H5N1 2.3.4.4b Loose Ends from OR, CO, AZ and TX and More Articles

Also, some mid-year thoughts as new information is minimized by seasonal trends and lack of transparency

The July 4th weekend as a mid-year time-point is a good time to take stock of many issues, including H5N1 2.3.4.4b. Outbreaks have mercifully slowed down, with a single outbreak reported last week on an upland game bird farm in Lancaster County Pennsylvania. The is the first commercial flock infection in more than 30 days since the Arizona dairy virus-related outbreaks. On the dairy side, a herd in Arizona was reported on June 24th, after the flurry of poultry flock outbreaks in Maricopa County.

So great news, this virus is burning itself out, right? Enhanced biosecurity is eliminating the risk from confined poultry operations as envisioned by Ag Secretary Rollins. Even Colorado’s NMTS “Affected” status only lasted for one week - maybe it was just a clerical error, although I have seen no confirmation of that. 21 states are now officially “Unaffected” via the NMTS Program.

Best of all, we have no new reported human cases. As reported by Bloomberg yesterday, the US Centers for Disease Control and Prevention (CDC) has ended its emergency response for bird flu as the outbreak has abated.

The US Centers for Disease Control and Prevention ended its emergency response for bird flu as the outbreak that sickened dozens of people, spread to cattle and drove up egg prices has abated.

The emergency designation ended in the last week, according to a person familiar with the matter who wasn’t authorized to speak publicly about it.

The CDC merged its bird flu updates with those routinely reported for seasonal influenza starting on Monday and will post the number of people monitored and tested for the virus also known as H5N1 on a monthly basis, the agency said. It will no longer include infection rates found among animals on its website.

States that were among the hardest hit have also dialed back their efforts. California ended its emergency declaration in April, a spokesperson for the Department of Public Health told Bloomberg. Washington, which had 11 human cases in 2024, is also downsizing its response, state epidemiologist Scott Lindquist said.

The CDC’s emergency bird flu response was deactivated to transition back to regular program activity, according to a spokesperson for the Department of Health and Human Services. Surveillance, readiness and response for bird flu will be included with existing efforts from the CDC’s Influenza Division and other agency programs, they said.

Has the crisis ended for humans, birds, and animals? Maybe enhanced biosecurity paired with solid immunity has served to shut down new outbreaks in dairy herds, preventing ongoing chronic dairy infections with occasional viral crossover into neighboring poultry operations. Have poultry farms now upped their biosecurity sufficiently to prevent infection from fewer infected wildlife? Or are we just in a high temperature, low migration, and just plain lower seasonal risk period of time? I’d argue we should hope fervently for the former, but plan as if we’ve just been really fortunate recently. I’ll get back to more prognostications later, but first I have some issues of interest that have arisen in research or news in the past few weeks to review.

Oregon

Avian Influenza A (H5) in Wastewater, July 2024 to February 2025 | Public Health | JAMA Network Open | JAMA Network

This piece of research didn’t receive much coverage, but I wanted to point out this piece in part as a tribute to Dr. Ryan Scholz, the Oregon State Veterinarian. I have written in the past regarding my concerns with undiagnosed H5 wastewater samples in states with significant dairy populations, including Oregon. Much of this positive wastewater data was being released prior to initiation of widespread bulk milk tank testing. Positive H5 samples in sewage were problematic in that milk processing was one of multiple possible sources of H5 virus in wastewater that needed to be addressed but was often ignored.

This published paper documents that Dr. Scholz and the Oregon dairy industry began monitoring Oregon bulk tanks during a period of positive H5 sewage sampling, with all 813 bulk tank milk samples remaining negative from late November 2024 onward, eliminating dairy processing as a likely source of the viral nucleic acid in the sewage.

Sewage sampling (and environmental sampling in general) is only as useful as our ability to tie results of concern to species of interest. Both over-interpretation and under-interpretation are issues when positive H5 samples cannot initially be directly tied to animals of interest. This technology is extremely cost-effective for screening; however, any positive results must be followed up with creative further testing to determine true risk from suspected sources. Kudos to Oregon officials for taking time to write up this important work as a proof of concept for effective use of environmental sampling! One further step that would be of great value would be sequencing of positive sewage samples and stream contribution analysis to further assist in source attribution.

Colorado

In my last column I spent some time discussing Colorado’s apparent loss of “Unaffected Status” under the National Milk Testing Strategy on June 20th. However, 1 week later, it returned to “Unaffected State” status on the June 27th and July 4th, 2025, maps:

I’d welcome an explanation from the APHIS Veterinary Services National Cattle Staff or from Dr. Maggie Baldwin, CO State Veterinarian. It seems to me that a positive result would require a 2-3 week series of negative bulk tank results post investigation to justify a return to negative status; however, it’s also possible there were recording errors or other extenuating circumstances related to the single positive report. Whatever the circumstances, some transparency in explaining a 1-week positive status “blip” would be helpful.

Arizona

An article in Feedstuffs provided more details on Hickman Farms layer flock losses in Arizona in late May through early June- Hickman details ‘slow-motion wreck’ from bird flu

…Hickman said a dairy operation near his farms has been getting H5N1 HPAI infections on and off all year, and although mild for the cows, it wasn’t so for his birds. “Our chickens got sick because of the proximity to this dairy, and we just had kind of a slow-motion wreck since May 16, with farm after farm after farm after farm dying to the point that we went from 6.5 million chickens to 300,000 in a span of three weeks.”

I wrote earlier about the release of D1.1 genotype poultry sequences collected from Arizona layer flock outbreaks. To my knowledge, neither USDA nor the Arizona Department of Agriculture have ever publicly commented regarding any linkages of the dairy and poultry outbreaks. Someone with sequence access shared phylogenetic analyses of AZ dairy and poultry sequences from recent outbreaks with poultry company sources, indicating possible multiple spillovers from infected dairy herd(s) to poultry flocks. The affected company is conducting its own epidemiological investigation to better understand how this virus spread so easily between multiple flocks in such a short time.

Additionally, a new AZ dairy infection was diagnosed (likely through bulk tank testing?) on June 24, after the poultry outbreaks. It will be interesting to determine whether that virus is a likely descendent of poultry or dairy infections, i.e. does this virus show phylogenetic evidence of spill back from poultry into a dairy herd or is it just another dairy herd to dairy herd transmission?

Texas

Current TX bulk tank testing reporting has been quiet, although I continue to question the process for reporting repeated bulk tank positive samples in the 7 “Affected” states (including TX). We know that affected states continue to have bulk tank positive samples to remain “Affected”; however, it’s not clear how or if these are individually reported when they are “ongoing” infections in previously infected herds.

Michael Coston in Avian Flu Diary once again wrote an excellent column reviewing a preprint letter the Journal of Virology: Avian Flu Diary: J. Virology: Phylogenetic Analysis of H5N1 Influenza Viruses Isolated from Dairy Cattle in Texas in December 2024. Read Michael’s entire column for excellent analysis of what we’re missing in our current “surveillance programs”. I’ll return to more of those topics later; here is the link to the Journal of Virology Letter itself: Phylogenetic analysis of H5N1 influenza viruses isolated from dairy cattle in Texas in December 2024 | Journal of Virology

…Texas reported several infected herds in the spring (1) and early summer of 2024 but saw fewer outbreaks during the second half of 2024, with reported outbreaks in July and December (2). Since September 2024, almost all reported outbreaks of genotype B3.13 viruses in dairy cattle have occurred in California. Here, we characterized self-submitted samples from a farm in Texas that experienced an outbreak in December 2024. This farm had purchased dairy cattle from several states in the US. We, therefore, asked whether the December 2024 outbreak in Texas was caused by B3.13 viruses that circulated undetected in dairy cattle or other species in Texas or resulted from the introduction of B3.13 viruses from California (having the highest number of affected farms at that time) or other states.

We received 38 milk samples from the Texas A&M Veterinary Medical Diagnostic Laboratory (collected on 6 December 2024 and 8 December 2024) from which 21 viruses were isolated (Table S1). All viruses were amplified in MDCK cells and embryonated chicken eggs. The virus stocks were then sequenced on the Oxford Nanopore MinION flow cell (FLO-MIN114) using Native Barcoding Kit 96 V14 (SQK-NBD114.96). …

The isolated viruses are closely related to B3.13 viruses isolated in Texas in the summer of 2024, supported by bootstrap values of >0.7 (Fig. 1). Phylogenetic analysis of individual viral gene segments demonstrated a close relationship between B3.13 viruses isolated in July and those isolated in December (Fig. S1)… Collectively, our analysis indicates that genotype B3.13 viruses continuously circulated in Texas, even though no outbreaks were reported between July and December 2024. It is unclear if the viruses were maintained in dairy cattle (apparently healthy or undiagnosed), or if they spilled over into other species and were reintroduced into dairy cows.

It’s interesting to me that the researchers postponed using “official tests”, i.e. PCR and sequencing at NVSL on these samples, in order to allow ongoing testing outside of the Federal Order and federal laboratory system. They grew the viruses on egg stock, then diagnosed them via Oxford Nanopore MinION flow cell (next generation sequencing). I imagine they likely reported infection after diagnosis, as required by the Federal Order, but had acquired whole genome sequences in the meantime for analysis.

Under the Federal Order, sequencing normally occurs in Federal Labs after VI and official diagnosis with the information held by USDA. This alternative approach is likely a bit of a gray area and illustrates the growing challenges that Federal Officials face in maintaining total control of diagnostics and information release related to reportable disease agents in the face of availability of new technology.

If these samples had been submitted via normal channels, the positive sample metadata linked to current and historical sequence data would likely have never seen the light of day; rather they would have been filed somewhere in internal non-public TX and VS NMTS records as an “ongoing herd infection” of a previously infected TX herd. That turns out to be the case, but this published analysis rules out an imported infection and provides a wealth of information related to sequential viral mutation events. This is important information that the larger dairy and livestock community should have access to with federally funded diagnostic data. My thanks to the dairy producers, their veterinarians, Texas VMDL and the researchers involved for taking the initiative to creatively obtain sequences on voluntarily submitted samples to answer questions of great interest to the livestock community. We need more collaboration between universities and interested producers and veterinarians seeking to voluntarily answer practical questions like this.

The major lesson reinforced from this work, as well as from the Idaho “reinfections”, is that H5N1 does stick around in many herds. We don’t have sufficient published work with closed herds, measured biosecurity, and repeated serological and PCR assessments of entire herd populations to understand under what circumstances the virus has niches for survival. However, under today’s typical management conditions it seems that sufficient non-immune populations are present in dairy herds to allow ongoing infections to fester at subclinical levels in subpopulations. This is very similar to what is seen with multiple influenza strains in subpopulations of swine breeding herds and even in some wean to finish swine populations.

3 Articles Worth Reading

The first article is important, not so much for any new information, but due to the weight and influence of the list of authors in the influenza community combined with the endorsement of the AVMA: Controlling bird flu is urgent—for dairy, wildlife, poultry, pets, and people in: Journal of the American Veterinary Medical Association - Ahead of print

We represent the Centers of Excellence for Influenza Research and Response,¹ a network of academic scientists funded by the National Institute of Allergy and Infectious Diseases at the NIH. A core mission of the Centers of Excellence for Influenza Research and Response program is to carry out research to address influenza outbreaks. Our network includes virologists, immunologists, clinicians, veterinarians, epidemiologists, computational biologists, and ecologists. We know a lot about influenza, and we want to make sure that communities affected by H5N1 understand the problem. Veterinarians are central to One Health and have important roles to play in getting the message out….

H5N1 is rewriting the rules and, in so doing, presenting major challenges to the veterinary profession. Interested veterinarians may get involved more by working with their clients and researchers to understand transmission to veterinary hosts and exploring avenues to mitigate the impacts of continued H5N1 circulation. To reduce the One Health risk H5N1 presents, affected communities need to understand the problem and come together to enact the best solutions.

The second article relates to a human pandemic worst-case fear of mine, i.e. human vaccine availability in the face of an H5N1 or other novel antigen human (or animal) viral epizootic. COVID would have been much more severe than it was if we had not had mRNA vaccines near-ready for development and deployment within a year of the onset of the pandemic. Unfortunately, some of our “leaders” seem to have learned the wrong lessons from our mRNA experiences, leading to preparedness shortfalls which could be extremely costly: Moderna’s mRNA vaccine contract should be restored. Here's why | STAT

…If we don’t invest in technologies like mRNA vaccines for pandemic influenza now, once a virus starts going human-to-human, it will simply be too late. Members of Congress, regardless of party, need to get these legally appropriated funds back into the hands of Moderna — recognizing that the next pandemic could become the largest mass casualty event in American history. To let such assaults on science and good governance stand is simply a travesty this country cannot afford.

The final article is a preprint that was released just recently from Great Britain: Detection of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus in a sheep in Great Britain

…A result of this testing was the first recorded detection of clade 2.3.4.4b H5N1 HPAIV in a sheep in March 2025, identified on an infected poultry premises in Great Britain. An initial seropositive result in a single ewe triggered further investigation, confirming serological positivity across repeated sampling and the presence of viral RNA in milk samples. This detection was confined to a single animal and was likely attributable to proximity to infected poultry and a presumed heavily contaminated environment. The implications of this ruminant detection are discussed in the context of interspecies transmission and surveillance strategies.

Mid-Year Outlook:

A few weeks back I penned the following points which I’ll repeat and modify a bit today, because I think they’re more important than ever as we relax a bit with fewer active poultry and dairy cases and NO human cases as the CDC stands down its H5N1 response infrastructure. H5N1 is still out there! USDA has released 101 new wild bird detections since July 1 (HPAI Detections in Wild Birds) and 3 new wild mammals (HPAI Detections in Mammals). Many were collected earlier in the year, but the point remains that our domestic environment remains highly contaminated with H5N1 2.3.4.4b. WE also know we have ongoing infection in an unknown number of dairy herds in at least 8 “Affected” states, and likely more the 25 provisionally unaffected and non-participating NMTS states. Finally, we have no negative test information on non-dairy cattle, sheep, horses, swine, etc. We do have a growing list of deceased cats!

The future H5N1 livestock narrative is out of our hands because we choose not to control or even measure it! Unknown changes to the virus and where it attacks next will drive the ongoing narrative, with surprises amplified by our willful ignorance and unwillingness to actively look for it:

1. Poultry flocks, especially layers, are the economic pinch point. Will B3.13, D1.X or other strains modify sufficiently, so that earlier dairy herd immunity fails to attenuate re-outbreaks sufficiently to prevent B3.13 or D1.1 spill-over to neighboring layer flocks in multiple states? So far, Arizona excepted, dairy (re)infections have been relatively mild in infected herds, keeping environmental loads below levels that threaten poultry. Will that continue? Will changing environmental conditions or herd viral loads enhance odds for spillover of domestic mammalian H5N1 infections (dairy or other species) to poultry flocks?

2. Will the virus remain quiescent in beef and beef on dairy feedlots? We know nothing publicly about the H5N1 serostatus of the U.S. cattle population. Will those operations provide a transient risk to their workers or to nearby poultry flocks or swine farms?

3. When, if ever, will we perform serological and PCR testing to assess disease status in non-lactating cattle and other livestock species on infected dairy farms?

4. The same question applies to other mammalian domestic livestock populations near infected poultry flocks. We know this virus goes both ways (see the British sheep preprint above and remember the Oregon pigs). We are tempting fate when we ignore domestic mammals, either wildlife or domestic, in the vicinity of infected poultry flocks. Remember, it’s also possible that those livestock populations may have played a role in infecting the birds (think Arizona last month). We know infected dairy herds and wildlife are a risk. Do we know that other species are not?

5. Will the virus stay relatively harmless to people? We keep ignoring a “few” red-eyed and runny-nosed undocumented workers who are more determined than ever to avoid routine sampling (and potential ICE detention). I’ve lost hope that we will be seriously testing workplace populations in the current political environment. But what happens if we diagnose H5N1 in a dozen kids in a day care with serious pneumonia and hospitalization? Or if a worker or a family member is hospitalized with a sequenced H5N1 isolate containing significant concerning zoonotic signatures? With early warning inoperative, the consequences of such cases “out of the blue” will be much higher.

6. Pigs and reassortment are a risky mix we are failing to address effectively. If the industry really is serious about surveillance, they need to commit to targeted herd surveillance surrounding positive dairy and poultry sites with whole genome sequencing of ALL matrix-positive swine samples (no prescreening with H1/H3 subtyping). Additionally, what happens if/when we find H5N1 positive pigs despite not targeting them? We may accidently find a “non-H1/H3” isolate at a county fair with sick kids this summer. What then? USDA, state officials, and the industry are overdue in making joint plans to address these contingencies. Finally, what ever happened to ARS feral swine studies and publication of H5N1 B2.3.4.4b inoculation work?

7. Will we continue to intentionally not test wildlife and environmental samples in real time for H5, while claiming we understand good biosecurity and exclusion principles? We now have a virus that is more or less endemic in our wildlife; yet we refuse to utilize our testing capabilities for risk assessments and real-time monitoring in high-risk areas, e.g. marshes near poultry farms. Finding an admitted endemic virus in the environment near production sites should not affect trade status; real-time H5 environmental testing needs to be negotiated as a best practice rather than allowing a positive finding to risk trade restrictions.

There are economic and policy-related questions inhibiting application of best practices towards minimizing animal and human risks from H5 or other zoonotic or pathogenic influenza agents. Frankly, they are more difficult to solve than the scientific questions! We KNOW what we should be doing - we don’t have the political will to do it…

I haven’t touched on vaccine use; frankly we ought to be vaccinating layer chicks now for protection this winter! Protocols for regular ongoing environmental and dead bird surveillance of vaccinated flocks should be in final planning stages. If we can negotiate 40% tariffs, we can negotiate poultry vaccines…

The dairy industry should be conducting widespread serological surveys to determine prevalence, with some vaccine trials utilized in chronically infected herds to assess efficacy in lowering reinfection risk. Smart producers likely know if they have H5N1 and what it is costing them. The market will tell them whether to vaccinate.

But hey, as for the big H5N1 narrative and taking responsibility for understanding and acting upon its implications, it’s all quiet today! What, me worry? Even our workforce immigration issues are solved! Don’t expect logic like this to lead us to better H5N1 solutions in agriculture.

My best guess is that we will look back longingly at the peace and quiet of July 11th. However, I could be wrong - viral threats DO die out, and this one could, also. Just be sure to ask some swine producers how that has worked out with PRRS…or influenza for that matter…or measles in people!

John