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Discussion thread: H5N1 avian flu in US dairy cows including human cases (poultry, dairy workers) - March 24, 2024 +
H5N1 2.3.4.4b D1.3 in Ohio-Indiana Poultry Outbreak with Associated Undisclosed Human Sequence Data
Background phylogenetic work on USDA raw sequence submissions reveals a surprise unpublicized emerging avian genotype (D1.3) as a common source in the large multi-state poultry outbreak
Welcome SeniorLearner! Thank you for posting this substack essay.
I also agree with this snip:
"I don’t want to drone on. We have a relatively new zoonotic H5N1 2.3.4.4b D1.3 genotype that has killed over 19 million chickens on 84 farms in a small area in less than 2 1/2 months! It put one poultry worker in the hospital. No one has even bothered to publicly announce the new genotype to my knowledge! CDC has likely sequenced it from the hospitalized human patient yet has failed to deposit the sequence or even inform the public of its findings."
Background phylogenetic work on USDA raw sequence submissions reveals a surprise unpublicized emerging avian genotype (D1.3) as a common source in the large multi-state poultry outbreak
H5N1 2.3.4.4b D1.3 in Ohio-Indiana Poultry Outbreak with Associated Undisclosed Human Sequence Data
Background phylogenetic work on USDA raw sequence submissions reveals a surprise unpublicized emerging avian genotype (D1.3) as a common source in the large multi-state poultry outbreak
more....
Update by the CDC today addresses the above issue (among others):
Milk tested for bird flu reveals a scientific mystery
Researchers across the country are studying the results
By: Danielle Prokop - April 4, 2025 10:00 am
...
New Mexico reported nine dairy herds in Curry County tested positive last April, and began milk testing its cattle in February following the rollout of a federal program.
The most recent results from milk-testing programs revealed that while more than 95% of the 93 cow herds in the state tested negative, a small set of inconsistent positives — all from three Curry County herds infected last year — remain, according to New Mexico State Veterinarian Samantha Holeck.
Enter the mystery: The cows themselves do not test positive, nor do they demonstrate the symptoms documented in the earlier avian flu outbreak, she said, such as huge drops in milk production.
“It’s been a real challenge to try to understand how it continues to circulate in some of these herds,” Holeck said.
...
New Mexico isn’t alone in experiencing the viral fragments, said Michael Payne, a food animal veterinarian at University of California, Davis, who noted there have been reports of similar persistent positives in quarantined herds there.
“I wouldn’t diminish the importance of it being small,” Payne said. “Yes, we’re talking about low levels of virus and yes, we’re talking about cows not getting sick, but it’s important that we’re not exactly sure where it’s coming from, and that in and of itself merits examination.”
...
Poultry vaccination a possibility for combating HPAI
A vaccination for poultry could be possible to help combat avian influenza, but there are challenges to a nationwide vaccination strategy.
The U.S. Department of Agriculture (USDA) is investing significant resources to fight highly pathogenic avian influenza (HPAI) through a five-pronged strategy, including $100 million into research and development of a vaccine.
American Farm Bureau Federation Economist Bernt Nelson said the ultimate goal of any vaccination against bird flu is protecting supply chains.
“So, when we think about these vaccines, more than 30 countries have now implemented some sort of a vaccine strategy since 2005,” he said. “Historically, when countries have done this, this has caused some major trade issues. Importing countries have a concern. They don’t want to risk an imported bird spreading the virus into the local flocks or wildlife.”
In addition to trade issues, vaccines pose a logistical challenge.
“One of the biggest limiting factors of implementing a vaccine strategy to poultry is that the only vaccines available have to be injected at least two to three times, and with our egg laying flock sitting at about 375 million birds, that’s just not feasible with the labor that’s needed,” Nelson said.
Nelson noted the infections are beginning to ease.
“Kind of looking at a slowdown this time of the year when we think about what’s happening with our migratory birds, the migrations have slowed down. We’re in nesting season, so there’s a lot less bird movement, and thus we have a lot lower case load of avian influenza,” Nelson said. “That’s about normal for this time of the year. We have had one major detection in the past, you know, week or two, and that was 700,000 egg layers in South Dakota.”
...
May 7th, 2025
A vaccination for poultry could be possible to help combat avian influenza, but there are challenges to a nationwide vaccination strategy.
The U.S. Department of Agriculture (USDA) is investing significant resources to fight highly pathogenic avian influenza (HPAI) through a five-pronged strategy, including $100 million into research and development of a vaccine.
American Farm Bureau Federation Economist
The US hasn’t seen a human bird flu case in 3 months. Experts are wondering why
By MIKE STOBBE and JONEL ALECCIA
Updated 12:00 AM CDT, May 19, 2025
...
The most recent infections confirmed by the Centers for Disease Control and Prevention were in early February in Nevada, Ohio and Wyoming.
... The possible natural reason bird flu cases are down
During a call with U.S. doctors this month, one CDC official noted that there is a seasonality to bird flu: Cases peak in the fall and early winter, possibly due to the migration patterns of wild birds that are primary spreaders of the virus.
That could mean the U.S. is experiencing a natural — maybe temporary — decline in cases.
It’s unlikely that a severe human infection, requiring hospitalization, would go unnoticed, said Michael Osterholm, a University of Minnesota expert on infectious diseases.
What’s more, a patchwork system that monitors viruses in sewage and wastewater has suggested limited activity recently.
New infections are still being detected in birds and cattle, but not as frequently as several months ago.
“Given the fact that the number of animal detections has fallen according to USDA data, it’s not surprising that human cases have declined as well,” the CDC said in a statement.
Are government cuts affecting bird flu monitoring?
Dr. Gregory Gray said he wasn’t concerned about the CDC not identifying new cases in months.
“I don’t think that anybody’s hiding anything,” said Gray, an infectious disease speicialist at the University of Texas Medical Branch in Galveston.
...
May 6, 2025
Clinician Update on Human Cases of H5N1 and Influenza A Virus Surveillance
At a glance
During this COCA Call, presenters will give updates on the current situation with human cases of influenza A(H5) and CDC's surveillance and monitoring efforts for influenza A virus infections among people in the United States.
H5N1 Dairy (Re)infections and the Bifurcated World of the National Milk Testing Strategy (NMTS)
Excerpts:
I had written quite extensively last week regarding questions I had regarding all the Idaho cases. Dr. Scott Leibsle, the State Veterinarian, was kind enough to briefly e-mail me some very helpful responses to inquiries I had sent him. I’d like to summarize his honest assessments to date of what is occurring in Idaho’s 4 counties with active infection:
First, he stated that it is in reality unknown how many cases are in previously infected herds versus newly infected herds because many dairies didn’t report having symptoms a year ago when the first wave of H5N1 came through Idaho dairies. His opinion is that nearly all Idaho dairies were either exposed to or affected by H5N1 in 2024….so it’s likely that the currently affected dairies are either getting it for a second time or never got rid of it.
He stated that B3.13 the only agent involved (no D1.x has been diagnosed)...
-snip-
Ultimate infected herd outcomes are critical, because we are still operating a cooperative H5N1 dairy “control” program based on the assumption that we can “isolate and exhaust” the B3.13 virus in infected herds. Evidence from Colorado and negative NMTS states would argue that could be possible. Idaho, Texas, and California repeat infections make that prospect look extremely unlikely.
-snip-
Finally, we have building evidence that H5N1 is an area spread whole herd infection, not confined on the farm to lactating animals only, as laid out in emerging work and thought by Lombard and others (The One Health challenges and opportunities of the H5N1 outbreak in dairy cattle in the United States - Journal of Dairy Science. This work would also implicate at least potential roles for beef cattle populations as reservoirs or amplifying sites for H5N1 outbreaks. No one has conducted serological or PCR sampling to date to my knowledge in areas with coexisting large beef cattle, dairy, and poultry populations with B3.13 H5N1 outbreaks in dairy and poultry (e.g. California, Colorado, Idaho, TX). Lack of testing does not equate to lack of the possibility for such occurrences with a virus that seems to spread indiscriminately in livestock dense areas to new dairy herds and poultry flocks.
May 23, 2025 Animal Health Body Says Vaccines Needed to Protect Humans and Trade
Excerpts:
"Vaccination is a tool, it's a very good tool when it exists, but it's up to each country, region, or group of countries to identify in which case it will be useful to use it or not," Director General Emmanuelle Soubeyran told Reuters ahead of the start of WOAH's general assembly on Sunday.
Bird flu has also spread to mammals, including dairy cows in the United States, and infected hundreds of people, raising concerns it could spark a new pandemic.
Avian Influenza in Cats: Latest H5N1 Updates with Ian Gill Bemis | AAHA HPAI Recap American Animal Hospital Association
13 Jun 2025 ---------------------------
Excerpts from the video:
Beis Gil Bemis from University of Maryland, expert on avian influenza outbreaks in cat:
-Publication soon to come, currently in the works on antiviral research
-Systematic review, we found a 90% approximate case fatality rate
-We have an ongoing serosurvey in outbreak regions targeting both domestic and rural cats and while I have not tested enough samples... we have found a sero prevalence that is relatively lowso far. So combined with our data that's very preliminary and the data that we found from the serosurveys and our systematic review, it appears that this is still an emerging pathogen, that this is not endemic in cats and when you consider the case fatality rate, it appears that it is unlikely to become endemic in cats...
----------------------------- See also:
July 7, 2025
H5N1 Dairy Crisis Enters Critical Phase as Economic Losses Exceed $950 Per Infected Cow H5N1 devastates milk yield with 900kg losses per cow while 90% spread silently. Your milking parlor = ground zero. Are you prepared?
EXECUTIVE SUMMARY: The dairy industry’s traditional biosecurity playbook just became obsolete—H5N1 has rewritten the rules by turning your milking parlor into the primary disease transmission vector, not wild birds. Cornell University’s groundbreaking research reveals that infected operations face catastrophic losses averaging $950 per clinically affected cow, with total herd impacts reaching $737,500 for large-scale operations[1][2]. Mathematical modeling confirms current industry interventions have prevented only 175.2 additional outbreaks, proving our response strategies are barely scratching the surface of this evolving threat. While Europe congratulates itself on zero confirmed cases, research shows European cattle breeds possess identical susceptibility patterns to U.S. herds, with the virus’s inevitable arrival being a matter of “when,” not “if”[1]. The virus spreads with alarming stealth—90% herd exposure despite only 20% showing clinical symptoms—making traditional visual monitoring completely inadequate for early detection[3]. Canada’s proActive program has successfully prevented H5N1 entry through mandatory biosecurity integration, proving that proactive preparation works infinitely better than reactive crisis management[1]. Forward-thinking producers must immediately abandon outdated poultry-focused biosecurity models and implement “Fortress Farm” protocols before this industry-defining threat reaches their operation.
KEY TAKEAWAYS
Eliminate raw waste milk feeding immediately to prevent 50%+ mortality in farm cats and potential viral amplification—switch to pasteurized alternatives or milk replacer to break the deadliest transmission pathway that most operations ignore. This single change can prevent catastrophic spillover events that transform your farm into a multi-species disease reservoir.
Implement dedicated milking parlor biosecurity with N95 respirators, dedicated gloves per cow, and complete equipment disinfection cycles after every session—the mammary gland-centered pathogenesis means your milking equipment has become the primary cow-to-cow transmission vector, not respiratory droplets. Operations ignoring this shift face inevitable herd-wide contamination within days of introduction.
Adopt Canadian-style “closed herd” philosophy with mandatory 30-day quarantine and pre/post-movement testing for all animal introductions—mathematical models show this approach prevents the interstate spread patterns that have devastated over 959 U.S. dairy herds across 16 states. The $28,000 USDA biosecurity support per farm proves prevention costs far less than outbreak response.
Install precision monitoring systems that detect rumination and milk production declines 5-7 days before clinical diagnosis—Cornell research confirms behavioral changes precede visual symptoms, enabling isolation protocols that could prevent the 90% herd exposure rates documented in infected operations. Early detection transforms potential $737,500 losses into manageable, isolated cases.
Prioritize genetic resilience in breeding decisions as H5N1 targets your highest-producing, most genetically valuable multiparous cows disproportionately—the virus’s mammary gland tropism means superior TPI scores amplify economic vulnerability, requiring breeding programs to balance production traits with disease resistance markers. This genetic shift protects decades of genetic investment from permanent productivity compromises.
Admittedly, the number of human cases in the United States has remained stable since February (although some cases may have been missed). If an agency felt the need to temporarily stand down - I can see why this recent respite would seem the ideal time to do so.
Complicating matters, farm workers are often reluctant to come forward - even when symptomatic - due to concerns over immigration entanglements or being fired (see EID Journal: Avian Influenza A(H5N1) Virus among Dairy Cattle, Texas, USA), and farmers remain reluctant to have their herds tested.
The USDA's Dairy Herd Status Programwebsite was last updated in late June, and still shows only 111 herds (out of an est. 36,000) from 20 states enrolled in the voluntary herd monitoring program.
We've also seen sharp decline in the number of wildlife H5 detections submitted by the states to the USDA in 2025. How much of this lull is due to an actual reduction in the virus in the wild, and how much is a result of reduced testing, is unknown.
Typically - at least in temperate climes - avian flu activity diminishes sharply during the summer months, but often resurges in the fall when migratory birds resume their annual southbound migration.
While we can never know what the next migration will bring, there is a high likelihood that avian flu activity will resume in the fall, and that new genotypes may accompany that upcoming wave.
Meanwhile, H5Nx continues to spread, and evolve, around the world. Any perceived drop in H5's threat level could easily prove temporary.
Of course, H5N1 isn't guaranteed to spark the next pandemic. It has loomed large several times in the past, only to recede back into the shadows. There may even be an insurmountable `species barrier' that prevents H5 from ever spreading easily in humans (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?).
But HPAI H5 is just one of many respiratory viruses with pandemic potential. Last summer the WHO unveiled an expanded Pathogens Prioritization report, increasing the number of priority pathogens to more than 30.
Additions included 7 different influenza A subtypes (H1, H3, H3, H5, H6, H7, and H10), 5 bacterial strains that cause cholera, plague, dysentery, diarrhea and pneumonia, and several coronavirus contenders.
In terms of likelihood of emergence, H5N1 is actually fairly far down the CDC's IRAT list. Currently the CDC ranks a Chinese EA H1N1 `G4' swine virusat the very top of their list, with 3 other North American swine variant viruses scoring higher than H5N1.
All reasons why it is important to keep a wary eye on more than just HPAI H5, and why pandemic preparedness should be based on dealing with the emergence of a wide range of respiratory pathogens, rather than just focused on the influenza subtype du jour.
All medical discussions are for educational purposes. I am not a doctor, just a retired paramedic. Nothing I post should be construed as specific medical advice. If you have a medical problem, see your physician.
We need proactive surveillance, not reactive surveillance. Since the beginning of the human cases in 2022 the US has failed. Our case list includes all full and partial test positive persons. Our count is 93. And not on our list are the reported dozen or so dairy cattle workers at the beginning of the known cattle outbreaks who had respiratory and conjunctivitis systems. The probable count is most likely over 100 and does not include unknown cases. Typically in outbreaks the known cases are a fraction of the real total - especially if the illness is mild.
When the first human H5N1 case was diagnosed in 2022 we should have instituted a very aggressive program to determine the real spread in the US - testing both wild animals, domestic animals, and humans. We can not go back now. That window closed.
As this site has said many times, do not wait for any government to "save" you. Not for hurricanes, or any other threat. They are often too little, too late.
No one knows what will happen with H5N1. Maybe nothing. Maybe all of the outbreaks are diminishing and the virus will disappear. I hope so but nature rules and we are not closely following her lead.
Take care of you (and your animals).
Last edited by sharon sanders; July 8, 2025, 04:06 PM.
Reason: Typo. Corrected to add the word "partial" in the 3rd sentence.
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