Estimating the Within-herd Transmission Rate of Highly Pathogenic Avian Influenza H5N1 Virus in a Dairy Herd using an Approximate Bayesian Computation Approach - Journal of Dairy Science

ABSTRACT

Since the initial detection in dairy herds in March 2024, Highly Pathogenic Avian Influenza H5N1 has spread extensively in the United States with over 1000 confirmed cases in dairy cattle across 17 states. Data on within-herd transmission of H5N1 are limited with fundamental knowledge gaps. We used a simplified disease transmission model and an Approximate Bayesian Computation (ABC) algorithm to estimate H5N1 within-herd transmission model parameters using disease morbidity, laboratory testing data from an outbreak herd, and experimental inoculation studies. The estimated adequate contact rate was used to simulate disease spread and predict the time to exceed various threshold fractions of cattle with clinical signs. The estimated adequate contact rate in the baseline model scenario was 0.78 (95% C.I.,0.64–0.97) per day and the estimated basic reproduction number was 8 (95% C.I.,7–11). Based on simulation model predictions for a known infected herd with 3,433 lactating cows, it took more than 2 weeks from disease introduction to attain a clinical signs prevalence threshold of 5 percent. The estimated parameters are essential for informing surveillance design, outbreak management approaches, risk analyses, and regional transmission models. Incorporating data from future experimental studies and outbreak herds may enhance model precision and help characterize the variability of transmission patterns…

The entire paper is well worth the read; it leads to many more questions which will require more research to answer. In my abbreviated summer hiatus format, here are some questions/comments that come to the top of my mind from this work:

1. How does herd immunity affect transmission, on a 0 to 100% scale?

2. Where does subclinical infection (assuming that low levels of infection exist) become undetectable either clinically or by bulk milk tank PCR?

3. This modelling was based on B3.13. Do the results extend to D1.1 and possible other subsequent B2.3.4.4b genotypes?

4. Effective herd cross-protection is welcome, but likely temporary. A sufficiently “different” virus will eventually enter a grossly negative chronically infected antibody-protected herd.

The future prospects for “freedom” from H5N1 infection in dairy herds really depends on strength of cross immunity and the degree of dairy herd susceptibility to new viral genotypes presented into the environment by wildlife. Time will tell what challenges the next season brings us…for all of our livestock species.

John

This is a must read for the Hantavirus update, more so to better understand public health’s ongoing challenges in clearly communicating risks for aerosol spread:

The Atlantic - The Close, Prolonged Contact Myth

Knowing how a virus spreads is essential to public health, but people keep getting it wrong.

By Joseph Allen

A man goes to a birthday party, sits next to someone with hantavirus, catches it, gives it to his wife, and dies. His wife then infects 10 more people at his wake. Another guest at that same birthday party has no interaction with the index patient except to say “hello” as they cross paths, but that person gets sick too.

One index patient, 33 subsequent infections, 11 deaths, four waves of transmission.

This is from a meticulously documented hantavirus outbreak in Argentina in late 2018 and early 2019, published in the New England Journal of Medicine (NEJM). Nearly the exact same Andes strain of hantavirus caused the recent outbreak on the Dutch cruise ship MV Hondius. Yet from the moment this latest outbreak hit the news last month, public-health officials have been claiming that this virus is spread through “prolonged close contact.” The evidence is not nearly so reassuring.

In any outbreak, the single most important question is: How does it spread? The answer informs the guidance for everything else, including how to stay safe, which protective measures to put in place, and who should be notified during contact tracing. Get it wrong and everything else breaks down.

Read: ‘This is not going to be the next COVID’

We made this mistake at the start of the coronavirus pandemic, and the cost was high. Health officials thought the virus spread on surfaces (“fomite transmission”) and through large droplets that dissipate quickly and can’t travel six feet. That’s why we spent a full year cleaning elevator buttons and putting stickers on floors telling people where to stand. But these interventions did little to halt the spread of a disease that in fact traveled through small particles that lingered dangerously in poorly ventilated and enclosed spaces.

We’re now getting it wrong again. “This is not a respiratory disease,” Mike Waltz, the U.S. Ambassador to the United Nations, said about the hantavirus in an ABC News interview on Sunday, adding, “It’s very rare to see it transmitted between humans.” Transmission of the virus “requires close contact,” Jay Bhattacharya, the acting director of the Centers for Disease Control and Prevention, insisted last week. The CDC’s official communications have continued to emphasize that “prolonged, close contact” is necessary for transmission, as have other public-health officials outside the Trump administration…

This outbreak is not likely to spark a pandemic, mostly because the hantavirus is less contagious than influenza, measles, and SARS-CoV-2. But given just how little experience we have with this virus, any certainty is hubris. Thankfully, despite the flawed messaging, the system is broadly working: Officials are investigating, passengers are quarantined, the seriously ill are getting treatment, and the risk to the general public is low. International and national public-health authorities are acting responsibly.

But what happens next depends on how well public-health officials communicate what precautions people should be taking. If people mistakenly believe transmission relies only on “prolonged close contact,” they may take risks they will soon regret.

Public-health officials have to be more honest and more humble about how this virus actually spreads. An essential lesson from COVID is that officials should be candid about communicating that we are often learning in real time, and we should shy away from making bold pronouncements that may prove dangerously misleading weeks or months later. When it comes to preventing an outbreak from becoming a pandemic, insisting on the wrong answer to that most central question—How does it spread?—may well be worse than not having an answer at all.

Perhaps no one wants to publicly admit the uncertainties that aerosol spread entail. We can avoid “prolonged contact”, disinfect fomites, observe safe distances, segregate infected fluids, etc. However, infected air (dust) is a non-mitigatable wild card to some degree. We WANT to reassure stakeholders that “X” distance or “Y” time is sufficient to prevent transmission. In our haste to provide reassurance, we build public overconfidence which then leads to a sense of betrayal when evidence proves reassurances to be overstated.

In light of my summer hiatus, here are 4 other recent articles of interest I’ve recently perused, with very limited “take-home” comments from me for now:

Serologic Evidence of Highly Pathogenic Avian Influenza A(H5N1) Virus Infection in a Veterinary Professional Exposed to an Infected Domestic Cat — Los Angeles County, California, December 2024–January 2025 | MMWR

1. Human infections are not necessarily clinically evident

2. Basing human PCR testing on self-reported clinical symptoms is likely “too little too late”, missing asymptomatic cases, and swabbing symptomatic cases after their highest chances for viral shedding

3. Note that the cat was infected with raw poultry product. How much chicken and turkey is passing through slaughter with infectious virus in the product? Our current pre-slaughter surveillance process does not prevent incubating birds from being slaughtered. Does the industry really have the desire to address this issue with <72 hour pre-slaughter molecular testing, or will the condemnation rates prove to be too expensive for a product that is actually likely to be “safe” with proper handling?

Fatal Human Case of Highly Pathogenic Avian Influenza A(H5N5) in a Backyard Flock Owner — Washington, November 2025 | MMWR

1. H5N5 has been found in the U.S. in other flyways; is it the same genotype? Has the same genotype spread further in the Pacific flyway? How much H5N5 wildlife sequence data is now publicly available?

2. Interesting that the environmental sampling was positive, while the birds were less so, indicating perhaps more of a historical infection in the ducks; the “pooling” effect of the environmental sampling proved to be powerful in linking the bird and human viruses.

Surveillance on California dairy farms reveals multiple possible sources of H5N1 influenza virus transmission | PLOS Biology

1. More follow-up work from this group adds to the picture of lots of aerosolized virus, especially in milking areas.

2. Evidence of sub-clinically infected cows with viral shedding in milk was interesting; mastitis seems to be an inconsistent sequalae rather than a primary step in the infectious process?

3. What is the real pathogenesis of this disease in lactating and non-lactating dairy cattle? In naive versus recovered herds? Why has dairy flu “died down” versus 2024-early 2025?

Avian Flu Diary: Sci Adv: Mammary and Respiratory Infection of Sheep with H5Nx clade 2.3.4.4b Viruses with Milk-mediated Transmission to Lambs

Michael Coston pulls highlights a recent research piece on sheep infected with the D1.1 H5N1 2.3.4.4b genotype as well as H5N5. We have a lot more to learn in multiple farm species beyond dairy cattle related to mammalian H5 influenza…

John

Avian Flu Diary: Eurosurveillance: HPAI H5N1 in Poultry & Domestic Cats and Occupational Exposure Among Veterinary and Other First Responders, Germany, February 2026

…I’ve provided the link, abstract, and some excerpts from the report below, but you’ll want to read it in its entirety. I’ll have a postscript when you return.

Open Access

Highly pathogenic avian influenza A(H5N1) in poultry and domestic cats and occupational exposure among veterinary and other first responders, Germany, February 2026
Aparna Dressler1,2 , Christiane Wagner-Wiening1 , Bettina Tegtmeyer3 , Susanne Haag-Milz3 , Bettina Demattio4 , Ralf Dürrwald5 , Timm Harder6 , Andreas Salditt7 , Judith Köster7

Highly pathogenic avian influenza (HPAI) viruses continue to circulate in Europe, causing outbreaks in poultry and wild birds and occasionally infecting mammals [1-4]. Although human infections remain rare, zoonotic transmission is a recognised occupational risk for persons involved in animal husbandry, outbreak control, and veterinary response activities, and sporadic human infections with HPAI A(H5N1) have been reported globally [5]. An HPAI outbreak in poultry and cats in a small, remote poultry holding in Sigmaringen in February 2026 triggered a One Health investigation with 17 exposed persons.

Here we describe the outbreak, assess potential zoonotic transmission and evaluate the public health response within a One Health framework.

Outbreak detection and initial investigation

On 19 February 2026, the local public health authority in Sigmaringen, Baden-Wuerttemberg, Germany, was notified of a suspected avian influenza outbreak in a small poultry holding following veterinary inspections triggered by animal welfare concerns. The holding, which had no biosecurity measures, comprised ca 21 chickens and nine free-roaming cats and was located in a remote rural area. The birds were in a poultry house but had access to the outside and contact with wild birds.

Between 16 and 18 February, veterinary inspectors found four dead chickens and one dead cat on the premises. A further cat showing severe neurological symptoms was euthanised (Tables 1 and 2). Laboratory testing using real-time quantitative PCR (RT-qPCR) confirmed HPAI A(H5N1) infection in all six animals, poultry and cats. All remaining poultry (n = 17) were culled as part of control measures. Subsequently, an additional symptomatic cat tested PCR-positive and was euthanised. The PCR-positive symptomatic cats presented with diverse clinical manifestations, including neurological signs, respiratory symptoms and general sickness…

I’m not writing columns on summer hiatus, but I do want to continue posting links to pertinent materials for readers’ references. The take home’s for me here:

1. H5N1 is international

2. Producer behavior is universal - no one wants to wear PPE or be tested for H5N1

3. Public health still has not caught on to the paradigm that H5N1 can be asymptomatic in people (and cats); PCR testing should extend to ALL direct mammalian contacts (not just symptomatic) on infected farms. “Symptomatic” is subjective and viral shedding often peaks pre-symptomatically in any event.

4. Cats remain a good standard sentinel carnivore!

Until the next news eruption,

John

Right out of the chute on my “hiatus”, a highly sourced and respected LinkedIn post comes along I have to share with my readers. Authorships don’t come any more respected than this MN-based group.

Here is the JAVMA article:

United States poultry flocks remain unvaccinated against H5 influenza—but why? in: Journal of the American Veterinary Medical Association - Ahead of print

John

97 - My Mother’s Final Year in This Life

My mother passed on April 14th after a relatively recent decline from dementia post-COVID pandemic. My family and I have shared the all too common “long good-bye” so often experienced with that disease. I have a huge collection of memorabilia to turn my attention and creative efforts towards in writing a family history honoring her and my father after her passing. Mom and Dad raised 4 boys, yielding 8 grandchildren, and 4 great grandchildren (to date); I want to electronically capture some of the wisdom and character we were surrounded with on that Iowa farm for the family to cherish.

75 - A Milestone Birthday

I turn 75 this year; I honestly feel more like 50 with a few extra wrinkles... I share with others what a wonderful long life my mother had, passing at 97; then I pause to realize that she bore me at 22! Simple math dictates that in 2+ short decades I’ll hit that same ripe old age… My health remains good, although I have a couple of upcoming “maintenance” procedures early this summer. Taking breaks from routines, even self-imposed ones like Substack columns seem like a prudent 75th year summer plan. If I don’t take time at 75 to make the trips to see the grandkids, watch the seasons turn in my garden, attend a nephew’s West Coast wedding, hold hands with my dear wife in our back yard at sunset, when should I plan to do it?

50 - Iowa State University Class of 1976

My graduating veterinary class is holding its 50th class reunion in Ames in September! I was one of the in-state “baby vets”, sailing through 4 years of vet school after 2 years in pre-veterinary medicine. I’m embarrassed to admit to today’s graduates that I paid in-state undergraduate tuition for all 6 years, graduating at 24 years old in May of 1976 with no college debt. I used unspent college savings to buy my first practice truck with a fiberglass box, then borrowed on a signature loan to buy a new 2-door Thunderbird…

I practiced in large animal medicine for a couple of years, but pigs were my passion, and that industry was on the cusp of a transformative revolution. Covering that topic and my real education is well beyond the scope of this section; the point I want to stress for younger readers is that cultivating your passion is the key to career development. That career may take many forms, as mine certainly has. Second, realize that knowledge in any field is now exponential, making continuous learning and collaboration essential as we all must specialize to maintain proficiency in more defined areas. State of the art production animal veterinary “practice” is almost unrecognizable today versus what I “knew” upon graduation. All that veterinary degree really did was buy me entry into further educational and collaborative endeavors; however, that entry was priceless!

I’ll be celebrating the 50-year reunion for all the good memories and honoring the opportunities veterinary medicine has brought to me and my classmates. However, the diploma never signified the end - it was only the beginning of a long life of learning that continues to this day.

2 - Years on Substack!

I’ve now been posting columns for 2 years. My initial posting went up on April 28, 2024, and this is #203. Those 203 posts in 2 years equates to about a post every 3.6 days. 24 posts of those posts generated over 1000 views on Substack and 3 generated over 3400 views! See the graph above for all views on all sources, according to Substack statistics. Frankly I’ve been overwhelmed by the readership’s response! The feed-back I’ve received and the new and renewed friendships this little exercise have brought me has been gratifying.

The whole process of putting ideas out for consideration engenders pressure that is both terrifying and clarifying. It forces me to defend my thought processes. I’d also like to think that it enforces within both me and the readers some degree of open-mindedness, especially as we veer into scientific uncertainty (welcome to RNA viruses) and appropriate policy responses (even more uncertain than viruses).

Rather than post on a set schedule, my plan has been to put together a column when something newsworthy strikes (really often). I especially look for multiple items that string together well to make a compelling narrative. I always try to attribute sources and acknowledge possible differing opinions or explanations. I can be exceedingly blunt in criticisms at times, but try not to make criticism personal, only relate my cocerns to policy decisions. I also know I have failed at times with too sharp a tongue.

I’ve never seriously considered charging a subscription fee for a couple of reasons:

1. 1) I didn’t want the pressure of meeting scheduling deadlines

2. 2) I wasn’t sure there was an ethical market for my information, which in the end is expert opinion, not rigorously independently researched materials

Perhaps the biggest overriding theme in the last 2 years over 203 columns has been - are we thinking beyond the old regulatory and scientific paradigms that worked before, but no longer fit the:

1. 1) influenza virus itself;

2. 2) scientific tools available to measure it;

3. 3) breadth of livestock species now affected; and

4. 4) degree of saturation of the wild bird and mammalian environment now harboring spillover threats.

Frankly, the entire “federal-state-industry system” has been even more resistant to needed modifications to meet the challenges H5 is throwing at it than I had thought it would be. Political forces are extremely resistant to foregoing “first to know” status for regulated diseases, on farm early detection capabilities not-withstanding. Opening testing approvals or official test research into non-confirmed infected species (non-lactating dairy, beef, sheep, goats, horses, even pigs) can only complicate messaging and marketing both for regulators and industry groups. None of the resistance should be surprising, however more complicated it may make control and human spillover in the event of viral reassortment. The system is really built to count on “staying lucky…”

Moving Forward for the Summer

First, I plan to return to what I have been doing on Substack later in the summer or early fall after a hiatus. Frankly, poultry outbreaks are likely to slow from here as the weather warms. APHIS moves at glacial speed; vaccine trials for poultry will likely not happen until more research is published. Human cases are non-discoverable right now in workers, and the current viral strain (D1.1) seems to not easily pass to people. Whatever is happening in livestock mammals will remain under wraps until somethings changes with the virus to make livestock sicker, or it reassorts to become widespread in pigs.

For the summer I plan to only post links to interesting events, with perhaps a comment or 2 of explanation. I’d entertain posting “guest” columns on my site at my discretion if anyone would like a crack at dialogue with the reading base. Otherwise, I will continue to use postings for brief updates, minus the more extensive comments I’ve usually placed with them. If a particularly pertinent issue should arise, I will spring back life on the keyboard with more commentary.

I’m pretty confident that something will eventually change with H5 to surprise us, wrecking plans to ignore it! We just don’t know when, where, or in what species. It may more likely be next fall-winter or later, when the birds are again moving with newly reassorted viruses from the Arctic mixing areas.

The other likely change is a return to divided government in the House and perhaps the Senate with the fall elections. That will mark a return to Congressional investigative hearings, putting Executive Branch officials back on the hot seat for a host of issues. Zoonotic H5, pandemic preparedness, and HPAI in poultry, including vaccination issues, will undoubtedly be of great interest to Democratic legislators salivating to grill the Administration. If disease events complicate the politics, USDA disease responses may take on an entirely different look with renewed political pressure.

I’ve truly enjoyed a really fast 2 years and plan to return to form later in 2026. In the meantime, look for a few sporadic “highlights” posts and stay tuned from other sources. I know I’ll still be watching, just not writing as much.

Stay the course,

John

Avian Flu Diary: EID Journal: Highly Pathogenic Avian Influenza A(H5N1) Virus RNA in Bovine Semen, California, USA, 2024

…Ten days ago, in Preprint: Bovine H5N1 Influenza Viruses Have Adapted to More Efficiently Use Receptors Abundant in Cattle, we saw new evidence that H5N1 was undergoing active and robust viral adaptation in cattle.

And yet there appears to be little sense of urgency among farmers, or regulatory agencies. Surveillance remains largely passive, and in some regions of the world, practically non-existent…

…While H5 may find a dead-end in cattle, we are tempting fate by ignoring the current trajectory, which suggests HPAI is increasing in - and adapting to - farmed mammals.

Posted by Michael Coston at 7:49 AM

Two years after it emerged, ‘cow flu’ is still circulating—and baffling scientists | Science | AAAS

After 2 years, the U.S. outbreak of the H5N1 influenza virus in cattle appears to be waning, easing fears that the virus could cause long-lasting damage to the dairy industry or mutate into a form that could cause a human pandemic. The last new detection of an affected herd occurred on 13 December 2025 at a Wisconsin farm, according to the website of the U.S. Department of Agriculture (USDA). Data from a USDA program that tests milk for the virus suggest 16 of the 19 affected states have gotten rid of the virus, which originated in wild birds.

H5N1 continues to circulate on farms in California and Idaho, those states’ agriculture departments told Science. Texas remains “affected” in USDA’s latest update, even though it has not had a detection since May 2025, because it has not complied with the National Milk Testing Strategy (NMTS) requirement that it sample all silos at milk-processing plants. In other states the virus may simply have escaped detection…

(Note - Texas gained unaffected status as of last Friday under the National Milk Testing Strategy Guidelines; 17 of 19 previously affected states are now classed as unaffected. Oregon, North Dakota, North Carolina, and Florida do not test to NMTS standards and are classed as “provisionally unaffected”)

But the virus remains ensconced in some farms. Veterinarian Edith Marshall, an epidemiologist with the California Department of Food and Agriculture, says a few have had cows that remain infected for more than 1 year. These cows could act as “superspreaders” of the virus to the new calves and heifers, which typically replace one in every three adult cows in a dairy herd every year. Infections could also result from infected cows that show no signs of disease and never are tested, or if tests produce false negatives…

…Data from several studies hint at other transmission routes. Air samplers at the California farms readily detected the virus, supporting the idea that the virus transmits through the air. And in a separate long-term study at 18 farms in California’s Central Valley, Melody found provocative, as-yet-unpublished evidence suggesting the wind can spread the viruses long distances.

Dairy farms in the southern part of the Central Valley had an explosion of the virus in the early fall of 2024, whereas those in the north were spared. Then in late November, a bomb cyclone walloped the state, sending strong southern winds across the northern Central Valley. Within 4 days, all 18 farms had an outbreak. Webby is now sequencing virus samples from those farms, which might confirm that their infections had a common origin.

Previous research has suggested the wind can give flu viruses wings. A study from the Netherlands showed it played an important role in the spread of a deadly subtype named H7N7 between poultry farms in 2003, and a 2025 report from the Czech Republic contends the wind moved H5N1 between poultry farms separated by 8 kilometers. “The head scratcher we all still have is how does it get from a particle blown in the wind into the udder of a cow?” Webby asks. But Melody is convinced cows’ noses are a main route for infection, even though nasal swabs often test negative.

Much remains to be elucidated regarding H5N1 viral ecology within and between larger dairy herds. Within herd prevalence is definitely quite low in most previously affected herds, perhaps completely gone. It’s unclear to me what the detection levels are used in the NMTS program. Are completely negative PCR and/or ELISA antibody assays required? What are the testing intervals for any given herd? Are mastitis or bloody nasal discharge cases targeted for PCR by producers? Is any whole herd H5N1 ELISA antibody screening being done to assess for subclinical or historical infections in at-risk herds?

Then there is the ongoing risk of new D1.X introductions from wildlife and neighboring poultry infections. NMTS can theoretically find those cases (as Nevada, Arizona, and Wisconsin did); however, detection requires regular surveillance at sufficiently frequent intervals via samples that are not over-diluted via milk silo blending. I don’t have sufficient expertise or knowledge of the methodologies being employed in NMTS to judge the rigor of the process. My impression is that individual states are in charge of state-specific standards, approved by VS federal staff. Regardless of the details, the entire process has been quite opaque outside of the regulatory community.

From my perspective we can state that we lack evidence of active H5N1 B3.13 or D1.X infections in all except 2 states in the U.S. at this point. Conversely, we lack proof of freedom from infection in the other 48 states due to lack of transparency and independent oversight in the National Milk Testing Strategy (NMTS) program!

In my former careers, I earlier served as an Iowa producer representative on the National PRV Eradication Committee. Each state had to meet producer-written PRV Program Eradication Standards, reporting results to a National PRV program staff, which reviewed them state-by-state with the Producer PRV Committee. Later I became a federal staff veterinarian leading those reviews. As an auditing process, each state program was subject to independent on-site reviews by outside producer-state animal health-federal officer expert teams, especially when state-level programs experienced setbacks or lacked progress. I only bring up this historical information to contrast it with the current opacity in the NMTS Program.

PRV is a stable Herpesvirus, amenable to a vaccination program to assist in eradication. Good biosecurity with separate site production and artificial insemination greatly aided in its elimination in swine. Even with that, PRV was eradicated with an asterisk*, because the virus is still present in feral swine and occasionally some backyard domestic pigs in contact with feral swine. While it can spread short distances by aerosol from large acutely infected populations, generally separation and good biosecurity are effective in blocking spread, keeping the bio-secure commercial production herd negative.

PRV serves as a good lesson is “knowing the enemy” when considering feasibility for viral elimination. Critically, the swine industry was committed to ridding itself of the production losses, vaccine costs, management constraints, and marketing restrictions the disease brought them. A stable virus with DIVA-capable highly efficacious vaccines against it made an eradication commitment possible. The same pork industry has failed miserably in bringing much more costly PRRSv under even regional control in pig-dense areas, despite more financial impetus for its elimination.

I don’t see dairy industry commitment to a formal scientifically defensible H5N1 herd eradication, nor is it likely to even be feasible. NMTS has served a purpose in getting the H5N1 acute clinical disease monkey off of most states’ and producers’ backs. However, it would be an overinterpretation of its opaque standards to conclude that negative NMTS status assures freedom from H5N1 infection in all cows in all unaffected states.

It seems more likely that H5N1 may persist at lower but less detectable levels in some herds. If so, the virus will continue to mutate under pressure from largely immune herds to infect new additions, calves with declining maternal immunity, and cows with declining titers. Completely “safe” animal movements from unclassified herds will require documentation of sending herd status via serological monitoring and targeted PCR testing paired with quarantine periods for stock after transfer from possible positive herds. Producers and SAHO’s can choose to look for these infections or to ignore them; sooner or later H5N1 may flare up again into clinical disease without vaccination to boost immunity as the virus continues to mutate. Time will tell…

As a veteran of PRV-Swine Brucellosis Cooperative Disease Eradication Programs, I don’t see dairy H5N1 as a viable target for formal eradication and state/national disease freedom claims with the H5N1 virus endemic and variable in geography, season, genomics, and species affected across the U.S. Individual herds can and should strive to document and maintain negative status to optimize animal and human health; however, that status will require more segregated bulk tank, serological, and targeted individual animal testing than is currently mandated via NMTS. Accomplishing that level of commitment across the entire industry is just not feasible at this point.

H5N1 Molecular Evolution in Cattle - 2 New Preprints Out

Molecular biologists have been at work analyzing the available H5N1 dairy sequences from the U.S. to study the dynamics of viral changes over time. 2 new large collaborative pre-prints were released in the past week, with some common authors, but differing emphases and objectives.

The first paper performed phylogenetic analyses of both B3.13 and D1.1 spillovers into cattle (the 3rd Wisconsin D1.1 spillover occurred too recently for inclusion in the analysis). Here is a link to the first collaborative paper, supervised by Philippe Lemey, Michael Worobey, and Andrew Rambaut: The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle

Abstract

Prior to 2024, highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses circulated predominantly in wild birds and poultry. In 2024 and 2025, 2.3.4.4b genotypes B3.13 and D1.1 were detected in United States dairy cattle. Using whole-genome and segment-specific phylodynamic inference, we estimate that B3.13 and D1.1 spilled over from wild birds into dairy cattle in late 2023 and late 2024, respectively. Spillover occurred shortly after the formation of the reassortant genotypes and was followed by months of cryptic transmission prior to detection. We found that both B3.13 and D1.1 evolved at higher rates in cattle relative to birds, primarily due to relaxed purifying selection. Site-specific analyses identified genomic sites under positive selection in cattle relative to birds, indicating adaptation and likely contributing to improved viral fitness after spillover. Intensified genomic surveillance in dairy cattle is essential as population immunity introduces additional selection pressures, with ever-changing risk for human emergence.

This is a highly technical paper well beyond my training level in molecular genomics! I can only rely on the authors summary in the abstract (as peer reviewed) for the practical take home message highlighted above - ongoing selection pressure will drive viral changes, which must continue to be monitored.

I did find this graphic interesting; the California B3.13 isolates are grouped independently on the tree. They are perhaps worthy of some independent epidemiological conclusions or at least questions as they continue to diverge from the original spillover.

The second point of interest is the 2 independent dairy D1.1 clusters from NV and AZ. I wonder where the WI isolate falls on the phylogram? Has anyone released any information of phylogeny on that virus? We also have multiple mammalian D1.1 isolates, including some human cases. Where do they fall on these trees? We know that one human isolate is closely related to the Nevada dairy isolates.

The second paper is confined to analysis of B3.13 isolates, looking at the role of mutations in the hemagglutinin (HA) segment in receptor usage in cattle as well as their likely effects on cross-species host ranges for the divergent HA genes. Here is the link to this paper, with Jack A. Hassard, Jiayun Yang, Bernadeta Dadonaite, and Jonathan E. Pekar named co-first authors: Bovine H5N1 influenza viruses have adapted to more efficiently use receptors abundant in cattle

Discussion

Host-specific glycan chemistry beyond sialic acid linkage alone represents a major but often underappreciated determinant of influenza virus adaptation during cross-species transmission. The ongoing H5N1 outbreak in dairy cattle provides a natural system to examine how these molecular features shape viral evolution during sustained mammalian transmission. Early adaptation of H5N1 in cattle was driven primarily by rapid changes in the viral polymerase complex. Here we show that continued evolution involves gradual selection and fixation of haemagglutinin (HA) mutations that enable recognition of sialic acid variants abundant in bovine tissues but absent in birds and humans. Several of the most prevalent substitutions enhance replication in cattle tissues while being neutral or slightly attenuating replication in human airway models. In contrast to NeuGc-preferring viruses such as equine H7N7, these mutations broaden receptor usage rather than switch specificity. This expanded receptor engagement may therefore preserve host range, consistent with spillover of H5N1 viruses carrying D104G and V147M into humans and poultry despite the absence of NeuGc in these hosts.

Enhanced binding to NeuGc-containing glycans may also reflect ongoing adaptation to bovine respiratory tissues and could facilitate more efficient respiratory replication and transmission, consistent with emerging reports of respiratory involvement in cattle infections. Such changes could alter transmission dynamics within dairy herds and complicate control efforts, while also increasing the risk of spread between cattle production systems. Several other influenza hosts, including horses, pigs and sheep, also express high levels of NeuGc. Although infections or serological evidence in these species during the current panzootic remain sporadic, adaptation in one host may increase spillover potential into others. These dynamics highlight the importance of rapid control of livestock influenza outbreaks, as prolonged circulation may generate evolutionary changes that expand ecological opportunities for the virus.

The somewhat speculative comments regarding possible increased respiratory transmission dynamics could play a factor in the increased herd to herd transmissions observed in the continuing California and/or Idaho outbreaks. More phylogenetic analyses of later outbreak isolates would be interesting in determining whether these changes were maintained in subsequent isolates.

The theoretical increased risk for spillovers into other species is certainly testable, both in lab transmission studies and also with increased serological surveillance in mammalian species surrounding dairy herd outbreak areas. However, both of those initiatives would require USDA and SAHO approval for testing and publishing of results. USDA-ARS in Ames has done a series of H5N1 experimental infections in pigs, with preliminary results shared informally; however, only a few of the early studies have been approved for publication. No work has been published to my knowledge regarding the behavior of H5N1 B3.13 or D1.1 in other ruminants, beef cattle, or equines in the lab.

H5N1 B3.13 - on the Road to Human Adaptation?

Michael Coston of Avian Flu Diary nicely summarized a dispatch regarding H5N1 B3.13 from an all-star zoonotic influenza research line-up in CDC’s Emerging Infectious Diseases Journal, adding links to several other pertinent reference articles as well: Avian Flu Diary: EID Journal: Tropism and Replication Competence of Cattle Influenza A(H5N1) Genotype B3.13 Virus in Human Bronchus and Lung Tissue

Here is the direct link to the recent EID article: Early Release - Tropism and Replication Competence of Cattle Influenza A(H5N1) Genotype B3.13 Virus in Human Bronchus and Lung Tissue - Volume 32, Number 5—May 2026 - Emerging Infectious Diseases journal - CDC

Conclusions

Viral titers and influenza NP-positive cells demonstrated that cattle-origin H5N1/439 and H5N1/98638 strains are better adapted to human upper airway tissues than avian H5N1/483 and have similar replication abilities as H1N1pdm/415742 in human lung explants.

The ability to bind α(2–6)-linked SA further indicates a shift of receptor affinities that are more compatible with upper respiratory tissues. Innate immune responses of H5N1/439 and H5N1/98638 viruses in human lung tissue fell between those triggered by H1N1pdm/415742 and H5N1/483 viruses, indicating that cattle H5N1 viruses could pose a human health risk.

Defining how these strains infect human tissues and shape immune responses is critical for anticipating outbreaks and reducing zoonotic transmission risks. Because influenza viruses continually evolve across diverse avian and mammalian hosts, sustained research and surveillance remain essential to prevent human infections.

There is nothing earth-shaking here - this virus remains “on the road” towards full human adaptability. Whether it makes the final steps towards pandemic status depends on future reassortments and mutations in its individual gene segments.

This was posted by Pathfinder on Flutackers.com last weekend, leading to the following local news post: Wild Instincts urges caution as fox kits tested positive for avian influenza after human interaction | Local News | wjfw.com

This case points the public’s connection with wildlife and associated risks with H5N1 infection. Individual human odds of infection here are low; however, the virus is nearly ubiquitous and likely in our livestock at times as well.

The human public health system in some states is becoming proactive enough to add H5 screening to H1/H3 influenza testing for humans in livestock dense areas, especially for Matrix positive - H1/H3 negative samples in sick patients. Human H5 diagnostics will continue to advance, and hopefully the U.S. will again provide and improve upon basic medical care and zoonotic screening for our immigrant friends caring for our herds and the communities that they and their families occupy.

A lack of zoonotic H5N1 human infections is not a cause for relief when testing denominators drop towards zero. A lack of large dairy infections and fewer large poultry flock depopulations have undoubtedly led to much less human H5 exposure, but I believe that we still likely have a significant number of farm workers with undiagnosed conjunctivitis and URI missing out on timely public health screening for a known public health threat. I continue to believe it would be prudent to conduct more asymptomatic testing of human contacts upon confirmation of new poultry farm infections, both for public health and for off-site biosecurity reasons. The human upper respiratory tract is one more potential fomite to be evaluated in a biosecurity evaluation.

Finally, I did note one piece of good news regarding H5N1 vaccine development on the world front! A research group in China reported on early success with an mRNA-based vaccine: Preclinical evaluation of an mRNA vaccine developed from the first human isolate of bovine H5N1: Cell Reports Medicine

Summary

Given the global threat posed by H5N1 clade 2.3.4.4b avian influenza, rapid development of effective vaccines is imperative. We design an mRNA vaccine encoding hemagglutinin (HA) from A/Texas/37/2024, the first bovine-to-human strain. In murine models, both wild-type and cleavage-site-modified HA vaccines elicit robust and durable humoral immunity, along with a balanced Th1/Th2 response, conferring complete protection against lethal homologous viral challenge. The vaccine, along with the World Health Organization (WHO)-recommended candidate (A/Astrakhan/3212/2020), elicits cross-clade binding antibody responses and demonstrates improvement against specific clades at a 1 μg dose. Pre-existing H1 immunity does not diminish H5-specific immunogenicity. In avian species, the vaccine also provides full protection against lethal clades (2.3.4.4b and 2.3.4.4h). Formulated with another ionizable lipid, the vaccine elicits responses comparable to benchmark lipid nanoparticles (LNPs) and shows a favorable safety profile in rats. This work establishes a rapidly adaptable mRNA-LNP vaccine prototype for pandemic preparedness against evolving avian influenza threats.

I imagine that other groups world-wide are also developing mRNA and other advanced vaccine technologies for influenza; however, this piece documents some longer-term hope for large-scale rapidly deployable vaccine platforms against an H5N1 or other influenza pandemic. The Chinese are adept at copying U.S.-led break-through technologies, even when we are too thick-headed to move it forward ourselves! Hopefully the United States will be back in the saddle soon on mRNA and related technologies for both people and animals at cost-competitive levels.

Summary of the Current U.S. H5N1 Surveillance Environment in Domestic Mammalian Livestock:

My last column detailed the OffFlu White Paper regarding the need for greater surveillance efforts in our mammalian livestock beyond dairy cattle, while this column describes officially disappearing dairy cattle H5N1 outbreaks in all but 2 states. We no longer suffer from the muti-herd dairy H5N1 B3.13 (or D1.1) influenza epizootics that occurred in 2024 and early 2025. That is indeed great news and suggests that solid herd immunity is likely a protective factor in preventing fulminant reinfections and rolling area outbreaks in dairy dense areas.

However, we have failed to conduct even rudimentary surveillance in either dairy cattle or other species for serological or antigenic evidence of subclinical or recovered clinical infections. Bulk tank and milk silo testing may approximate subclinical testing at times, depending on dilution factors and testing intervals. Those parameters have not been openly disclosed, but we know that testing intervals increase over time without outbreaks. Initial serological sampling strategies in targeted at-risk groups and species would provide clues for more informed antigenic surveillance if indicated; however, there is little or no appetite in the U.S. to allow such prospective sampling in the absence of “trouble”. We can’t really expect any different outcome from a political standpoint, where no stakeholders have an interest in finding a problem not currently on the radar.

However, odds favor that we’ll find eventually more H5N1 in U.S. livestock whether we want to or not! New positive influenza findings may show up in people exposed to undiagnosed H5N1-infected domestic mammalian livestock. Alternatively, livestock samples may be tested independently of the U.S. regulatory testing system for influenza with positive findings (next generation sequencing-NGS or ELISA antibodies reported independently or internationally (e.g. the positive H5N1 swine titers in Canadian feral swine). As the Dutch discovered, dead cats are also a great sentinel for infected milk in dairy farms or infected raw meat diets, and cat owners are often concerned enough to request necropsies with rabies/H5N1 checks. Raw meat or rendering products generated from multiple species (including beef and pork) is also a wild card for bringing H5N1 to zoos, wildlife preserves, fur farms, etc.

Finally, there is no guarantee that H5N1 will remain a quiet background viral pathogen in any livestock species. Reassortment is possible in swine, horses, dogs, and cats, leading to much more obvious clinical illness, including viral pneumonia and encephalitis. It could develop into a more potent co-infection in the shipping fever complex in feedlots, where the continuous flow of feeder cattle into populations would provide ongoing “fuel for the fire” to maintain an endemic mutating influenza infection in feedyards. Endemic swine influenza H5 re-assortants are always a possibility, most likely arising in backyard or show swine with poultry/wild bird ties, but then moving into commercial production until detected. And…no one has paid any attention to sheep and goats; are milking goat herds (and goat milk) as big a risk as dairy cattle herds?

In the meantime, back to the poultry, broilers this time: Arkansas has first case of HPAI in commercial poultry of 2026 | WATTPoultry.com - 191,200 broilers.

Until next time,

John

Before launching into a separate topic, I’d like to provide a more recent update on the main topic in last week’s column. The Wednesday, March 25th, U.S. Animal Health Association Daily News Briefs featured the following:

5. Largest Animal Health Emergency in US History Continues as HPAI Hits Indiana Hard

By Eric Pfeiffer

WWBL.com

March 23, 2026

Since the beginning of March, highly pathogenic avian influenza has claimed over 350,000 birds in Indiana.

“We’re asking all of our producer partners, whether it’s layers or broilers or turkey or dairy or any other adjacent production system, please be vigilant,” says Dudley Hoskins, Under Secretary of Agriculture for Marketing and Regulatory Programs. “We need sound biosecurity practices. It’s not just what’s happening on that one facility, there’s risk of lateral transmissions.”

Full text: https://www.wwbl.com/2026/03/23/largest-animal-health-emergency-in-us-history-continues-as-hpai-hits-indiana-hard/

The Indiana tragedy was featured in my column last week; as of Thursday evening, March 26th, here is the updated March poultry count for Indiana:

The 350,000 birds listed about a week ago has now grown to nearly 400,000 depopulated poultry today.

Here are the 2025-26 HPAI Indiana monthly totals by flock type:

March will go down as the second most deadly month of the 25-26 season in total poultry losses but the worst month for the duck industry. The state has lost over a million layers in multiple “smaller” flocks and over half a million ducks, predominantly in 2 counties in north Indiana! (3/31 update - Indiana BOAH has subsequently reported 4 more infected duck flocks totaling 27,120 birds through March 31st)

Moving briefly to another hard-hit state, I want to compliment Pennsylvania’s apparently quite successful effort to bring an ugly outbreak in Lancaster County under relatively rapid control! NVSL has only reported 3 Lancaster County PA outbreaks (plus one on neighboring Cecil County Maryland) since the 20th of March. I consider that really effective area outbreak shutdown, given the earlier scope of infection and the poultry density in that area. (3/31 update - NVSL reported 1 more infected Lancaster County duck flock totaling 18,000 birds on March 27th.)

Additionally, both Pennsylvania and Indiana have publicly stated that they are individually testing dairy herds (via milk sampling) in outbreak areas. No dairy herd infections have been reported in either state. It would be great if officials provided negative counts to document their dairy monitoring activities; however, the lack of reported cases is reassuring.

Mammalian Infections with H5N1 2.3.4.4b

State commitments to testing dairy herds in the immediate areas of poultry flock HPAI outbreaks remind us that this virus easily crosses into multiple mammalian species. I’ve included a couple of links to papers I reviewed this week that add to this body of information:

Detection of antibodies against influenza A viruses in cattle | Journal of Virology

This paper was published about a year ago but was not widely covered.

Unexpected outbreaks caused by the H5N1 highly pathogenic avian influenza virus (HPAIV) in dairy cows in the United States (US) have raised significant veterinary and public health concerns. When and how the H5N1 HPAIV was introduced into dairy cows and the broader epidemiology of influenza A virus (IAV) infections in cattle in the US remain unclear. Herein, we performed a retrospective study to screen more than 1,700 cattle serum samples collected from different bovine breeds in the US from January 2023 to May 2024 using an enzyme-linked immunosorbent assay (ELISA) targeting the nucleoprotein (NP) to detect IAV infections, and the positive samples were further tested by hemagglutination inhibition (HI) assay. Results showed that 586 of 1,724 samples (33.99%) from 15 US states were seropositive by the NP ELISA assay, including 78 samples collected in 2024 and 508 samples collected in 2023. Moreover, the HI assay revealed that 45 of these ELISA-positive samples were positive to human seasonal H1N1 and H3N2 and swine H3N2 and H1N2 viruses, and some were positive to two or three tested IAVs. Surprisingly, none of these ELISA-positive samples were HI positive for the circulating bovine H5N1 strain. Our results demonstrate that IAVs other than H5N1 can infect cattle, infections are not limited to dairy cows, and that bovine infections with swine and human IAVs have occurred prior to the H5N1 outbreaks. All results highlight the value in monitoring IAV epidemiology in cattle, as the viruses might adapt to cattle and/or reassort with the currently circulating H5N1 HPAIV, increasing risk to humans.

The results only reflect the time period sampled (January 2023-May 2024) and the areas from which the cattle were drawn (almost exclusively Missouri (1400+ samples), Illinois, Arkansas, Kansas, and Oklahoma-see map below). Lack of H5N1 titers is actually not surprising, given the May 2024 sample cut-off for a disease that first appeared in Texas in late March or early April 2024.

The more enlightening information from this paper is the high percentage of nucleoprotein (NP) ELISA positive samples, indicating influenza A exposure of some sort, with a significant number (45) showing HI titers to human and swine viral antigens.

The work provides further evidence of cattle susceptibility to influenza viral infection from multiple H subtypes and mammalian plus avian sources of virus. Further serological and antigenic studies, including H1, H3, and H5 across much broader populations of cattle would be useful, but unlikely to readily occur, as I’ll discuss later.

Michael Coston recently highlighted a report from Europe regarding detection of influenza A (H1N1) in a European bison: Avian Flu Diary: Vet Research Comms: First report of serological and molecular detection of influenza A (H1N1) in European bison (Bison bonasus). This adds one more piece to the body of evidence, including documented viral molecular detection, of the ability of influenza to at least sporadically infect ruminant species.

USDA Surveillance and Reporting of H5N1 Mammalian Infections

USDA has maintained a web site for some time now showing H5 isolates in “non-livestock” mammalian species in the U.S.: HPAI Detections in Mammals.

The dataset includes wildlife, including marine mammals, plus domestic cats. Sampling is based on passive and some active surveillance of affected animals, dependent upon voluntary mortality sampling conducted by federal, state, and local wildlife officials for the most part. Some samples may also be collected from peridomestic species collected near poultry and dairy HPAI outbreak sites. Positive results can reflect area incidence, but more likely reflects sampling intensity, or the lack of it, in many areas, e.g. most of the SE United States.

All positive farmed domestic mammalian livestock samples in the U.S. are found at this site: HPAI Confirmed Cases in Livestock | APHIS. With the exception of 1 backyard swine case in Oregon and 1 alpaca case in Idaho, all confirmed cases have been dairy cattle herds.

USDA-APHIS provides Testing Guidance for Influenza A in Livestock. Despite the growing scientific consensus for a wider sampling effort, this document is silent on testing production animals other than lactating dairy cattle. Slightly more guidance is found in the following on-line document:

National Animal Health Laboratory Network (NAHLN) Frequently Asked Questions Highly Pathogenic Avian Influenza (H5N1) in Dairy Herds: Updated July 25, 2025

• Livestock HPAI TO (task orders) can be used for IAV-A testing in any species, including peri domestic mammals and birds, associated with a livestock premises. This includes cats. Any bovine IAV-A testing including FADIs can be charged to this TO.

• What testing is paid for by NAHLN? Samples taken from other animals including cats with potential exposure (from dairies, exposed to raw milk, etc.) or reported clinical signs associated with this disease event.

• Can NAHLN labs forward fluA non-negative samples from other livestock and companion species (e.g. horses) for characterization by sequencing? Yes. NVSL appreciates receiving these samples for further characterization.

• Are positive test results for influenza A in all species reportable? All influenza A, with the exception of H1/H3 in swine should be reported to USDA.

In summary, USDA APHIS makes provisions for testing non-dairy livestock and cat samples for influenza through the HPAI “Dairy” Program at NAHLN labs and NVSL. However, those provisions are buried in a NAHLN “Dairy” FAQ document. Sample testing is not part of any coordinated approach towards risk-based sampling of livestock exposed to infected dairy herds, highly- infected HPAI poultry production localities, or to areas with high risks for wildlife H5N1 exposure.

OffFlu Discusses the Mammalian Livestock Surveillance Gap

Early last week OffFlu released a paper under the sponsorship of its parent organizations, WOAH and FAO:

Beyond poultry: Rethinking monitoring and control of HPAI H5Nx anticipating spillover risks for mammals - OffFlu

The paper provides this opening Disclaimer:

This document does not provide normative standards or prescriptive guidance. It presents technical considerations and illustrative response options intended to support risk-based decision-making by competent authorities. This document provides the point of view of independent OFFLU experts and does not necessarily reflect the position of the parent organizations FAO and WOAH.

The introduction then is presented in summarized “Problem” and “Solution” summary statements:

Problem

Surveillance systems for high pathogenicity avian influenza (HPAI) urgently require adaptation to protect animal and human health in the context of a rapidly changing ecological risk landscape. This need is driven by the emergence and global spread of HPAI H5 clade 2.3.4.4b viruses of the Goose/Guangdong lineage (hereafter H5Nx), which have fundamentally altered the epidemiology of HPAI. H5Nx viruses have acquired increased fitness in wild aquatic birds, enabling sustained, year-round circulation and global spread. This ecological shift has led to recurrent incursions into poultry populations and a growing number of spillover events into diverse mammalian species, including companion and farmed mammals in close contact with humans.

The current surveillance paradigm, which remains largely focused on poultry, is no longer sufficient or reflective of the epidemiological reality. H5Nx viruses can no longer be regarded solely as “poultry-centered” or even “avian-centered”, highlighting the urgent need to expand surveillance efforts to include mammals. The continuous circulation of H5Nx viruses in wild aquatic birds for several decades suggests that these viruses are entrenched and unlikely to disappear in the near future. At the same time, it remains uncertain how ongoing viral evolution will affect host range, virulence, and transmissibility in different host species. This rapidly changing epidemiological landscape highlights the urgent need for versatile surveillance systems that are ecologically informed, cross species, and aligned with a One Health approach.

Solution

Many countries have well-established, regulated systems for the early detection and control of HPAI viruses in poultry, designed to prevent onward transmission and to minimize economic and animal health impacts. In addition, several countries have implemented surveillance programmes in wild aquatic birds to assess viral circulation, evaluate impacts on wildlife populations and ecosystems, and guide mitigation strategies aimed at reducing spillover into poultry.

However, dedicated HPAI surveillance strategies targeting wild and domestic mammals are largely absent in most countries. This gap is particularly critical for farmed mammals, which often live in close proximity to humans, are kept at high densities, are highly interconnected through trade and transport networks, and represent substantial economic value. Despite these risk factors, significant blind spots remain in monitoring programmes for HPAI virus infections in farmed (mammals), and in some settings such programmes are absent altogether.

A practical and scalable solution is to build upon existing avian surveillance systems that are already aligned with the WOAH Terrestrial Code and embedded within the One Health framework, by adapting these systems to include relevant mammalian hosts. ‘Relevant’ species are those whose biological susceptibility and ecological or geographical context place them at risk of involvement in H5Nx ecology, recognizing that what constitutes a ‘relevant’ species will continue to evolve over time and space due to viral evolution and changing exposure patterns.

Such integrated surveillance could aim both to detect H5Nx infections in mammals at an early stage and to prevent further spread, thereby reducing impacts on ecosystems, animal health, and human health.

The paper then provides more detailed background summary information, well worth a close read, before moving on to a section entitled “Detailed Solutions”, which the authors further break down across 4 broad groups: 1) mammals housed and managed in groups (e.g. livestock, fur farms, catteries, zoos), 2) individually managed companion animals, 3) free-ranging mammals (defined as limitedly- or non- managed mammals, living in free-ranging conditions, including both wild and feral mammals) and 4) humans. I’ll limit my thoughts to the group’s recommendations related to a subset of the first group- livestock and fur farms, where many of us are or were employed.

Please read the entire document closely - it is not excessively long. In zeroing in on the livestock-related recommendations, it occurred to me just what a heavy lift the group is requesting of the livestock industries in practice. Let’s look at some of the detailed recommendations to explore why few of these recommendations can occur without significant further international discussions and more creative surveillance paradigms.

Under the “Spillover” Prevention section the authors advocate for surveillance for “evidence of virus circulation in wild birds surrounding farms.” U.S. regulatory authorities have not provided for “real-time” reporting of H5 status in wildlife populations near farms; private monitoring for HPAI infection is not allowed. We can and do monitor wild bird population movements and densities and may get results of mortality testing for HPAI weeks or months after the fact. However, we lack assessments of the viral status of wildlife populations or the environment surrounding farms during periods of high risk. This is likely due to the risk that reporting a diagnosed wildlife HPAI infection in trade areas could adversely affect interstate or international trade in domestic poultry in some situations. H5 is now endemic to some degree in most areas in most countries involved in poultry trade; however, international agreements rules have not evolved to accept real-time wildlife status documentation for improved risk management without potentially penalizing reporting with possible trade restrictions!

Another statement in that section states: “Likewise, consideration may be given to reducing or phasing out intensive farming practices involving multiple species (e.g. poultry and pigs) on the same premises.” Multi-species single premise production may well increase risks for interspecies spillovers; however, recommendations for their phase-out would be viewed very dimly in the U.S. under our legal systems guarding free enterprise in agriculture. Our biggest multi-species on premises “violators” are likely our smaller producers! Additionally, repeated dairy to poultry premises to premises spread in 2024 demonstrated that understanding other factors in stemming “area spread” may be as critical as ending multi-species co-location on premises in mitigating cross-species spillover. Distance is not the only and perhaps not always the most important factor in limiting interspecies spread.

In the section titled “Early detection Through Targeted or Syndromic Surveillance”, the OffFlu group advocates for both broader testing of unexplained differential diagnostic cases, as well as targeted serological and PCR testing, especially in high-risk areas on appropriate slaughter animals and contact animals near where H5N1 is known to be circulating.

This section is where the good intentions and the most powerful recommendations of the OffFlu Working Group run head on into the realities of U.S. and international commercial agricultural production. Frankly, in the U.S. and EU, modern diagnostic methodologies and surveillance protocols and authorities are mature enough for full implementation of these recommendations. Next generation sequencing applied to “unexplained morbidity and mortality events (UMME) and targeted surveillance for HPAI in areas where HPAI is raging in poultry / wild bird populations have NOT been fully employed because we lack political will and compelling policies for implementation.

The paper claims routine implementation in the UK and the Netherlands; however, I have to wonder about its effectiveness in the Netherlands, given that nation’s track record on the H5N1 cat mortality-dairy farm traceback timeframe and associated dairy cattle PCR testing delays. I don’t bring this up to condemn the Dutch; I’ve also criticized U.S. officials for failing to test non-poultry species (swine and beef cattle) on quarantined HPAI premises. Zoonotic disease surveillance failures in livestock production units are a repeated occurrence in agriculturally mature developed countries. We can’t even pull raw cheese epidemiologically tied to E. coli infections (The Atlantic) from the market anymore!

We have little hope for significant consensus in sampling for H5N1 in livestock species (beyond our rapidly retreating dairy effort) until agricultural interests and regulatory officials are comfortable that sampling can be undertaken without jeopardizing interstate or international agricultural trade and market values.

The OffFlu paper moves on to suggest “Control of outbreaks through predefined response protocols”, stating “Suspicion (instead of detection) of H5Nx infection in any mammal could be made immediately reportable. The subsequent response measures could be determined based on risk assessment and local epidemiological context, rather than automatically prescribed.”

Key management options for consideration are similar to those implemented for other infectious diseases. Isolation may be applied, including defining minimum quarantine periods and clear criteria for release from isolation…

Culling may also be an option, and the benefits of preparing regulations for control measures in advance of outbreaks—rather than solely in response to outbreaks—may warrant consideration, with prioritization of the key species indicated earlier.

Ironically, the U.S. swine industry valiantly attempted to define many of these parameters for a possible H5N1 outbreak in swine herd(s) about a year ago, coming to consensus on an early draft for review by APHIS-VS. The effort basically went nowhere in APHIS, with so many questions outstanding regarding just how an uncharacterized novel agent of completely unknown zoonotic potential might need to be handled. My personal “take-home” was that it’s very difficult to prebuild a response plan for an H5N1 or reassorted virus of unknown infectivity and unclear zoonotic potential. Those factors alone make reporting infection or doing next generation sequencing of undiagnosed cases a tough decision, because the needed response is unknowable in advance of understanding the virus involved.

In the “Decrease impact when spillover has occurred” section, one final recommendation that will likely cause heartburn in the U.S. is: “Limits on animal numbers allowed on farms may improve control and response capacity…” Once again, economics and design solutions for large-scale viral outbreaks, whether HPAI or other diseases, will partly drive unit size decision-making. Ironically, ASF in China has seemed to drive even larger production units, right or wrong. Governments may choose to limit indemnification levels per site or emission levels per site; however, animal numbers per site based on disease risk is likely not the best way to solve an international diease problem.

The group made 4 final Considerations that work across these different phases:

• Acceleration of poultry vaccination efforts, when combined with appropriate biosecurity measures, could help to reduce overall viral burden and spillover risk.

• The development of best practices for mammalian influenza diagnostic techniques for viral (RNA) detection and antibody detection, including point-of-care diagnostics, could support improved detection capacity.

• Increased implementation of real-time genomic sequencing of viruses, alongside the sharing of genetic sequences from detections in all mammals (including free-ranging mammals) in the public domain, could support the rapid identification of adapted or reassortant viruses and enable genomic epidemiology, thereby improving risk assessment and response capacity.

• Consideration of inequalities and the establishment of financing mechanisms to support low-resource countries could strengthen the global response to this threat and support sustained reductions in overall viral burden and spillover risk.

I have supported all of these, especially 2 and 3; I’ve discussed both topics multiple times in multiple columns in the past.

An APHIS-coordinated NAHLN-based H5N1 integrated multi-species UMME and targeted surveillance process could be a powerful early detection and genotype monitoring tool in mammalian livestock species. It would meet most of the objectives of the OffFlu paper. I’m concerned that the current U.S. ‘Foreign Animal Disease Investigation” HPAI diagnostic monopoly is functionally limited in the production animal sector to poultry and dairy. It needlessly limits samples, ties up data, slows diagnostics, and prevents the widest and earliest possible dissemination of the broadest amount of H5NX 2.3.4.4b genomic information and associated metadata possible.

However, I also recognize that the agricultural meat and products trade industry may prefer to maintain the system just the way it is. We risk consumer or trading partner confidence in our meat and poultry products should unmonitored diagnostics in more species produce concerning results which are published “prematurely” from less controlled sources. Wide-spread cross-species H5N1 infection research studies and serological surveys are rarely conducted because approvals for conducting official tests in “off-target” livestock species must be granted by USDA-APHIS and resident state animal health officials. Neither individual states nor commodity group stakeholders want to volunteer as the next dairy industry H5N1 poster child!

Regardless, I personally believe that in the era of Oxford Nanopore and “Citizen Science”, trying to “manage” information through exclusive data channels is a longer-term futile proposition. We WILL have more H5 human hospitalizations/deaths and more sick livestock and wildlife as this virus keeps mutating and reassorting in birds and mammals. Viruses will be sequenced and associations made, some of them beyond the control of “official testing” performed exclusively in the regulatory-NAHLN-NVSL nexus.

Maybe it’s the optimist in me on behalf of my grandkids, but I’m increasingly confident that we are imminently approaching the onset of a resurgence in ethics and excellence in the U.S. and across the world that will sweep away much of the rot that currently governs us. Minneapolis showed the way for the rest of the world to follow. As this new mindset emerges across our society, we will collectively find the courage in agriculture to search out H5 and beat it, not bury it! Just like we beat brucellosis, TB, PRV, Salmonella enteriditis, and even E. coli in "no longer raw” cheese!

In U.S. animal health, we solve our problems, we don’t hide them!

John

I want to use this blog to review the numbers regarding the 2025-26 outbreak in 3 somewhat unique counties in northern Indiana, partly to illustrate just how difficult the HPAI situation becomes when we collectively fail to upgrade our responses to a viral enemy with enhanced capabilities. H5N1 2.3.4.4b has adapted to poultry and mammalian immune system defenses with increasing success; it is thriving on our inability to as quickly adapt our detection, response, and prophylaxis (vaccine and therapeutic) processes in domestic animals to meet its challenges.

The Northern Indiana 2025-26 HPAI Outbreak Area

Here is the area involved:

If you google the counties involved, you get a plethora of beautiful pictures and descriptions of the Amish rural lifestyle we all cherish. You also can read of the agricultural background of the area, including its egg and duck meat production, made up of smaller farm production units. Meat ducks are handled by 2 major corporate processors in the area; this small spot in Indiana is one of the 2 largest duck meat production areas in the U.S.

Here is a breakdown of the 2022 NASS Ag Census data for layers and duck farms in these 3 counties, as sourced from USDA/NASS QuickStats Ad-hoc Query Tool:

The real take-home message for me is that a total of 1350+ poultry farms are shoehorned into 3 counties, with an extremely infectious H5N1 virus increasingly subject to tracking and area spread risks for the resident poultry flocks.

2025-26 Outbreak - the Big Picture

Here is a table of the outbreak for the 3 counties derived from NVSL and Indiana BOAH reporting of cases to date spanning the entire current “season”:

It’s hard to comprehend this small area enduring 83 outbreaks with over 1,000,000 dead birds in slightly over 2 months in Wave 1. Now, they have 27 new outbreaks with another 250,000 dead birds in less than 1.5 months as Wave 2 intensifies.

Here is another way to view it as a more classic epidemiologic curve for sites infected:

We’ll see what the coming weeks bring; the NVSL confirmed case line list doesn’t yet reflect 6 cases shown here as reported in recent Indiana BOAH SitReps. Here is my compiled line list for Indiana’s 20 March cases reported through Sunday evening the 15th. All but 4 cases (pink) in Indiana have occurred in Elkhart and LaGrange Counties (I zeroed out the bird totals on those 4 for accurate Northern Indiana spreadsheet counts):

15 farms, 87,000 chickens, 102,000 ducks in 15 days in March in 2 counties…The dollar economic loss is undoubtedly much higher when a single 3 million head layer site is infected; however, it’s hard to put a price on what a disease disaster like this does to small close-knit agrarian-based communities dependent on these birds to maintain their way of life. Further, this is the second time this has happened in 4 months in these counties!

We don’t know to what degree the same farms may have been infected twice; however, do the math. The counties house about 2.8 million hens, and since October 892,000 have been depopulated- that is nearly 32% of the 3-county 2022 NASS hen inventory lost! The duck picture is even more dire, with an inventory of 1.214 million birds, 439,000 have been depopulated, over 36% of the area’s duck inventory gone!

It’s one thing for a once in a hundred years’ loss to be incurred by any business; hope springs eternal for those of faith and sufficient reserves to carry on. It’s another thing entirely when owners lack any assurance that the situation will not repeat itself on an uncertain but much more frequent timeline.

Dispassionate analysts will undoubtedly blame the high rates of infection in these counties on some or all of the following factors:

1. higher shedding rates and asymptomatic preclinical infections in ducks

2. poor within/between farm biosecurity practices by “less educated” producers

3. excessive production sites built too close together

4. lack of wild bird control around production facilities

5. etc., etc., etc.

We have no way to intelligently judge from the outside what steps might be necessary to resolve this situation; we cannot “fix” this crisis for them. However, this segment of the poultry industry deserves to be heard and considered as much as the integrated egg, turkey, and export-oriented broiler producers regarding policies and tools available to battle this virus. Early detection, surveillance, reporting, and vaccination policies are devilishly difficult to navigate across all stakeholders’ needs; these producers and others like them make up another critical stake-holders group we all must keep in mind in crafting needed changes.

Lack of Predictability Is the Real Risk

From here I need to backpedal really quickly, because I have not been on infected poultry farms in Northern Indiana or anywhere else to guide me in specific recommendations. My experience comes from older experiences in swine populations, especially related to recurring PRRS infections, which I believe applies here to H5N1 in poultry more than we would like to admit.

Cyclic PRRS outbreaks on my single site 700-sow farrowing operation in Iowa back in the 90’s drove me out of the swine business, teaching me unforgettable lessons regarding the treachery of mutating RNA viruses (sound familiar?) and their effects on operational pig flow, cash flow and ultimate profitability. I figured out too late that 90% PRRS control in a single site operation was not good enough, because 10% of the time my farrowing operation was unpredictably pig-starved and thus totally cash-starved. Conversely, integrators could have the same 90% PRRS control rate across 20 farrowing sites with 18 sites still in production while a couple were down, while budgeting a more predictable annual 90% cash flow system wide. It took me years of reflection after exiting the business to understand what I had missed in failing to network into a larger production network that diversified PRRS and other risks and opportunities across multiple sites and management strengths.

The industry STILL has not figured out how to consistently keep PRRS out of farrowing sites in finishing site dense areas, although top-notch biosecurity and air filtering has greatly helped. I’ll leave vaccine discussions aside, since I’m really unqualified to discuss PRRS versus H5N1 vaccine prospects for success. Suffice it to say that PRRS vaccines have been at best a management aid for viral load control, not a panacea for viral elimination.

Endemic PRRS in Northern Iowa / Southern Minnesota and many other swine dense areas remains a humbling case study for application towards the H5N1 model in poultry epidemiological principles, particularly related to viral infections in larger bird populations. Many of the area animal and viral density and spread concepts that I and others have referred to were refined with innumerable public and private PRRS virus epidemiology studies for nearly 40 years now.

This personal story in production and financial unpredictability illustrates the conundrum that our Indiana Amish friends and many other non-site-diversified poultry producers face with H5N1 today. No one can long survive high incidence, uncontrollable production wipe-outs in independent economic operations! Many economic risks can be offset or hedged - this one cannot. If producers briefly forget it, their bankers are there to quickly remind them…

How Do We Restore Predictability for the Poultry Industry?

I’d venture to say that no one knows the answer to this question today; however, we do know that the status quo is not working! Consensus seems to be building for at least some experimentation with vaccine usage to increase flock resistance to viral incursions and lower viral log levels in flocks that do become infected, while aiding in lessened shedding and potential transmission. I do worry that some are looking at vaccine as a panacea, which could lead to inevitable disappointment.

However, we cannot further develop vaccines as useful tools as long as we keep them totally off-limits. Their true efficacy will emerge and improve as producers put them to the test in real world conditions, paired with intensive surveillance testing measures to assess their efficacy.

Surely, trade issues can be negotiated in today’s H5N1 environment where every major trading country is facing the same issues. Scientific reason would argue that poultry meat (with surveillance) from judiciously risk-based vaccinated poultry flocks sourced from endemic H5N1 wildlife countries (all countries today) are less likely to be infected than non-vaccinated birds in the same circumstances!

I also sense (and urge) a movement towards much earlier, broader-based pooled environmental sampling in order to look for early signals for HPAI incursions in wildlife and flocks prior to development of clinical signs and fulminant viral shedding. We can’t remain 3 steps behind the virus, waiting for sick birds to initiate official testing. This strategy only encourages onward spread. This may be especially true in duck flocks?

It seems that there remains regulatory reluctance to encourage “unofficial testing” in any form for fear of leaking (or conversely of hiding) unofficial results. I personally believe that it’s presumptuous to believe that we officially manage H5N1 access so well that only our national labs can confirm infection of a virus that anyone can obtain on a beach in California or near a lake in many states, or in the air from a quarantined egg layer. An inadvertent disclosure of a non-official test result for a highly endemic virus is not earth-shattering, when domestic flocks would still require official testing for regulatory classification. We tie ourselves in knots trying to discourage sequencing of the enemy we’re all trying to learn more about! The Republican Party has always been supportive of “deregulation”; HPAI is overdue for that approach, Secretary Rollins, as the trade issues are resolved. It’s possible zoonotic dynamics add another layer of complexity but that can’t be used as an excuse to keep more wide-spread sampling cost-prohibitive or inaccessible.

To be completely fair, the U.S. swine industry has not been hobbled with many of the regulatory constraints for PRRS faced by the poultry industry with H5N1; however, PRRS has not been conquered yet in the entrepreneurial pork production industry. We need to consider that even with more relaxed vaccine approaches and intensified sequencing efforts, H5N1 will remain a formidable threat to the poultry industry for quite some time.

Regardless, changing nothing only guarantees us more of the same results- endless cycles!

https://share.google/8AqRdXs5HtCtLGf6D

John

NVSL posted these new commercial farm H5N1 outbreaks this morning. Cecil County Maryland borders Lancaster County PA, which continues under quarantine with multiple HPAI cases. State lines are poor biosecurity barriers!

https://www.researchgate.net/figure/Location-of-the-Big-Elk-Creek-Basin-Pennsylvania-and-Maryland_fig1_265539525

Additionally, those of us subscribed to Indiana’s SitReps know of 5 additional farms in the queue from that state. I’ll have more on those later today.

John

A post by Pathfinder last night in Flutrackers covered an article in the LA Times written by Susanne Rust regarding the outbreak in sea mammals:

H5N1 bird flu spreads to sea otters and sea lions along San Mateo coast, wildlife experts say.

A quote from the article was added in a nested FluTrackers post from Commonground:

The strain the animals have contains a mutation allowing it to more easily transmit between mammals. It is also a different variation than the ones found in dairy cows and commercial poultry. This one is Eurasian in origin, first seen in 2022. It has been detected in birds that fly along the Pacific Flyway and is responsible for a mass mortality event in 2023 in northern fur seals on an island in eastern Russia, said Christine Johnson, director of UC Davis’ Center for Pandemic Insights, during a press conference Thur​sday morning.

Johnson said researchers think this is the first detection of the A3 variation of the virus on the Pacific Coast and therefore likely a new introduction into North America, she said.

First, thanks to NVSL for a great readable update of the GitHub site. I stumbled onto it again in looking for more information on the “A3 variation” of the H5N1 2.3.4.4b virus described above, which was initially unfamiliar to me. According to GitHub - USDA-VS/GenoFLU: Influenza data pipeline:

The current “D” genotypes represent reassortants of GenoFlu A3 that emerged in the late fall/winter of 2024 (Figure 1 and Table 1). Genotype D1.1, a four gene reassortant of A3 with North American genes, including N1, replaced previous B3 genotypes by late 2024 and is currently the most frequently detected genotype since the start of this event. Circulation of genotype A3 remained limited to the Pacific flyway until late fall and winter of 2024, when A3 and the “D” genotypes expanded eastward, affecting wild birds, poultry, and wild mammals across all four migratory flyways.

In reviewing the GitHub genotype reference table, it appears that A3 produces long lists of “children” isolates - over 60 “minor” genotypes, some of which may become successful enough to gain “D-lettered” status. We’ll see if A3 itself or a D-descendent becomes a “King Kong” in marine mammals…like D1.1 has done in domestic poultry and wildlife currently.

So more to come on the phylogeny of these viruses, as well as what mammalian adaptation SNPs may arise as H5N1 likely replicates within the marine mammal populations on the Pacific Coast. Will it spill back into avian species? Into other marine or shore mammals? What is the human and companion animal risk?

Stay tuned.

John

Highly Pathogenic Avian Influenza Detected in a Kent County Commercial Flock

The confirmation of the turkey flock infection from NVSL clarified the picture; however, this west-central Michigan area appears to also house a number of large egg layer facilities which also remain at risk from this development. HPAI is active in the county and many other poultry dense areas currently.

Stay tuned for further reports - the virus is on the move and indiscriminate. Infection has been especially active again about 100 miles south in Northen Indiana in duck and smaller private layer flocks. I’ll provide a better picture (under development) of these cases and the really dire situation these smaller producers face as it appears that some of their newly repopulated flocks may well be re-breaking before they can even return to full production. “Carrying on” with current tools is not a viable option!

John

This is just unfolding, but it is highly suggestive of area spread within the egg layer industry in SE Wisconsin. Recall that a large Daybreak Farms site housing 1.2 million birds in the midst of restocking was depopulated last week- Overnight - Wisconsin Layer Reinfected by H5N1, while Southern Indiana Layer Flock Quarantined. It’s too early to know the bird count on the newly infected farms, if layers are indeed involved as the infected sites.

Stay tuned.

John

Evening update: 3.1 million layers affected in 2 Daybreak Farms flocks

'We've seen this before': Bird flu again hits Wisconsin poultry farms - WPR

(Note: these numbers are already out of date, due to delays in publishing on my part…I plan to run another follow-up after the February totals are in from NVSL, by the end of next week)

February is already the highest mortality month, courtesy of layers in Pennsylvania for the most part. Flock counts peaked earlier in November-December, due to the rash of northern Indiana duck and layer cases (smaller flocks).

Here is a state-by-state break-down; Indiana still leads in number of cases per state by a wide margin, but Pennsylvania has lost the most birds:

• Indiana has 25% of the cases, but only about 6% of the national bird mortality

• Pennsylvania represents 38% of the losses, mostly in the past 3 weeks with multiple large layer house infections. Large layer infections have a disproportionate effect on state level mortality (e.g. Wisconsin)

• 41 states in total have been infected, 31 with commercial and/or backyard and 10 with backyard flocks only

Pennsylvania has been the prominent outbreak state since January 1st, as northern Indiana finally exhausted new infection sites in the local 3 county area.

Here are the Pennsylvania infections since January 1st, 2026, derived from the published NVSL line list:

This has certainly finally caught the attention of politicians in Pennsylvania: Gov Shapiro and Secretary Redding Host Roundtable on HPAI | Commonwealth of Pennsylvania. This press release refers to an even larger bird death toll of 7.6 million, perhaps reflecting NAHLN-provisionally positive flocks not yet confirmed at NVSL.

The scope and power of this outbreak in such a poultry dense area was predictable after the initial large egg site outbreak, as I repeatedly pointed out:

1/29/2026: Bulletin: First 2026 HPAI Million Bird+ Layer Infection Reported in Lancaster County PA

2/3/2026: Korslund-LinkedIn-Lancaster County (2nd layer- Lancaster County “in trouble”)

2/17/2026: More Egg Layers Break Over Weekend in PA (more layers - full scale multi-county out-break)

I’m not trying to be a “know-it-all” here; however, we are nearly a month into this with 7.5+ million depopulated birds and the Governor is finally pulling all the stops. I have no idea of where this ultimately ends; weather will play some role; as will biosecurity compliance and plain old luck, of course.

The most concerning trend in Pennsylvania right now is the epi curve, with 12 cases in the past week alone (11 Lancaster County plus one in Dauphin):

The slope of the epi curve is just beginning to bend upward, with a denominator of over 10,000 poultry farms in Lancaster County housing 26 million hens and large populations of broilers and turkeys according to 2022 Ag Census Data. The HPAI fire has nearly unlimited kindling for sustained spread in the near term. (Note: the NVSL line list as of 2/28/2026 only shows one additional PA case in broilers on 2/24 for the current week; however, NVSL confirmation dates are not always current on the web site, especially over weekends.)

This same runaway H5N1 outbreak situation occurred late last year in Northern Indiana (with nearly 90 cases) and early in 2025 in East Central Indiana and West Central Ohio. Our current surveillance, detection, response, and elimination processes have repeatedly been no match for the spread of this virus in poultry dense areas during seasonally high- risk periods (fall-winter-early spring).

Upping our Bio-surveillance Capabilities

I and many others have repeatedly written about our time-to-detection deficiencies for HPAI and other highly infectious high consequence viral diseases with significant preclinical shedding periods. Preclinical shedding allows the virus to repeatedly gain a foothold with further spread in new areas prior to official diagnosis based on central lab PCR testing of animals showing clinical signs of infection.

An extensive review of multiple sensing modalities now available and/or under development for diagnosis of HPAI was released last week in npj Biosensing:

Multimodal sensing technologies for HPAI biosurveillance in poultry production systems | npj Biosensing

The introduction states:

This review outlines the molecular pathobiology and transmission kinetics of contemporary HPAI strains and evaluates diagnostic bottlenecks. Then, we explore how molecular amplification, electrochemical detection, and acoustic anomaly analysis can be combined into a single approach for in situ disease recognition. Finally, we describe how behavioral and physiological signal integration can enhance biosensor accuracy and support adaptive One Health biosurveillance systems for anticipatory and scalable field responses.

…Yet conventional surveillance approaches, which rely on clinical signs or periodic laboratory sampling, are hampered by significant logistical and statistical limitations. Sampling a statistically representative subset of a commercial flock of tens of thousands of birds is logistically challenging, and the inherent delays in sample transport and laboratory processing (often > 24 h) create a critical window for viral spread¹⁹. In addition, existing surveillance often fails to capture rapidly fluctuating infection dynamics or low-prevalence carriers, meaning early-stage outbreaks can be missed entirely. Environmental persistence of pathogens, such as virus contamination on surfaces or in dust, further complicates detection, as these reservoirs are rarely sampled in routine protocols. Given the increasing complexity of disease emergence patterns at the animal–human–environment interface, there is a need to move beyond static, protocol-based models toward dynamic, real-time monitoring systems capable of complementing standard biosecurity measures.

Real-time PCR (qPCR)

During the 2022 U.S. outbreak, confirmatory qPCR results frequently required 48–72 h after collection, by which time the virus had already spread within or between flocks; similar bottlenecks were documented in Europe during peak outbreak periods⁵⁵. Given that HPAI can cause flock mortality reaching 100% within 48 h of infection, such delays severely constrain outbreak response. These limitations highlight the urgent need for rapid, low-cost, and portable diagnostic methods—such as isothermal amplification or CRISPR-based assays—that can complement qPCR by enabling decentralized, on-site detection during fast-moving outbreaks.

Isothermal amplification

Isothermal nucleic acid amplification techniques, such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA), provide thermocycler-independent alternatives to qPCR by enabling nucleic acid amplification at constant temperatures (37–65 °C)⁵⁶. These assays target influenza gene segments (e.g., HA, NP, M) and support diverse detection modalities, including colorimetric, turbidity, fluorescence, and even lateral flow-based or smartphone-compatible readouts. With reaction times of 30–60 min and detection thresholds ranging from 10 to 100 RNA copies per reaction, they offer rapid, portable diagnostics well-suited for on-farm deployment, often using minimal equipment such as heat blocks or handheld devices with lyophilized reagents⁵⁷. Relative to qPCR, isothermal assays generally demonstrate reduced sensitivity, limited quantitative resolution, and higher susceptibility to nonspecific amplification or contamination, though they may tolerate crude samples with less processing. Integration with CRISPR–Cas systems, microfluidic cartridges, and multiplexed detection strategies is being actively pursued to overcome these limitations and enhance specificity⁵⁸. While isothermal platforms are highly promising for on-farm use, their most effective role may be as a complementary component within a multimodal surveillance framework that balances speed, accessibility, and diagnostic robustness during HPAI outbreaks.

CRISPR-cas12a-based assays

CRISPR-Cas12a–based diagnostics represent an emergent class of programmable nucleic acid detection systems with exceptional analytical specificity and on-farm use⁵⁹. Functionally coupled with isothermal amplification platforms such as RT-RPA or RT-LAMP, these assays enable sequence-guided detection of AIV gene segments (e.g., HA, NP) with sensitivities approaching qPCR⁶⁰. Upon target recognition, Cas12a undergoes conformational activation and triggers collateral trans-cleavage of labeled reporter oligonucleotides, producing signals detectable by fluorescence, paper-based lateral flow strips, or smartphone-integrated readouts⁵⁹. With time-to-result typically under 60 min and detection thresholds as low as 2 copies/µL, CRISPR platforms combine rapid turnaround with near-gold-standard sensitivity. Key advantages include modular programmability—allowing rapid reconfiguration to track emergent genotypes, point mutations, or antiviral resistance loci—and compatibility with low-cost, decentralized testing formats⁶¹. However, current implementations still require pre-amplification, careful contamination control, and stable reagent formulations, which limit widespread field deployment. Ongoing advances in one-pot chemistries, lyophilized reagents, and cartridge-based integration are expected to overcome these barriers. Within an HPAI surveillance framework, CRISPR-Cas12a offers a promising bridge between laboratory-grade sensitivity and true on-farm usability.

Serological tools

Serological assays are essential components of avian influenza virus (AIV) surveillance, enabling retrospective exposure assessment, vaccine efficacy evaluation, and DIVA (Differentiating Infected from Vaccinated Animals) strategies^22,62. While they do not detect active infection, these tools measure host humoral responses, primarily IgM (acute phase) and IgG (long-term), against viral antigens such as HA, NA, and NP. ELISAs are widely recognized as the reference method for high-throughput, quantitative antibody detection. Strain-specific or DIVA-compatible ELISAs⁶³ targeting non-vaccine antigens (e.g., NP, M1) facilitate differentiation between vaccinated and naturally infected birds. IgM-specific ELISAs identify recent infections, while IgG-based assays inform exposure history or vaccine-induced immunity^22,64. Despite moderate turnaround times (2–3 h), their reliance on centralized laboratories and trained personnel introduces delays in sample transport and result reporting, reduces accessibility in resource-limited regions, and creates diagnostic bottlenecks during outbreak surges⁶⁵.

The hemagglutination inhibition (HI) assay remains a subtype-specific reference test, endorsed by international agencies, and quantifies neutralizing antibodies that block HA-mediated red blood cell agglutination. While inexpensive and rapid (~30 min), HI has lower sensitivity than ELISA and limited DIVA compatibility unless paired with updated antigen panels²².

Lateral Flow Immunoassays

Lateral flow immunoassays (LFAs), in contrast, are immunochromatographic strip-based assays that provide portable, low-cost, and rapid (10–20 min) detection of antibodies or viral antigens. For AIV surveillance, LFAs commonly target conserved NP-specific IgG or detect viral proteins directly from swabs, making them well-suited for on-farm testing and wildlife monitoring^66,67. However, they are qualitative, lack subtyping capability, and cannot differentiate infection timing. Antigen detection assays, including ELISA and LFA formats, enable direct identification of viral proteins (e.g., HA, NP) from poultry specimens such as oropharyngeal or cloacal swabs. Though less sensitive than molecular methods, they deliver results within 15–30 min and exhibit specificity > 90%, supporting rapid triage during outbreaks. Antigen detection platforms such as LFAs⁶⁸ provide rapid results but can experience variable sensitivity⁶⁹.

More Advanced Detection Processes

The review article goes on to describe more futuristic electrochemical and acoustic detection concepts which may have future applications for HPAI and bird health in general, beyond the scope of where this article is headed today. The technological capabilities and alternatives are rapidly developing, leaving the legal and regulatory questions yet to be considered.

Please read the entire article for much more detail, especially on some of the more exotic electrochemical and acoustic methodologies which may hold promise, especially in integrated continuous building health monitoring applications.

What is Available (or Nearly Available)

Antigen ELISA “Snap Tests” or Lateral Flow Assays are available for H5 screening in poultry flocks; however, variable sensitivity with these products has likely discouraged their routine use in routine surveillance. In my view this may partly be due to over-reliance on “negative” results when used as part of an ongoing early detection system across flocks to continuously flag for possible developing infections during high-risk periods. With repeated testing in a disciplined process, “false negatives” will soon be caught by a succeeding positive test, providing earlier detection value for the entire system versus no surveillance at all. Individual negatives mean nothing, but positives would certainly trigger official testing earlier than no system in place whatsoever. Regardless, the industry apparently has not embraced currently approved ELISA LFA’s as sufficiently sensitive or cost-effective for use in routine HPAI screening of asymptomatic or pooled poultry mortalities or environmental samples.

However, there are new technologies and refinements available now or under development that will aid in preclinical viral diagnostics and thus provide better opportunities for interrupting transmission cycles.

Alveo Technologies

The following link features a branded product that is currently under licensure review by USDA for possible domestic use in yet to be prescribed formats. This is a kit-based LAMP technology, linked to the web for connectivity for reporting results to appropriate parties. The products would not be utilized as an official test; rather it’s use would be for rapid screening of multiple samples in the field to prioritize confirmatory testing of non-negative screened flocks. The following link feeds to a real-life example of a use case in Europe for HPAI: Alveo Technologies The Real Cost In Highly Pathogenic Avian Influenza

I don’t personally endorse products; however, I commend Alveo for aggressively moving this product towards licensure. I hope it can officially be licensed with its use encouraged by industry, state, and federal regulatory officials to signal possible field infections 72 hours or more earlier than is currently possible with clinical signs-based sampling and shipping for PCR-based official testing.

Barnwell Bio

Another player in H1N1 diagnostics (among many other agents) is: Barnwell Bio

This company works with individual farms in developing non-invasive barn environmental sampling plans for tailored whole meta-genomic sequencing of emerging or endemic disease agents of concern.

Environmental sampling and next generation sequencing (non-official testing) of environmental samples for multiple agents would likely not fall under existing regulatory authorities unless it led to scientific suspicion of the presence of a reportable disease via sequence evidence. If a highly pathogenic influenza (including H5N1) is uncovered through environmental sampling and metagenomic sequencing processes on a farm, owners and veterinarians would be responsible for contacting regulatory officials to report the results for official testing via existing program standards.

Issues will undoubtedly develop regarding sequences derived and possibly reported from environmental samples via NGS, versus official diagnostic sequences later reported by NVSL. There will be great temptations by regulators to suppress “unofficial” results via one route or another. I’d argue that required full and early disclosure (reporting) is the only sustainable option, given the fungibility of the technology. We’ll see how this all develops…

BASE₂BIO

I had the opportunity to listen to a webinar on 2/16/2026 by Claudio L. Afonso, with a link at the following site:

UGA Poultry Science & PDRC Avian Seminar Series - University of Georgia Kaltura

This webinar provided background information regarding the promise of next generation sequencing as a transformative diagnostic tool and a new commercial service for both researchers and producers now being offered by this company:

BASE₂BIO provides next-generation sequencing and other bioinformatics data analysis services, as well as full-service project consultation, to researchers, producers, and animal health specialists. We have experience in a wide range of areas, including pathogen genomics and eukaryotic genomics and proteomics. We can help you manage and analyze your second- and n^th-generation sequencing data and provide custom solutions to fit the needs of your research.

Much of the presentation found on the link above is beyond my retirement “pay grade”; my understanding is that the company works with farms and consultants to analyze “random short-read sequencing” (Oxford Nanopore) data for next generation genomic analysis.

Once again, the technology and its capabilities are outracing regulators’ abilities to manage information release “in the public’s interest.” The key goal must be to keep the information release on a level field for all, not slowed for the comfort levels of governing bodies, regulators, and industry stakeholders.

Summary

I’m sure there are other promising hardware, services and data services pipelines on the horizon - these are 3 that I have had the opportunity recently to hear more about. I am confident that other commercial screening products and concepts now under development will be available soon to further foster innovation, drop costs, and add flexibility to field-based preclinical sampling and near-the-field next generation diagnostics and sequencing capabilities.

Surveillance experts must aid in developing systemic high-risk sampling and pooling protocols for use as repetitive cost-effective screening protocols for high-value surveillance targets. The challenge is to get potential H5N1 genomic material from animals and the environment into the devices and sequencers before the barns have dying birds!

AS importantly, we need those sequences into the hands of our phylogenetic bio-informaticists much closer to real time at volume and representativeness levels that are useful for their analyses! Diagnostic lag times are critical; however, phylogenetic analytical lag times are even more important as our experts attempt to assess pandemic risks for viral mutations and reassortments.

While official testing will always be a legal regulatory function by necessity, much of the supporting work related to surveillance, viral characterization, and analysis is begging to be accelerated, deregulated and democratized to open the information flow and speed responses. We now have collection and characterization tools adapting to the speed of the virus, if we choose to embrace them. The real payoffs in our advances lie beyond our regulatory processes. Let’s make sure that our regulators, legal authorities, and industry advocates vocally support diagnostic innovation and transparency in a positive way to allow our technological advances to keep up with H5N1!

John

Bird flu has been detected in a poultry flock owned by the egg producer Daybreak Foods in Jefferson County, the third time in six months the virus has been found in its birds there, according to the Wisconsin Department of Agriculture, Trade and Consumer Protection.

The facility, located in the town of Palmyra in between Madison and Milwaukee, has been quarantined to limit movement of poultry products, and birds on the farm will be killed to prevent spread of the disease, according to the state agency. The U.S. Department of Agriculture is working with the state to contain the virus.

The same Daybreak Foods location was released from quarantine in November, after bird flu was reported twice last fall in the company’s Jefferson County flocks, according to a spokesperson for the state’s agriculture department. One of the culled flocks then had more than 3 million birds.

Crawford County commercial egg farm quarantined after highly pathogenic avian influenza detection - Dubois County Free Press, Inc.

A commercial egg-laying operation in Crawford County with 49,727 birds is under quarantine after testing positive for highly pathogenic avian influenza, state officials announced 27 February 2026.

The detection triggered active control and surveillance zones spanning portions of Crawford, Dubois, and Perry counties in Indiana. A 10-kilometer control area affects portions of Crawford and Dubois counties, while a 20-kilometer surveillance zone extends into Perry County…

Other mammalian species, including humans (though rare), dairy cattle and wildlife, have also been diagnosed with the virus. The current, ongoing HPAI event is the United States’ largest animal health emergency in history…

BOAH staff will reach out to flock owners within surveillance zones to offer testing of nearby flocks to verify the virus has not spread in the area. USDA Wildlife Services and the Indiana Department of Natural Resources are assisting with surveillance of wild birds in and near the control areas.

Indiana Grade A dairy farms in control areas will be tested for HPAI. Lactating dairy cattle must have a negative test before interstate movement under a federal order, and USDA has expanded surveillance through testing milk at the farm or processor level to establish the health status of herds and states…

Finally, an infection was also confirmed in Pottawatomie County Kansas on February 24th in a 24,000-hen commercial breeding facility by NVSL. The relief we have seen in H5N1 layer losses may have been a temporary phenomenon and not a managed trend with this widespread extremely infectious virus.

I have another more dated column related to Pennsylvania and case count updates almost completed but wanted to get this breaking information out for your review. It’s really hard to keep up. As the USDA likes to tout- The current, ongoing HPAI event is the United States’ (and world’s) largest animal health emergency in history…

John

3 Layer breaks over the weekend in SE Pennsylvania significantly accelerated their HPAI issues over the weekend, with over 5.5 million birds now affected, plus the count pending on another table egg layer in Dauphin County. The affected area remains in SE PA, but the outbreak control and surveillance areas have significantly increased with the new outbreaks:

Once again, here is a reference to an older column describing livestock concentration in this part of the Keystone State:

Bulletin: First 2026 HPAI Million Bird+ Layer Infection Reported in Lancaster County PA

It’s likely safe to say that H5 is not finished with poultry in PA, and the state might want to keep an eye on bulk milk samples and swine herds in the affected area as well. Cats and people are a given, if officials choose to proactively test them! Wildlife? Of course!! And can we share sequences please, Pennsylvania?

John

However, in the past 15-20 years or so we’ve fell into a self-imposed crisis here in the U.S. and worldwide resulting from a confluence of intellectual hubris and selfishness in the “leadership” class combined with desperation and envy in the “followership”, resulting in a crisis in effective shared democratic governance. We’ve come to the point where revenge and scoring-settling is now more valued in many circles than even short-term societal gains. Solving this woeful state of affairs is beyond my skillsets but look at this example!

Who would have ever thought that the current Secretary of Health and Human Services (a nephew of a beloved assassinated president no less) would say the following:

The off-hand drug abuse admission is troubling enough; just as troubling is that the United States Health and Human Services Cabinet Secretary was attacking a pandemic response public health guideline (social distancing) while minimizing SARS-CoV-2 infection risk in such a flippant way. We can agree that lockdowns in some situations may have been excessive given what we know now, but maybe not, given what we knew then? Never trust a know-it-all medical professional, let alone one who is actually a trial lawyer posing as a pandemic expert!

Even more troubling than Kennedy’s lack of thoughtfulness on pandemic policy in the face of unknowns is his pure malignant ignorance related to public health and widespread disease (pandemic) threats in general. He apparently fully believes microbial threats can be kept at bay with “MAHA principles” alone. Thus the new edict for NAIAD strategic planning:

Staff members at the United States’s premier infectious-disease research institute have been instructed to remove the words “biodefense” and “pandemic preparedness” from the institute’s web pages, according to e-mails Nature has obtained.

The directive comes amid a broader shake-up at the US National Institute of Allergy and Infectious Diseases (NIAID), one of 27 institutes and centres at the National Institutes of Health (NIH). The NIAID is expected to deprioritize the two topics in an overhaul of its funded research projects, according to four NIAID employees who spoke to Nature on the condition of anonymity, because they are not authorized to speak to the press.

NIH director Jay Bhattacharya explained the restructure at an event with other top agency officials on 30 January. “It’s a complete transformation of [the NIAID] away from this old model” that has historically prioritized research on HIV, biodefence and pandemic preparedness, he said. The institute will focus more on basic immunology and other infectious diseases currently affecting people in the United States, he added, rather than on predicting future diseases.

About one-third of the NIAID’s US$6.6-billion budget currently funds projects involving emerging infectious diseases and biodefence. The research studies pathogens of concern and monitors their spread, and develops medical countermeasures against threats from radiation exposure, chemicals and infectious diseases.

Nahid Bhadelia, director of Boston University’s Center on Emerging Infectious Diseases in Massachusetts, says the decision to deprioritize these areas will leave people in the United States more vulnerable to pathogens that are constantly evolving in wildlife around the world and spilling into human populations, sometimes sparking outbreaks. “Just because we say we’re going to stop caring about these issues doesn’t make the issues go away — it just makes us less prepared,” she says….

To restore trust, Bhattacharya, Taubenberger and Taubenberger’s senior adviser, John Powers, outlined a “new vision” for the institute in a commentary¹ published in Nature Medicine on 16 January.

“NIAID’s work clearly neither prevented the pandemic nor prevented Americans from experiencing among the highest levels of all-cause excess mortality in the developed world during that time,” they wrote. “Given the increasing prevalence of allergic and autoimmune disorders and the burden of common infections in the population over the past few decades, the NIAID must focus research on these conditions with a greater sense of urgency.”

It would be interesting to compare America’s (and the world’s) all-cause excess mortality during the pandemic and up to today, if the great mRNA vaccine project had not been accomplished. That is a miracle that RJK Jr and his buddies are desperately trying to reverse! With more evidence piling up that “long COVID” and other late life viral infections are a factor in dementia and other senior living morbidity-mortalities, I thank God every day as a multi-vaccinated 74-year-old that mRNA COVID vaccines beat RFK to HHS. We can only hope the mRNA technology is only sidelined for a short time by the current bureaucratic shit shows here in the U.S.

Moving On to an Ongoing Erosion in USDA Expectations…

USDA and Iowa State researchers published the following brief report, first published online February 13, 2026:

Detection of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus in cull dairy cows with underlying respiratory and systemic disease - Daniel J. Righter, Erin B. Howey, Chris L. Siepker, Eric R. Burrough, Drew R. Magstadt, Marta Mainenti, Asha Fears, Aaron D. Lehmkuhl, Gleeson Murphy, Kimberly Lehman, Mia Kim Torchetti, Suelee Robbe-Austerman, Carrie E. Schmidt, 2026

Brief report First published online February 13, 2026

Abstract

Highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus was identified in 4 cull dairy cows condemned by the U.S. Department of Agriculture because of pneumonia with accompanying systemic changes. Histologic findings were bronchopneumonia in 3 cows and embolic pneumonia and nephritis in 1 cow. In addition to detection of HPAI A(H5N1) virus by reverse-transcription real-time PCR in various formalin-fixed, paraffin-embedded tissues, influenza A virus was detected by immunohistochemistry and in situ hybridization in the pulmonary respiratory epithelium of 2 of the cows with bronchopneumonia and in renal medullary tubules of the cow with nephritis. A PCR panel screening for common bovine respiratory pathogens in the cows with bronchopneumonia revealed variable coinfections with Histophilus somni, Pasteurella multocida, Mannheimia haemolytica, Mycoplasmopsis bovis, and bovine coronavirus. We describe the distribution of HPAI A(H5N1) virus in naturally infected cows while highlighting the need for research on the roles of coinfection and immune response in influenza viral replication…

Scope of the Study

In April 2024, 3 cull dairy cows originating from a known HPAI A(H5N1) virus-positive herd were condemned by the USDA’s Food Safety and Inspection Service (FSIS) by in-plant personnel because of severe pneumonia and lesions consistent with infectious systemic disease. FSIS, the Animal and Plant Health Inspection Service’s National Veterinary Services Laboratories (NVSL; Ames, IA, USA), and the Iowa State University Veterinary Diagnostic Laboratory (ISU-VDL; Ames, IA, USA) performed ancillary testing to investigate infection with the HPAI A(H5N1) virus. Preliminary HPAI A(H5N1) virus PCR results from these 3 cows led to the implementation of an exploratory study of the distribution of HPAI A(H5N1) virus in tissues of cull dairy cows condemned during inspection. This exploratory study targeted dairy cows with an unknown HPAI A(H5N1) virus herd status that were condemned because of pneumonia, septicemia, or both by Public Health Veterinarians (PHVs) during routine inspection at U.S. slaughter facilities. From 2024 Apr 3 to 2024 May 13, PHVs sampled at least 10 condemned dairy cows at each of 11 targeted high-throughput cull cow slaughter facilities, operating in 8 states (California [2], Idaho, Michigan, Minnesota, Pennsylvania [2], South Dakota, Texas [2], Wisconsin) for a total of 111 cows.

Conclusions from Findings:

Our findings demonstrate viral replication within respiratory epithelium of the lung. The results further reveal co-infection of HPAI A(H5N1) virus with common bovine respiratory pathogens in cows with bronchopneumonia. Interestingly, the kidney of one cow with embolic bacterial nephritis had possible HPAI A(H5N1) viral replication within a few tubules of the renal medulla. Initial pathogenesis studies suggest that HPAI A(H5N1) virus is not a primary cause of respiratory disease in dairy cows.^1,6 Unfortunately, we cannot confirm whether these animals had viral mastitis, because no mammary gland tissue or milk was sampled at slaughter. Furthermore, it is unclear if a bacterial bronchopneumonia developed secondary to an underlying HPAI A(H5N1) viral infection, or if damage to the lung tissue by bacterial pathogens created conditions that facilitated viral replication…

Our study is unique in that natural infection and replication of HPAI A(H5N1) virus were identified in the lungs and kidney of dairy cows brought to slaughter. Pneumonia in cows at postmortem inspection is common and often multifactorial in etiology (e.g., shipping fever). However, until recently, IAV was regarded as an unlikely contributing pathogen. Collectively, our findings raise questions about the circumstances surrounding HPAI A(H5N1) virus replication within the respiratory epithelium of the bovine lung. Can the virus cause primary pneumonia or does the virus take advantage of already diseased tissue? It also raises questions about the immune response and degree of influenza viral replication, given that most cows with shipping fever have at least some degree of immunosuppression. Finally, if replication of HPAI A(H5N1) virus is occurring at high rates in bronchial and bronchiolar epithelial cells, is horizontal transmission via respiratory droplets possible in these herds? Although the detection of IAV by ISH and IHC in the kidney was potentially an outlier, IAV RNA has been detected in urine from a cow on an affected farm.⁸ Further studies on interactions betweenHPAI A(H5N1) virus and a host immune system that is under the stress of coinfection are warranted.

Comments:

Briefly, FSIS and NVSL in collaboration with Iowa State in April of 2024 tested 3 cull cows from a H5N1 positive herd (identified via lab markings to be from Idaho) delivered to a slaughter plant and condemned for severe pneumonia and septicemia. This was within 1 month of the initial confirmed H5N1 index case diagnosis in Texas and led to a follow-up study of 110 cull dairy cow slaughter condemnations at multiple plants in the next 40 days. One additional positive animal (from Michigan) was discovered, making a total of 4 animals included in this study.

The obvious USDA “Erosion of Expectations” which I refer to relates to the February 2026 release date of this May 2024 study! This report documents that USDA had extremely good evidence by late June 2024 that nucleic acid was found in lung tissue with a CT value as low as 16.9 (Eurasian H5 PCR) in the randomly sampled condemned cull Michigan cow:

Yet the entire agency’s unified talking points remained steadfast that this virus was “nearly exclusively” transmitted by ascending udder infections through mechanical transmission of virus or movement of people, animals, or fomites farm to farm through the balance of 2024 and into early 2025. New D1.1 genotype isolates in cows in Nevada and Arizona finally forced officials to admit likely oronasal transmissions in those cases. Prior to that Lombard, Melody et al had demonstrated H5N1 2.3.4.4b viremia in preclinical naturally infected dairy cows in California. Even prior to that, a very early study by Diehl et al had shown evidence of nasal and urine shedding in an early infected Ohio cow.

So now, more than 2 years after the H5N1 dairy outbreak began in Texas (the meandering 4-week index case diagnosis is another “eroded expectation”), USDA finally quietly released this “brief report” showing awareness nearly from the start that the course of infection for B3.13 infection in cattle is likely quite similar to that seen in other mammalian species, with early oronasal colonization rapidly followed by lung and systemic involvement prior to the well-characterized mastitis in a portion of infected lactating dairy cows. This wider systemic infection has much broader implications for non-lactating dairy and beef cattle involvement, which was conveniently ignored in testing and movement requirement considerations.

These implications succinctly explain why the dairy and beef industries, along with state and federal regulatory agencies gravitated towards the “lactogenic/mechanical viral transfer” hypothesis for cattle-origin H5N1 2.3.4.4b B3.13 as the least troubling paradigm for both the spread and control of bovine influenza A infections. Perhaps more than a conscious choice, it was the “least painful-best fit” combination of evidence that would allow ongoing trade and commerce for multiple species while maintaining some semblance of credibility with existing early prominent clinical symptoms in lactating dairy cattle. By concentrating testing, movement, and talking points on lactating dairy cattle, the disease process quickly self-perpetuated as a lactating dairy story line, with little or no serological or PCR testing pursued to mess with the narrative under USDA and state regulatory-controlled testing protocols.

However, there were increasing challenges in maintaining this “special route” hypothesis as contrary evidence continued to mount through 2024:

1. early work form Iowa State (the Magstadt Curve) demonstrated rising PCR levels in bulk tanks a week or more prior to onset of clinical mastitis in affected herds, indicating herd infection was preceding disease longer than would be expected if ascending udder infection was the instigating source of virus.

2. the virus spread quite easily back to poultry farms from infected dairies; common shared fomites (workers, clothes, and housing) biosecurity shortfalls were generated to explain the spread through non-case-controlled studies but never with smoking gun evidence.

3. explosive area dairy farm spread in Michigan, then Colorado, Idaho, and finally the grand-daddy of them all, California, was incompatible with much slower physical-mechanical contact as the most plausible means for rapid spread, especially as poultry B3.13 outbreaks continued to occur in areas with infected dairy herds.

4. selected dry cows were found to be infected with B3.13, either by sporadic ELISA testing (which was never really approved or allowed in volume), or through sporadic PCR testing, which was routinely encouraged only in milk samples. When official diagnostic testing is limited to milk from lactating cows, confirmation bias continues for milk as the sole source of infection; however, sporadic positive PCR results in other research and field sample types kept adding to doubts.

5. finally, researchers could not demonstrate consistent repeatable natural mechanism(s) for an ascending H5N1 viral flow through the teat canal “upstream” to the udder parenchyma. Experimental infection required intramammary cannulation and such infections routinely failed to generate more than localized infection within infused quarters.

The biggest research impediment to accepting traditional oronasal transmission of H5N1 in dairy cattle has been repeated failures to reproduce ongoing transmission in controlled BSL-3 experiments in adult cows. Infection has transmitted to calves via infected colostrum; however, direct lab-reproducible mechanisms have been unsuccessful, despite multiple attempts. Regardless, repeated field epidemiological and post-mortem data, such as this information finally released last week show that under some as-yet undefined conditions, H5N1 2.3.4.4b very easily and rapidly spreads between naive cattle in large groups.

Fortuitously for USDA and the cattle industries, this 2-year fable has bought them the time needed to dodge more painful regulatory measures up to what now appears to be an improved cattle H5N1 national herd immunity profile combined with today’s increasingly lax regulatory and zoonotic risk environment. More states are attaining negative NMTS as chronically infected herds apparently finally stop shedding H5N1 virus at detectable PCR levels with bulk milk testing. Both Arizona and Nevada dropped off the affected states list this past week, about a year after they had been infected with D1.1. We really have no public knowledge of how long or how many herds in these states remained positive or how the viral sequences changed over time. That information is all proprietary to the states and to USDA. Other states with formerly positive B3.13 herds have also attained official negative status. Only TX, ID, CA, and WI remain as affected states, with WI’s publicly available weekly negative testing data indicating it’s well on the road to negative status as well.

It’s important to note that the public has essentially lost access to most relevant dairy H5N1 data at this point! Positive samples in “previously infected herds” are not reported as new infections, and additions of new sequences to GenBank or GISAID from dairy herds are almost non-existent. H5N1 is now an endemic dairy infection without reporting in any remaining affected states. New cases may be reported from negative states, if the 50% lowered testing levels in provisionally negative states are frequent enough to capture transient PCR blips in herds with partial immunity. We really have no idea of the immune status of the U.S. dairy (or beef) herd, because we have not officially validated or utilized H5N1 ELISA testing in cattle for questions we’d rather not ask.

The only remaining paths for checking milk for H5N1 are regular retail milk sampling or environmental (sewage) H5 testing. The total disarray in HHS-CDC-FDA pretty much assures that any effective surveillance will not occur until the next pandemic is well upon us and the reefers are full of corpses. (How soon we forget…) If you doubt that- read this -

CDC early warning systems have gone dark. Here’s how to fill the gap | STAT

Back to the cattle, dairy herd immunity to H5N1 2.3.4.4b is likely much higher than 2 years ago, and evidence would indicate that prior B3.13 infections may protect against D1.X and vice versa. So perhaps there is enough subclinical H5N1 bouncing around in dairy herds to maintain low levels of immunity with only occasional clinical illness and mastitis with insufficient virus to trigger positive PCR samples in bulk tank sampling until it is discontinued. We really don’t know because we don’t check antibodies; further, we cut bulk testing frequency in half because every participating state is now “successful” in program implementation.

So, to summarize, USDA never had truly high expectations for controlling zoonotic Highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus in cattle; 2 years later we have successfully made the problem go away! underground! In my view we have 3 likely outcomes moving forward:

1. the virus remains a quiet ubiquitous respiratory semi-commensal in dairy and beef cattle herds;

2. the virus remains ubiquitous in cattle, but mutates to become highly infectious in other mammals - e.g. people, cats and dogs, sheep and goats, etc.; or

3. the virus mutates and/or reassorts into a newly pathogenic strain to cattle, which may or may not be infectious to poultry and other mammals.

The real kicker is that H5N1 2.3.4.4b is so dynamic world-wide right now; D1.X is everywhere in the U.S., as Nelson and Crespo-Bellido reminded us. We really have no clue regarding how this virus will interact over time with cattle or any other mammalian species moving forward.

D1.9?

I received an email from a national reporter asking for my comments on information she received from the Washington State Department of Agriculture related to a H5N1 cat mortality in Grant County collected back on January 9, 2026:

“Testing confirmed that the virus was H5N1 avian influenza, specifically clade 2.3.4.4b, genotype D1.9. This genotype is very closely related to D1.1, which has been detected recently in wild birds.

The virus is consistent with strains currently circulating in wild bird populations, and no genetic changes or adaptations were identified that would suggest increased transmissibility to humans. Wild bird exposure remains the most likely source of infection for the cat.

USDA-VS curates and maintains the H5N1 genotype naming system found at the following link: github.com/USDA-VS/GenoFLU. The last update to the nomenclature was made 1/30/2025. NVSL has apparently updated Genotype naming conventions in the past 1+ years but has not had time to publicly update GitHub to reflect the naming conventions.

I feel badly for NVSL in dealing with the workload pressures they must feel with the onslaught of avian influenza samples they handle under current testing protocols. I’d refer you back to Nelson’s and Bellido’s paper: Emergence of D1.1 reassortant H5N1 avian influenza viruses in North America

Figure 1. H5N1 genotype D1.1 samples from North America, 2024-2025.

D1.1 is a monster right now! Look at the lower right corner of the table above to see all the sequences which cannot be analyzed because NVSL has been unable to curate the data for GenBank-GISAID! This was through about August 2025. We must be much further behind with the avalanche of cases since September 1, 2025, in poultry, wild birds, and mammals reported.

H5N1 is a “reportable disease” with legal testing limited to NVSL for non-human samples. The entire scientific community depends upon NVSL for access to sequences and metadata for analysis of U.S. viral isolates. Time and manpower are obviously always in short supply; however, those excuses wear thin when it comes to higher volume data and software automation processes, which could be applied if open access choices were prioritized.

Most people accept that some metadata should be withheld / masked to protect markets and business interests for trade sensitive commodities. However, having served in USDA-APHIS-VS for too many years, I strongly argue that this modification is abused all too often to “lock up” data for all sorts of other more dubious reasons, often not openly stated.

A person who shall remain unnamed sent me the following quote, which is right on target: “There’s absolutely no reason why the wildlife H5N1 and companion animal sequence data shouldn’t go straight to GenBank. There is no sensitive livestock/business concern there. Totally bonkers.”

Regardless, nothing is going to change tomorrow at VS-NVSL, any more than policies will change before the elections at HHS-CDC-FDA. Governmental data access issues are complex and fraught with hidden agendas. Thinking that unmonitored preclinical disease surveillance and environmental sampling for HPAI are slam dunks because they make so much sense haven’t yet dealt with the realities of dealing with the “system”.

Information yearns to be free, but those who control it know its value!

When I get discouraged, I go back to my roots for perspective and inspiration, today from the Apostle Paul:

We MUST bend our thoughts towards the lovely - at our roots, we are love!

And one more bit of inspiration which I had never seen before, but which I find brilliant; from a brilliant man whose intellect has saved more lives than RFK Jr. will ever snuff out through his brain parasite and cocaine-induced ignorance…

Let us all evolve onward!

John

Here is an English translation of the Dutch government’s announcement from last Friday: Antibodies to bird flu virus found in dairy cow

News item | 23-01-2026 | 19:01

Avian influenza antibodies have been detected in a dairy cow at a dairy farm in the municipality of Noardeast-Fryslân, province of Friesland. No evidence of active viral circulation of avian influenza among the dairy cows on this farm has been found. There are also no signs of avian influenza spreading to other dairy farms.

On December 24, 2025, the Netherlands Food and Consumer Product Safety Authority (NVWA) received a report of two sick cats. One of these cats tested positive for avian influenza and died two days later (see the letter to Parliament here). Following this report, the NVWA conducted source and contact tracing. This investigation revealed that the cat came from a dairy farm.

On January 15th, the dairy cattle on that farm were screened with a random sample. There were no sick animals present at that time. Analysis of the milk samples by Wageningen Bioveterinary Research revealed that no active virus was present. The presence of antibodies was also tested, which were found in the milk samples from one cow. This indicates a previous infection with the virus in that cow.

The Netherlands Food and Consumer Product Safety Authority (NVWA) visited the farm again on January 22nd. Blood and milk samples were taken from all cattle present. These showed that there was no avian influenza virus on the farm. The results of the antibody tests are expected next week. This will tell us whether more animals have come into contact with the virus. Other mammals on the farm, such as dogs, cats, and horses, are currently and have not shown any symptoms. The people on the farm and the veterinarian are being tested by the Municipal Health Service (GGD).

As far as we know, antibodies against avian influenza have not previously been demonstrated in dairy cattle in Europe. However, there have been numerous avian influenza outbreaks among dairy cattle in the United States. Individual infection of a dairy cow with the avian influenza virus can occur. It is important to know whether this leads to spread within and between farms. There is no evidence that this has occurred.

That information is intriguing on its own; however, Michael tracked down and translated additional information as reported in his Saturday blog, from a letter from the MOA to Parliament, and a separate clarification note/addendum to that letter.

Below you’ll find some translated excerpts from that letter, where we find that the cow in question was sick with mastitis and respiratory symptoms in December, and that 5 PCR tests must be repeated due to errors in the initial testing.

On December 24, 2025, the Netherlands Food and Consumer Product Safety Authority (NVWA) received a report of two sick cats. One of these cats tested positive for avian influenza. The cat in question died on December 26, 2025. The second cat tested negative and has fully recovered. I informed your House of this in my letter of January 13, 2025, with Parliamentary document 28807, no. 322. Following this report, the Netherlands Food and Consumer Product Safety Authority (NVWA) conducted source and contact tracing. This revealed a relevant contact with a dairy farm; the cat in question originated from this dairy farm.

On January 15th, the dairy cattle on this farm were screened. Milk samples were taken from several of the cows present, and a sample was also taken from the bulk milk. At the time of sampling, no animals showing symptoms of illness were present on the farm. The samples were sent to Wageningen Bioveterinary Research (WBVR) for analysis. The results of the PCR tests, which detect the virus in milk, were negative for both the individual samples and the bulk milk sample. This confirmed that no virus was present in the dairy cattle on the farm,

In addition, the samples were tested for the presence of antibodies. On January 20, the WBVR reported that one cow had antibodies against H5N1 avian influenza. The presence of antibodies indicates a previous infection with the virus. The cow in question had suffered from mastitis and respiratory problems in December.

These are symptoms that can be observed in a dairy cow infected with avian influenza. At the time of sampling, this cow had recovered.

Following this positive antibody test, the NVWA (Netherlands Food and Consumer Product Safety Authority) revisited the farm on January 22nd. During this visit, blood and milk samples were taken from all cattle present. A bulk milk sample was also taken again. Today, January 23, 2026, the PCR results of these tests were received.

All but five samples tested negative for individual PCR tests. The bulk milk was also PCR negative. The five remaining individual milk samples resulted in a test error in the laboratory and will be retested this weekend. Based on the PCR results available so far, from last week and today, there is no indication of active avian influenza virus circulation among the dairy cattle on the farm. The results of the antibody tests are expected next week. This way we know whether more animals have been in contact with the virus. Other mammals on the farm, such as dogs, cats and horses, have no symptoms at the moment and in the past period. The people on the farm and the veterinarian are tested by the GGD. The final five PCR results will be available this weekend. If these unexpectedly result in a positive outcome, I will inform Parliament immediately.

“Immediately” turned out to be during discussions last Friday (January 30th) in the Dutch Parliament as reported here (via Google translation):

Five cows with antibodies against bird flu in Noardeast-Fryslân - Omrop Fryslân

At the dairy farm in Noardeast-Fryslân, where it was found last week that a cow had antibodies against bird flu, another four cows have been in contact with the virus.

This is what outgoing Minister Wiersma told the House of Representatives tonight in a debate on zoonoses and animal diseases. On (last) Friday it became clear that one cow had antibodies against the bird flu virus H5N1, which indicates that that cow has been infected with the virus. After that, the NVWA (Dutch Food and Consumer Product Safety Authority) took samples from all cows on the farm to test them for antibodies. “Now it appears, and this is new information, that antibodies have been found in five different cows,” Wiersma said in the House. She did say that there is currently no bird flu virus active on the farm. (Note from John: this would indicate that the 5 PCR samples retested were declared as negative status)

Exposed by sick cat (John’s comment- published header totally backwards! Cows’ milk likely exposed the cat)

That there has been bird flu on the dairy farm in Noardeast-Fryslân became clear after the NVWA received a report about two sick cats. One of these cats tested positive for bird flu and died two days later. It turned out that the cat came from the dairy farm in Noardeast-Fryslân. The dairy cattle on that farm were then examined. Initially, that study showed that one cow had antibodies, but after additional research it now appears to be a total of five.

The people on the farm who are exposed to the cows and the sick cat all test negative for the virus, says Wiersma.

For the first time in Europe

It was the first time in Europe that antibodies against bird flu were found in dairy cattle. In the United States, this has happened before.

The risk that the bird flu virus H5N1 that is prevalent in Europe will spread from animals to humans is very small, according to the RIVM. The risk of people getting bird flu from eating pork, eggs or beef, or through dairy products, is also very small. The milk is pasteurized and with that the virus, if it is already in the milk, dies.

Member of Parliament Laura Bromet (GroenLinks-PvdA) asked Wiersma whether it is safe to drink raw milk from other companies. “I wouldn’t necessarily say that that milk is unsafe,” was Wiersma’s answer. She added that she wants to ask for more clarity from experts next week.

Time-out here! Let’s follow the timeline:

• 12/24 - 2 sick cats reported

• 12/26 - 1 cat died and diagnosed with H5N1 avian influenza infection, other cat negative and recovered (No follow-up to farm at this point! Incomplete clinical history taken? Dairy exposure not questioned or not admitted?)

• 1/13 - disclosure of H5N1 feline infection/death to parliament - genotype not disclosed (and still not shared to my knowledge); parliament likely asked “how was the cat infected-which prompted formal investigation?

• 1/14? - cats were discovered (or admitted) via formal traceback to originate from a dairy farm in Friesland

• 1/15 - epidemiological investigation and testing of “several” cows and bulk tank at dairy farm; no virus confirmed in samples tested; other animals on farm (dogs, cats, horses) “did not display clinical illness” and were not tested via PCR or for antibodies. No testing of any peridomestic species done or at least not disclosed at this time. No discussion of poultry or wild bird morbidity/mortality in the immediate area. One of how many? samples taken was positive by ELISA serological testing.

• 1/22 - farm revisited - blood and milk samples taken from all (x no.?) lactating cattle on the farm (non-lactating not discussed); all were PCR negative, except for 5 requiring retesting due to testing errors. Serological results on all serum samples collected will be released this week (1/26/2026).

• 1/26 - Q and A in parliament as reported above reported 5 positive ELISA results, but negative viral antigen results in cattle and negative H5N1 titer results in people and the other sick cat. Experts will be responding with more formal risk assessments regarding H5N1 in raw dairy milk in NL next week.

The world has had the benefit of watching the U.S. struggle with H5N1 2.3.4.4b B3.13 and the later D1.1 in dairy cattle, birds, and mammals including cats for nearly 2 years. Despite the obvious lessons learned most stakeholders, domestic and foreign, continue to operate in the “see no evil, hear no evil, speak no evil” mode regarding H5N1 interspecies spillovers and onward transmission into livestock on their local turfs!

My father used to say that the worst way to dock an animal’s tail, if it must be done, is repeatedly, one inch at a time, which is how the Dutch government has chosen to disclose this whole situation! However, this approach to handling public relations is all too typical in every burgeoning outbreak, sacrificing potential longer-term credibility losses for short-term issue minimization in the hope that the worst inferences will somehow be avoided in an effort to avoid panic.

It’s important to note that much remains to be determined on this case! We lack the following information:

1. explanation as to why a more formal investigative process was not initiated at the time of initial diagnosis of H5N1 in the cat in late-December, which would have allowed much timelier testing of the dairy herd.

2. the ELISA results of the whole herd serological test drawn on January 22nd. 5 out of how many total tested? What about non-lactating animals? What were the readings (scale of positivity)?

3. Any serological or PCR tests performed on other domestic animal species on the farm or wildlife species associated with the farm? Additionally, any investigations of herd contact farm investigations? Did any dairy animals leave the farm during the last half of December?

4. Genotype and phylogenetic information on the H5N1 isolate from the farm cat associated with this case, along with its relationship to any wildlife or domestic poultry samples collected from cases in the area of interest and in NW Europe in general.

5. Any plans for H5 mastitis screening in dairy and/or H5 encephalitis screening in cat mortalities and other small pets in the Netherlands or elsewhere in the EU?

If the Netherlands authorities are to be fully transparent, these pieces of information are essential in adding to the narrative. They would serve as a lesson in transparency to the rest of the world in how H5N1 cross-species investigations should be conducted, in contrast to many of the weaknesses of the U.S. efforts to date.

Nontransparency Issues: Turning Back to the U.S.:

A paper was published online by Pekar, Jonathan E. et al., on January 23:

Can H5N1 avian influenza in dairy cattle be contained in the US?: Cell

Unfortunately, the material is currently behind a paywall for many of us without institutional access or willingness to pay. I obtained a full copy from a colleague with access for a close review. Although I can’t share as much as I usually would without violating possible copyright issues, I’ll summarize much of the work here to compare and contrast with some of my thoughts on the Netherlands lack of speed and transparency above.

The U.S. differs in that we have suffered thousands of dairy herd and feline H5N1 infections since April of 2024. This article provides a critique of the data available and missing for public analysis in GenBank related to both the B3.13 and D1.1 dairy herd infections. Below are somewhat low-resolution images taken from the paper which were shared in the abstract. The left one shows the B3.13 clades developing from the single spillover into TX cattle. There are some interesting pieces of information generated from that data, e.g. the entire California outbreak originated from a single introduction of an infected animal from Idaho into California in late summer 2024. Also, the large Colorado outbreak moved south into the state from Wyoming. This illustration provides a good example of how phylogeny combined with epidemiological and movement data can be utilized to inform spread analysis and improved biosecurity measures when combined with critical analyses.

The right panel illustrates some holes found in the USDA sequencing data when the authors lined up the existing state-level outbreak line lists with available sequences in GenBank through mid-November. We are missing genetic sequence data on the following reported outbreaks:

1. California in July and August of 2025 (assumed to be B3.13)

2. Arizona in February-March and July of 2025 (likely D1.1)

3. Michigan in February 2025 (genotype unknown)

4. Texas in May 2025 (genotype unknown)

We also must assume that some affected herds in the NMTS “affected” states of CA, ID, AZ, TX, and NV had ongoing “repeated” outbreaks as detected by bulk tank positive samples, leading to their states remaining “affected” status. However, we lack recent publicly shared “metadata-anchored” sequence data in these states or herds to compare with earlier isolates to assess ongoing genomic mutations in those herds.

The paper also points out the urgent need for improved cattle movement data if the spread of highly contagious diseases such as H5N1 are to be first understood and ultimately brought under control.

The following paragraphs conclude the paper and highlight the challenges we face in the U.S. currently in understanding and responding to H5N1 in dairy cattle and livestock in general:

Cattle become a new source for H5N1 spillover

Dairy farmers seek information on how to protect their animals from H5N1 but need more clarity on how the virus spreads among animals on farms as well as from farm to farm. Greater clarity on the mechanisms of disease transmission is needed in order to develop actionable guidance on how to prevent the virus from getting onto farms, spreading among cattle, or spilling over into other hosts. In multiple species, influenza is a respiratory disease that transmits between hosts by sneezing and coughing. In wild birds, influenza is shed in feces and spreads via the oral-fecal route. Influenza spreads in dairy cattle via a new medium: milk. High viral loads in the cow’s mammary glands (udders) and secreted milk facilitate transmission to milk-lapping barn cats and workers exposed to milk splashes. How milk spreads cow-to-cow is less clear. How wild birds become exposed to secreted milk is also less clear. Experimental transmission studies on live cows under stringent BSL-3 laboratory conditions are limited because they are challenging to conduct, but they have already demonstrated that cows can be infected via the mammary gland and potentially infected via contaminated milking equipment. A role for non-lactating animals, including calves, has not been ruled out, nor has respiratory transmission. Anecdotal evidence of H5N1 transmitting between dairy farms without movement of live animals raises additional questions about modes of transmission between farms. Wild birds could, in theory, spread B3.13 between farms, but additional spillovers into cattle are not visible in the phylogenetic tree. Wind gusts could potentially spread airborne viruses between neighboring farms, or fomites could travel between farms on shared vehicles or workers’ clothes or equipment. Fomite transmission could potentially explain the high frequency of B3.13 spill overs from dairy farms into poultry farms (e.g., chicken, turkey, and duck) in California, Michigan, Colorado, and elsewhere (Figure 2), but more study is needed. High B3.13 transmission and mortality in poultry farms require mass culling of all birds on the premises. As a result, lower biosecurity on dairy farms could present a threat to neighboring poultry farms that share workers and are visited by the same delivery vehicles. New biosecurity protocols are cumbersome and costly, and more scientific data are needed to help dairies identify which interventions provide the maximum benefit.

Future directions

In September2025, Nebraska became the 18th US state to report H5N1 in dairy cattle. While fewer H5N1 outbreaks were reported in US dairy cattle in 2025 compared to 2024, the detection of new D1.1 spill overs and the expansion of B3.13 into new states shows that the virus is not in retreat. Furthermore, dairies experiencing a repeat H5N1 outbreak were not (re)reported in 2025, reducing the total number of reported outbreaks in 2025 and making it difficult to gauge the duration of post infection immunity. A major question is whether a H5N1 vaccine will be licensed for US cattle as the outbreak wears on. States with ongoing B3.13 outbreaks such as California and Idaho may welcome a H5N1 vaccine to reduce disease severity in dairy cattle, but the national market remains unclear, particularly in light of potential trade implications for poultry. It is also unclear whether the current levels of surveillance can monitor the impact of vaccination on virus evolution and silent circulation. Another looming question is whether there will be major H5N1 outbreaks in cattle outside of the US. Preventing H5N1 spillover from wild birds into cattle in other countries is difficult without greater knowledge of the circumstances of spillover in the US. More data are also needed to understand the particular features of the US dairy system that sustain H5N1 transmission in dairies over the long term, including long-distance cattle movements and biosecurity. Determining how US dairy cattle become infected—including the roles of wild birds, domesticated birds, other cows, winds, fomites, flies, and other mammals in general—can inform biosecurity protocols and make dairies around the world more resilient to future outbreaks. While the NMTS represents an important step forward in active monitoring of H5N1 activity in US dairy cattle, detection does not equate to control, and successful outbreak response requires real-time infrastructure that rapidly links genetic sequence data with animal movement, symptoms, sera, and epidemiological data, supported by greater collaboration between scientists and farmers. Scientists, policy makers, producers, and other stakeholders must work together toward eradication before a rapidly changing H5N1 virus delivers its next surprise.

The Curse of Official Testing, Disease Reportability, and Widespread Animal Disease Incidence

It’s somewhat telling to look closely at the authorships of several of the recent papers discussing the lack of actionable sampling and associated data related to H5N1 in the U.S. and world-wide. Long-standing well-intentioned policies place the Federal government (USDA, in partnership with relevant state partners) in control of information generated related to sensitive “Reportable Diseases”. This reporting system generates sets of protocols requiring that all diagnostics be performed on “approved samples” collected by “official methods” through “official testing at approved labs (NAHLN and NVSL)”.

This is a workable system for disease agents with: 1) a relatively rare incidence with clear case definition; 2) highly technical diagnostic and confirmatory testing requirements; 3) single species or limited cross species susceptibility; and 4) limited wildlife disease reservoirs. With pathogenic avian-mammalian influenza (HPAI), none of these assumptions are true!

Official testing requirements ensure accuracy and precision but also add expenses and severely limit sampling volumes and turnaround times. Moreover, as shown repeatedly by recent publications such as the one referenced above, government entities consistently fail to allow timely open access to even reasonably redacted data for crucial analyses.

I believe that our friends in APHIS-VS and their state partners truly believe that the agency is being as transparent as possible, and/or that the data will be released in due time/when staff is hired to analyze it/when the paper is published/ etc. I also suspect there is a bit of the “MY DATA” syndrome involved…

The reality is that this is “everyone’s data” when it comes to solving the H5N1 production loss and zoonosis issues! The samples originate from individual owners, are collected, assayed, recorded, etc., in government facilities with taxpayer dollars. We DO owe confidentiality to individual producers, but we’re a long way from violating that with date and state or even county data in most cases. The taxpayers should expect reasonable and timely transparency within the bounds of personal confidentiality.

There is tremendous power in phylogeny paired with the epidemiology or time and space. We may need every bit of that power to stay even with H5! Every molecular epidemiologist that has an opportunity to run that next algorithm helps lay the path for the next breakthrough.

Better yet, we should recognize that H5 is truly endemic across the U.S. and elect to open up testing, sequencing, and GenBank depositions independently to all qualified diagnostic labs (with appropriate quality controls). We could quickly build mounds of data that might find those concerning mutations much faster in wildlife or livestock not currently being sequenced. Many NAHLN labs can now sequence independently, as can other research facilities. We don’t need the constraint of NVSL as an unnecessary regulatory bottleneck to adding H5 animal-sourced sequences from the U.S. to the world’s dataset. It’s a numbers game, as we slowly discovered with swine influenza sequences in the USDA Swine Influenza Surveillance Program!

It’s a game of Clue, and H5 is leaving us millions of new leads each day to investigate, if we choose to use them. We can look at subsets of the viruses now or wait at cadavers after the zoonosis has begun. The more we know and the sooner we know it and share it the better!

John

Avian Flu Diary: Netherlands: NOS.NL Reports 5 Dairy Cows Have Now Tested Positive for H5N1

Netherlands: NOS.NL Reports 5 Dairy Cows Have Now Tested Positive for H5N1 (ELISA)

#19,035

Although I have yet to find any official statement posted on a NL government website, NOS (Nederlandse Omroep Stichting) - the Netherland’s Public Broadcasting Network - is reporting that last night Agriculture Minister Femke Wiersma notified the House of Representatives that testing now reveals Five cows with antibodies against bird flu in Northeast Friesland.

This story has also been picked up by AgriHolland and BoerderiJ.

The last official statement I can find was on January 23rd (see Netherlands: NVWA Announcement on Avian Flu Antibodies Detected In Dairy Cow), after an investigation into 2 sick barn cats (1 died from H5N1) led to the detection of a single dairy cow with antibodies to HPAI.

Initial reports strongly suggested this was an isolated incident, stating `No evidence of active viral circulation of avian influenza among the dairy cows on this farm has been found. There are also no signs of avian influenza spreading to other dairy farms.‘

Despite this reassuring report, a separate letter to Parliament indicated that 5 tests came back with “errors” and would be repeated (see excerpt below).

All but five samples tested negative for individual PCR tests. The bulk milk was also PCR negative. The five remaining individual milk samples resulted in a test error in the laboratory and will be retested this weekend. Based on the PCR results available so far, from last week and today, there is no indication of active avian influenza virus circulation among the dairy cattle on the farm. The final five PCR results will be available this weekend. If these unexpectedly result in a positive outcome, I will inform Parliament immediately.

NOS quotes Minister Femke Wiersma as stating during a debate on zoonoses last night at the House of Representatives; “It now appears, and this is new information, that antibodies have been found in five different cows.”

Hopefully we’ll get more information in the hours ahead.

Every indication that this was a “classic” bird to dairy spillover that led to the fatal cat infection. Unfortunately, delayed traceback to the dairy farm didn’t allow for viral isolation from the cows; however, seroconversion indicates at least some portion of the herd was infected based on known information.

We need dairy (milk) surveillance of some sort anywhere in the world where cows (and maybe sheep and goats) are at high risk of spillover infections from H5N1 2.3.4.4b-infected wildlife.

John

Here is a map for the Pennsylvania Department of ag web site showing the location of Lancaster County in Pink: Highly Pathogenic Avian Influenza-PA Dept of Ag

Looking at the 2022 USDA Census of Agriculture data, Lancaster County is home to over half of Pennsylvania’s layers (13.7 of 26.9 million). Additionally, the county has significant broiler and turkey populations, as well as 77,000 dairy cattle (16.6% of the state’s inventory of 465,000 head).

Hopefully, this will be a “one-off” infection; however, this area just suffered a major winter storm which likely disrupted wild bird habitats, as well as complicated both biosecurity protocols and response and recovery efforts. It remains extremely cold and challenging in SE Pennsylvania currently.

We all hope for the best in a very challenging situation.

John