The eradication project was estimated to cost $11 million. (SHIC Swine Disease Global Surveillance Report September 03rd – September 30th 2024)

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 ASF testing in invasive wild pigs in Canada.

Transport of Invasive Wild Pigs in the U.S.A

Researchers from the USDA National Wildlife Research Center and the University of Saskatchewan recently released findings on a study of the rapid range expansion of invasive wild pigs in the U.S. The project specifically looked at “purposeful human-mediated movement of feral swine”.

Almost 19,000 samples were analyzed using an AI software program to identify feral swine that had been translocated (moved). Approximately 20% of the samples were identified as having been translocated with some individuals being more than 1,000 kms away from their predicted origins.

Recently, the state of Ohio introduced a bill in the state senate that requires anyone who shoots a feral pig to notify USDA Wildlife Services, bans importing feral swine and prohibits garbage feeding to feral swine.

In South Carolina, a pilot project in a small area was completed after 3 years where invasive wild pigs were trapped and removed. In the first year 860 pigs were removed, in the second year 290 and in the last year 125. Scientists estimate the project removed 70% of the population. (Pig Progress)

PRRS

PRRS now costs US pork producer $1.2 billion per year: An Iowa State University study found that PRRS caused an estimated $1.2 billion per year in lost pork production in the U.S. from 2016 to 2020. This is an 80% increase from a decade earlier. An earlier study in 2012 had estimated losses from 2006 to 2010 were $664 million per year.  Changes in market prices, increased cost of production and the size of the U.S. pig inventory account for $108 million of the $536 million increase. The remaining $408 million increase is due to the portion of the herds affected and the difference in productivity between affected and unaffected herds. Another difference found between the early study and the recent study is that there was an increase in amount of production losses from growing pigs. The earlier study found 55% of the lost production was from growing pigs and the new study found it was now 68% of the losses. One of the study’s authors, Dr. Holtkamp, attributes part of the increase to new more virulent PRRS strains. (Pork, Jennifer Shike, August 06th 2024)

Mosquitos and Pigs:  Recently, the Swine Health Information Center (SHIC) hosted a webinar on mosquitos and their impact on swine health. High amounts of rainfall in the spring and early summer in Iowa and Minnesota created an ideal environment for mosquitos to multiply. There were four different speakers. Dustin Swanson spoke on mosquito biology. A few points Dustin made were: females can lay rafts of 80 to 100 eggs several times in, on or near standing water, some eggs can survive several months during dry periods and reemerge after a rain, mosquitos can cause harm to pigs through physical bites and blood loos, possible transmission of viruses, anemia, reduced weight gain and allergic reactions. Dr. Bernie Gleeson from SunPork in Australia spoke on the Australian experience with the emergence of Japanese encephalitis virus, JEV, in pigs and people in 2022.  Mosquitos carry JEV between wild birds, pigs and people. Dr. Natalee Judson from pipestone shared her experience in the upper midwest. Processing plants were seeing some loads of pigs with between 20-80% of the pigs having physical blemishes on the hides. Dr. Judson recommended that producers target all stages of the mosquito life cycle to reduce the population.

Targeting just the adult mosquitos in the finishing barn is too late. Dr. Chris Rademacher from Iowa State gathered information from different sources and stakeholders to develop a factsheet titled Management of Site Insect Levels to Minimize Carcass Impact which is available on the Iowa Pork Industry Center website. A few of the tips include: removing sources of standing water, turn off outdoor lights at night, lower the temperature settings for stir fans in barns to create more airflow, cut down tall grasses and weeds around barns because some species of mosquitos do not fly far and will shelter in these plants during the day, trap the mosquitos and have an entomologist identify the species because there are differences for example some species can fly 2 kms, understand what insecticides and larvicides can be used, target the larval stage if possible.  (SHIC August 26th 2024)

Cleanliness in the farrowing room: Two recent studies looked at cleanliness in the farrowing rooms. The first study was funded by SHIC and led by Dustin Boler at Carthage Innovative Swine Solutions. The purpose of this study was: to determine the areas in the farrowing crates with the greatest surface contamination risks and determine the correlation between microbial counts and relative light units as detected by ATP bioluminescence.

The study was done in April and May 2024 on a 5,600 commercial sow operation. The farm had recently eliminated PRRS and Mycoplasma but was struggling with Rotavirus. Each week the farm farrowed approximately 200 litters in four farrowing rooms of 54 crates each. The rooms were washed with high pressure hot water, visually inspected and then an accelerated hydrogen peroxide disinfectant was applied.

5 crates from each room were swabbed for ATP testing as well as the entryway floor. Six locations within the farrowing crate were swabbed. In total 105 crates from 21 rooms were tested. 13 of the 21 rooms were also swabbed in the same location to measure bacterial levels, (total colony forming units, CFU) to compare to ATP testing. The study set a threshold of CFUs to rank areas as high bacterial contamination.

The study found the highest levels of contamination of the entryway floor, (93.8% of the samples) which is expected, followed by the sow feeder, (93.1%), sorting bar, (49.5%), back wall, (13.8%), piglet floor mat, (11.8%), and corners, (10.5%).  There was good correlation between the ATP testing and bacterial swabbing.

The researchers concluded that ATP luminometers could be used as a tool to measure on farm cleanliness. They also recommended that extra attention be paid to the sow feeder and the piglet sorting bar. (SHIC, August 05th 2024)

Another study in Ireland looked at if enhanced cleaning in farrowing could reduce antibiotic use and disease incidence in the pigs during nursing and post weaning. Two methods of cleaning were used in the trail: high pressure cold water with no disinfectant versus using a detergent, a disinfectant and drying. Crates were swabbed for bacterial counts and ATP swabs were taken. The study was small involving 47 farrowings.

The study found lower bacterial counts in the farrowing crates that were washed with a detergent, disinfected and dried. The number of cases of diarrhea was 75% less with the improved wash/disinfection program and antibiotic treatments were reduced 79%. Pigs from the improved wash/disinfection program had heavier weaning weights and improved ADG preweaning. ADG was also higher from weaning to 49 days post-weaning, but this did not carry through to finishing. (Halpin et al., Transl Anim Sci 2024, Jn)

How can you Participate in OAHN?

Look for the 2024 Q4 veterinary clinical impression survey that will come out the first week of January 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.