Indiana, France --- Ducks and Chickens and Vaccine -Same Old Same Old but Concerning Infections in Vaccinates
Canada researchers find H5N1 titers in feral swine while ARS apparently chose not to report a 2024 feral swine H5N1 surveillance project earlier in progress, publishing a TX H1-H3 study instead
Several of the recent H5N1 detections in the U.S. have thankfully occurred in smaller backyard poultry holdings with much less total industry economic hardship; regardless, each case is a calamity for owners of the affected flocks. However, the brunt of the H5N1 burden this fall continues to fall on our colleagues in a 2+ county area in Northern Indiana in the heart of the Amish poultry communities, with a total of 77 poultry flocks affected in less than the past 60 days!
I had written a few weeks back about the developing situation in Indiana: A Grim Week -H5N5 Death in WA, ProPublica Piece Documents Likely OH-IN H5 Aerosol Spread as Situation Now Repeats in N. Indiana. In that piece I projected possibly 80 cases by November 30. Indiana BOAH SitReps actually reported 66 NAHLN-positive flocks through 11/30, with another 11 logged through December 5th.
Note in the illustration below that NAHLN confirmatory reporting lags state sitrep reporting of positive flocks by 2-10 days. NVSL reported 5 November infections as December confirmations, and totals on the web site as of the evening of December 9th are not yet posted for 7 flocks.
(As of December 11th all flocks above are confirmed on the NVSL website with dates of 12/5,12/8, and 12/9 listed)
Keep in mind that most official reporting data utilizes “Date Confirmed Positive”, which is a very poor substitute for “Date Collected” from an epidemiological standpoint. Official confirmation can trail date of infection for even a “promptly reported” highly infectious diseases by 30 days or more. National diagnostic lab confirmation will trail infection by a week under the best of circumstances with clinical signs-based sample collection:
Each step of the above process could and should be time-stamped for process accountability. Just adding date of sample collection would be a very helpful additional epidemiological piece of information; however, that data paired with the confirmation date brings unwelcome accountability into the reporting system. Those of us involved in internal disease program analysis over the years often struggled mightily to troubleshoot the entire sample and information collection/transfer system to address “delayed” testing and reporting issues. All of those process questions are avoided publicly when only confirmation date is provided. Regardless, as the above illustration shows, confirmation dates are likely at best a week and at worst a month after the infection dates for any given highly infection disease case.
Just to wrap up Northern Indiana briefly, new SitRep’s have quieted recently with a single new case reported by BOAH on December 10th, the first since December 5th; perhaps the virus is burning itself out with few or no new flocks to attack in the immediate area. All parties involved in that area have to be exhausted. I have not seen any recent estimates of the outbreak’s effects on the regional or national Holiday duck supply or other economic effects of the outbreak. The layer losses are not a large percentage of total U.S. egg supply; however, I can imagine that local niche-based egg markets must have been severely impacted.
I want to transition from here into the larger world-wide view - how do we begin to address this nightmare world-wide for the innumerable other poultry-dense areas so susceptible to these types of H5N1 viral cloud storms flaring up to engulf entire multi-county production areas?
Let’s cross the Atlantic…
Avian flu hits poultry farms in 13 European states | WATTPoultry.com
Over the past week, almost 90 of the region’s commercial poultry flocks have been confirmed with infections of the H5N1 highly pathogenic avian influenza (HPAI), while cases in wild birds have been found even more widely across Europe. So far this year, a total of 577 highly pathogenic avian influenza (HPAI) outbreaks on poultry farms have been reported in 23 countries across Europe.
The total has now surpassed the figure for the whole of 2023 and 2024, which were 451 and 521, respectively. This is according to the European Commission (EC), whose latest update of its Animal Disease Information System (November 26) covers listed animal diseases in European Union (EU) member states and selected adjacent countries. These include Türkiye, but exclude Great Britain. In 2025 to date, presence of the H5N1 serotype of the HPAI virus has been detected at each location.
According to this database, Germany’s total count for the year to date is the highest, currently standing at 144. Next come Hungary and Poland (each with 107), France (65), Italy (36), and the Netherlands (21). The other 17 countries have each recorded fewer than 20 outbreaks in this category.
The disease situation in Great Britain is not monitored by the EC System. As of November 30, cases have been confirmed in 117 flocks, according to the government agriculture department, Defra. This figure includes commercial farms, backyard poultry, and other captive birds, as well as outbreaks in Northern Ireland.
Many new farm outbreaks in France, Germany
Based on the EC’s database, the greatest increases in new poultry farm outbreaks confirmed over the previous week were logged by France at 32, and Germany with 22.
…Also noteworthy is that 21 of these outbreaks involved ducks that had been vaccinated as part of France’s national HPAI vaccination strategy.
Vaccine Failures and Real-World Protection
This real-world data from France regarding vaccinated duck flocks is concerning, given all the hope that has been placed on poultry vaccination as a tool towards better management of H5 HPAI going forward for the U.S. and world poultry industry.
A paper was released on December 5th in Vaccine by French researchers: To what extent may the duck population be protected after vaccination against highly pathogenic avian influenza? Contributions from a modelling approach and French field data - ScienceDirect. While the entire paper is behind a paywall, the full abstract is available:
Abstract
Faced with increasingly disastrous avian influenza crises, and considering the associated zoonotic risk, France launched a vaccination campaign against highly pathogenic avian influenza on duck farms with more than 250 ducks in October 2023. In the context of this paradigm shift in the fight against HPAI, our study was designed to (i) provide an overview of the vaccination campaign over the first six-month period and (ii) evaluate the level of assumed vaccine protection at population scale through a simple modelling approach – using actual duck population dynamics, data related to the recommended vaccination protocol, and biological data on vaccination-induced humoral responses obtained from experimental studies - and real-world data on how vaccination was actually implemented in the field between 1 October 2023 and 31 March 2024, corresponding to the level of compliance with the vaccination protocol. Vaccination compliance appeared satisfactory, with high vaccination coverage at flock level (more than 95% of duck flocks being vaccinated at least once during the studied period). Ages at vaccination and time between doses were in line with the vaccination protocol. Regarding the assessment of the level of assumed vaccine protection, both theoretical model and actual vaccination data indicated that, at any given time point, maximum 40–50% of duck batches were considered fully protected, through either the second dose or the booster, while 30–40% of the vaccinated flocks were either considered only partially protected (primary protection through the first dose) or their protection was seen to wane six weeks after the second dose. Our work can inform the testing and optimisation of vaccination strategies and complementing our data-driven approach with serological monitoring, evaluation of vaccine efficacy, or spatio-temporal modelling of coverage across territorial scales would be pivotal to fully capture the interplay between vaccination, population dynamics, stakeholder decision-making, and epidemiological dynamics.
It appears that the researchers have concluded that less than half of vaccinated flocks were considered to be fully protected post-vaccination. Given the high susceptibility of ducks to H5N1 with less than stellar vaccine protection indicated with this study, the vaccine failures seen this year in France are perhaps not so surprising. Stay tuned as more details emerge both about this study and about vaccine performance and development in general.
I don’t believe that these results by themselves condemn vaccines to the trash bin. Were there differences in efficacy between vaccine protocols or brands? Successful vaccine development for RNA viruses is a long journey with trial and error. What about mRNA or other genetically enhanced or modified products? Regardless of setbacks, we need to: 1) develop regulatory and trade frameworks compatible with vaccine use; and 2) pair vaccine approvals with robust surveillance to match further vaccine advancements with the inevitable viral escapes we’ll see to vaccine barriers erected against the virus.
The fact remains that we have a world-wide extremely transmissible endemic mutating virus embedded in wild bird populations. Biosecurity is essential, but likely not sufficient in preventing its onward transmission, especially in poultry and livestock dense production areas. The world is growing meat, milk, and egg production capacity to meet the protein demands for 8.2+ billion people. We are not about to “de-industrialize” agricultural production in response to H5N1, which would not end the threat in any event. We can and should greatly improve our production siting decisions from a biosecurity standpoint. We can also engineer improved viral barriers and kill processes (filters, electrostatic, UVC, etc.). However, these are longer term and individual site refinements that cannot solve the immediate crisis by themselves.
All this argues that vaccines, anti-virals, and/or other countermeasures for H5N1 in poultry and likely other livestock are a top research and implementation priority now. Trade barriers and strategic inaction that conflict with moving these countermeasures forward are a basic threat to adequate human protein supplies in the near future! This is before we even consider the One Health threats posed by ongoing uncontrolled outbreaks of possibly zoonotic H5NX influenza in poultry and livestock populations in close contact with human caretakers!
It’s only early-December and Indiana and Minnesota-SD-ND have been our canaries in the coal mine. All of Europe (as well as Canada) are battling the same virus. What exactly is our agricultural leadership waiting for to initiate planning for our vaccine defenses?
Feral Pig Influenza Serology Studies
Finally, this week I want to highlight 2 research papers recently released regarding influenza serology studies in feral swine. The first is from a collaborative effort of Canadian university, provincial and CFIA veterinarians looking for serological evidence of H5N1 in Canadian feral swine collected in Alberta from 2022-2024:
Abstract
Influenza A virus (IAV) can infect a wide range of hosts, including wild and domestic pigs. Swine play an important role in influenza evolution and epidemiology due to their ability to get infected with both avian and human influenza viruses, potentially leading to reassorted virus variants. Interactions at the wild-domestic swine interface have been documented on multiple occasions, raising concern about pathogen transmission and the emergence of novel influenza strains. This study investigates the occurrence and subtypes of IAV infecting invasive wild pigs in Alberta, Canada. A total of 267 wild pigs were captured between 2021–2024. Exposure to IAV was initially detected by cELISA, with further confirmation of exposure to the H5Nx virus by hemagglutination inhibition (HI) and virus neutralization (VN) assays. Although no IAV genetic material was detected by qPCR, the seropositive samples by cELISA (4.17%; 5/120) coincided with the 2022–2024 highly pathogenic avian influenza virus (HPAI) H5N1 epizootic in Alberta, which involved outbreaks in wild species and domestic birds. These findings, combined with the epidemiological context, suggest interspecies transmission of HPAI H5N1 clade 2.3.4.4b to wild pigs. These results highlight the potential role of wild pigs as a new host in Canada and emphasize the need for continued surveillance of IAV in wild pig populations to assess the risk of spillover events at the wildlife, livestock, and human interfaces.
One interesting piece of information for me was the lack of evidence for any H1/H3 titers in feral swine in the Canadian Prairies, where these pigs apparently lacked exposure to H1/H3 influenza from domestic swine populations. All 5 cELISA positive pigs were negative by HI for H1 and H3. Note that 4 of the samples were positive by HI at 32-64 and the fifth was positive by virus neutralization (modified) at 1280. It’s important to note that these are not validated HI or VNT tests for H5, because no one has sufficient known positive samples for full serological test validation. However, I believe the paper does a nice job of providing fairly compelling evidence that the titers are “real”; i.e. these pigs did become infected and seroconvert to H5 2.3.4.4b virus when it was concomitantly antigenically found in wildlife in the same area.
Then there is USDA…
Longer term readers may recall a column I wrote a bit over a year ago describing work in progress by USDA ARS (in collaboration with Wildlife Services) prior to when the new administration took over in January 2025. Here is a link to that old column:
California H5N1 Dairy Outbreak Explodes - Time to Talk Feral and Outdoor Swine Risk I wrote in that article:
Despite testing assay knowledge gaps, ARS is currently funding a feral swine H5N1 surveillance project with a goal of testing about 8000 serum samples collected by Wildlife Services harvests for H5 antibodies. Dr. Arruda presented the following results to date:
While 3% are NP positive, these likely includes pigs seropositive from H1 and H3 endemic infections. These samples are then tested via H5 Hemagglutination Inhibition (HI) testing at NVSL; the data shown would indicate that 4 animals have shown positive HI titers. While it’s possible or perhaps even likely that these pigs may have been exposed to H5 B3.13, that cannot be determined with certainty, given that other high path and low path H5’s also may exist in the environment and diets of feral pigs and cause HI cross-reactions. Without serum from known infected pigs to evaluate seroconversion properties (positive controls), it’s difficult to interpret the significance of these findings.
So, over a year ago, USDA had at least 4 known HI positive H5 samples (unvalidated) with about half of their planned samples tested. This likely included few or no Fall 2024 samples from California, where both H5N1 HPAI influenza and feral swine were found in high concentrations!
Then with the 2024 election everything went silent within USDA in the HPAI world as the poultry massacre intensified to add to the dairy woes in California. Feral swine surveillance was totally dropped from everyone’s radar. Eventually Secretary Rollins was confirmed just in time to unveil a new poultry biosecurity initiative as spring brought the winter HPAI outbreak to a merciful end.
Fast forward to November 2025, and we get a USDA ARS feral swine study released:
Elevated Exposure to Influenza A Viruses in Wild Pigs (Sus scrofa), Texas, USA - PubMed
Abstract
Detections of highly pathogenic avian influenza viruses in mammals have increased globally, underscoring the need to assess influenza A virus (IAV) exposure in species that bridge wildlife, livestock, and human interfaces. We collected serum from 396 wild pigs (Sus scrofa, hybrids of wild boar and domestic swine) between October 2022 and May 2023 on a cattle ranch in north central Texas, USA, to estimate IAV seroprevalence and identify ecologic correlates of exposure. Using commercial blocking ELISAs and hemagglutination inhibition assays, we report high recent exposure of wild pigs to IAVs (seroprevalence 40%, n=396). Seropositivity was highest in individuals that were female, >2 yr old, sampled during spring (compared with fall or winter), and/or sampled <1.5 km from surface water. Almost half (46.3%, 57/123) of the samples were positive for at least two hemagglutinin clade representatives, and 13.8% (17/123) had titers against both an H1 and an H3 strain. These results indicate a hotspot of IAV circulation in wild pigs in north central Texas and highlight elevated exposure near water bodies, where wild pigs may contact wild waterfowl. Enhanced surveillance of wild pigs at the wildlife-livestock-waterbird interface is warranted to better understand ecologic and epidemiologic pathways for IAV transmission and reassortment.
Unfortunately, I couldn’t access the entire paper because this government-funded project is behind a paywall. Regardless, the abstract is simply a statement of the obvious! The earlier 8000 sample H5 incidence objective seems to be reduced to 396 samples in North Texas measured for H1 and H3, an area where domestic swine are numerous enough to allow for the feral populations to be endemically infected through occasional contact. H5 is certainly a risk, but the abstract avoids mention of any H5 serological swine sampling!
Note that the conclusion in the abstract stated: Enhanced surveillance of wild pigs at the wildlife-livestock-waterbird interface is warranted to better understand ecologic and epidemiologic pathways for IAV transmission and reassortment. It’s interesting to read that comment in light an Avian Flu Diary blog today covering H5 detections in wildlife reported by the Texas Parks and Wildlife Department (TPWD): Avian Flu Diary: TPWD Wildlife Health Alert: HPAI Detected in Multiple Areas Throughout Texas. Wildlife Services as has repeatedly reported positive H5 samples (by PCR sampling) in the same area where the 396 serological samples were pulled for the study:
Yet USDA-ARS seems to have consciously made a decision to not run or not report (non-validated) serological Hemagglutination Inhibition or Virus Neutralization H5 assays on these or any other samples collected. This is not an indictment by me of the paper’s authors, many of whom I consider extremely talented colleagues and friends! I believe they are in an impossible situation, where political censorship from senior leadership is likely being applied to logical scientific inquiry.
Maybe more complete work is pending and soon to be released? Regardless, it’s strange that USDA work on feral swine serology for H5 has been “scooped” by the Canadians. NVSL possesses actual live virus from the Oregon infected pigs to allow generation of positive serological samples from controlled experimental infections for more formal validation processes. That would be one step towards standardizing swine serological assays internationally. Are those collaborations underway as a priority for world-wide standardized swine serological H5 HI assays?
Finally, I’d like to express my personal thoughts on the role of serological results in isolation to keep some perspective in the discussions. Positive serological results are not smoking guns!! Immune systems are extremely sensitive markers for exposure; I suspect that currents strains of H5N1 may mildly infect pigs and promptly clear without lasting illness, generating a serological response. So positive serology by itself without a complete clinical picture, including information on associated contact infections and isolate sequence analyses does little to assess the true risk of swine titers in either pigs or on their animal or human contacts. That is the beauty and the challenge of One Health - any single piece of information in a vacuum is of little value; knowledge only comes from multi-centric synthesis of related data, information and expertise!
It’s possible that USDA elected not to publish feral swine serological results over concern that non-validated positive results would be overinterpreted by trading partners and the general public as that “smoking gun” implying more concern for positive serological results than the results deserved. Regardless, I’d hope USDA might be more transparent on the fate of the earlier disclosed 2024 H5 feral swine surveillance project, whether it is still in the hopper or was discontinued for whatever reason they choose to disclose. Thank goodness we can rely on the Canadians for the needed work.
John