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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...
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