Re: update dairy influenza

On 5/16/2025 10:36 AM, RonO wrote:

On 5/15/2025 12:55 PM, RonO wrote:

On 5/12/2025 8:34 AM, RonO wrote:

This is a post that I tried to send 5/4, but no new posts loaded since 4/30.
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I've been on the road for most of April, but in terms of the H5N1 dairy epidemic the USDA and CDC seem to be continuing to downplay the situation and continue to refuse to say if the continuing infections of cattle are the D1 (wild bird) or B3.13 (dairy) genotype.
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https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/
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According to the GISAID phylogeny the infection of the Nevada dairy worker with the D1 genotype (supposedly infected by infected dairy cattle) and the Wyoming patient that had to be hospitalized with the D1 infection got infected by a virus that is the same lineage as the D1 genotype that infected some of the Washington poultry workers back in October 2024.  These were the poultry workers that were detected 10/23 and not with the first group detected 10/09.  The 10/23 group were likely the group that was detected because they went to Oregon and tested positive.  It looks like some infected Washington poultry workers went to Wyoming and Nevada and infected animals there so that the Wyoming patient (02/11/2025) and the Nevada dairy worker (02/04/2025) could be infected.  The D1 infection was established in Nevada before the Wyoming patient was infected with the same lineage, so the D1 virus may have gone from Washington to Nevada, and then to Wyoming and Arizona.  Washington did not restrict poultry worker movements even though they knew that some of them were infected. Nevada wasn't restricting worker movements even though they knew that dairy workers were getting infected.  No contact tracing was attempted.

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https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/
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They do need to do a proper epidemiological analysis of the H5N1 genome sequences.  The USDA needs to supply the dairy locations where the samples were collected and the workers were working at.  If the workers were working at multiple dairies and or poultry farms that should be noted.
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The California sequences are much more divergent than those states infected by Texas.  They need to remove the possible recombinant virus from the analysis.  A/Texas/37/2024 was known to be an abberrant sequence when it was first produced, and it looks like having that sequence in the phylogenetic analysis is messing up the analysis and making the B3.13 wild bird sequences root within the Texas samples. Just from divergence estimates it looks like the dairy root should be closer to or within the California sequences.
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Multiple California samples are still listed as being collected 1/1/2024.  This would predate the Texas infection that was first detected in March 2024.  It would make the initial transfer from birds to cattle likely occurring in California.  If the collection date is an error it should have been detected and reported by now.
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The GISAID data indicates that humans carried the D1.1 genotype to Nevada and or Wyoming from Washington.  The Washington poultry workers known to have left the state for Oregon were carrying a virus that is the same lineage as was later found in Nevada, Arizona (likely infected from Nevada) and Wyoming.
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Ron Okimoto

 I posted something yesterday that never showed up.
 https://www.aphis.usda.gov/livestock-poultry-disease/avian/avian- influenza/hpai-detections/hpai-confirmed-cases-livestock
 The USDA has confirmed 10 more herds in Idaho infected with H5N1, but they continue to not disclose what genotype.  This is the second round of infection for Idaho.  Idaho was one of the first states infected by the Texas strain in early 2024.  Contact tracing done by California detected an infected Idaho herd in Oct 2024.  At that time California was claiming that the infection came from Idaho, but the Idaho herd that had contact with California cattle were found to have the California lineage of the virus, and it was not closely related to the Texas lineage that had initially infected Idaho.  Idaho stopped testing their cattle in 2024 and the Texas virus likely infected most of the herds in Idaho.  Idaho just refused to test the cattle to confirm that all their herds were likely infected.  These infections would have likely burned out by Oct.  The California strain is now plowing through the Idaho herds because they are not restricting dairy workers from working on more than one farm even though they know what happened in California and Colorado where over 70% of the herds got infected even though they were restricting cattle movements.  This just should tell anyone that if they tested the herds that have not yet been infected by the California strain that they would find seropositive cattle for H5 at most of the Idaho farms due to the Texas infection that they went into denial about and stopped testing the cattle in 2024.  The current herds are only being dectected because the USDA program for bulk milk tank testing.
 If they restrict cattle, and dairy worker movements they should be able to contain the infection, but as stupid as it may be the CDC never implemented dairy worker testing and contact tracing, and only recommend that workers not go to other farms.  It has also been found that veterinarians have been infected, and could have taken the virus to other farms.  So they need to test all the people with contact to infected cattle, and their contacts in order to bring the transmission down to zero.
 It should be noted that the CDC claimed to be implementing wider dairy worker testing back in Nov. 2024, but they lied, and nothing ever happened.  California ended up with over 80% of their herds infected, and 17 million commercial birds infected in just 2024.  They have lost over 40% of their commercial layers.
 The USDA should have been doing monthly epidemiological analysis of their sequence data, so that they would know by now how the herds and commercial flocks were being infected.  They have known since the first commercial layer flocks went down in Michigan and Texas that dairy workers from infected farms also worked at the infected poultry farms, but they refused to to the testing and contact tracing to confirm human to bird transmission.  The sequence data that they put out is pretty worthless for analysis because they refuse to give the location where the sample came from.  They have been told that it is worthless to just keep claiming USA as the location, but they refuse to identify where their samples come from, and they refuse to do the epidemiological analysis themselves.  An epidemiological analysis would likely show that the Nevada D1.1 dairy infection came from Washington poultry workers. The same lineage as Nevada was found in the poultry workers detected because they went to Oregon after being infected.  My guess is that some of the infected workers went south undetected.
 Someone needs to look at the GISAID sequence phylogenies.  Several California samples nest within the California sequences, but they are claimed to have been collected 1/1/2024.  This would predate the Texas infections, and would mean that California was the first state to have the Dairy infection.  If this is a labeling error it should have been corrected by now (those sequences have been used for several months) The branch length divergence phylogeny seems to confirm that California was the first state infected.  California has the longest branch lengths for their viral lineages.  It looks like using A/Texas/37/2024 is messing up the phylogenetic analysis.  This sample should be removed from the analysis.  From the beginning it was known to be an aberrant sequence, and it may be chimeric or some type or reassorted virus. Using it likely makes the dairy root falsely lie within the Texas lineages.  My guess is that if A/Texas/37/2024 is removed from the analysis the divergence of the lineages indicate that the root may fall near the California sequences.  The new node would probably make the California branch lengths shorter and the Texas Branch lengths longer.

https://www.cidrap.umn.edu/avian-influenza-bird-flu/quick-takes-h5n1-dairy-cows-and-poultry-polio-5-nations
Along with the 10 herds in Idaho Texas is now producing positive herds again, but they aren't saying what genotype.  It may be the D1.1 from Nevada and Arizona, or it could be the California strain of B3.13.
The official count is 1,065 herds infected, but that probably isn't close to the real number of infected herds.  States like Texas, Michigan, Minnesota, Arizona, Idaho, etc did not report all their infected herds, and relied on voluntary reporting which was obviously stupid.  Most of the herds in those states were likely infected in the first round.  California and Colorado are the only ones that tested all of their herds and they found over 70% of the herds infected in Colorado, and over 85% infected in California, so all the rest of the states that only reported a few infections like Oklahoma were really under reporting.  Now that the USDA is bulk milk tank testing in most states (Wisconsin and a couple others do not want to be tested. Wisconsin likely got infected during the first round of infections in 2024, and they have even had infecterd poultry farms and a poultry worker infected, but they deny having any infected herds and refuse to be tested).  Multiple states never reported positive herds like Florida, and a veterinarian that did not work in a state that had reported positive herds was infected, so the number of infected herds of this dairy epidemic is a lot higher than the 1,065 confirmed.  I recall that Wisconsin is supposed to have the third largest number of dairy cattle, and they just do not test their cattle.
Brazil had a poultry farm go down with H5N1.  They are not saying what genotype, but it is the same clade as B3.13 and D1.1.
Ron Okimoto

 

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Nothing about the relationship between the Washington poultry worker strain and the Wyoming and Nevada infections has been announced because the CDC and USDA refuse to do the epidemiological analysis of the samples that they obtain, and the USDA continues to put out useless data and continue to refuse to state where the samples came from except that they came from the USA.  The human infections can be tracked because the CDC does supply the location information with the sequence, but they have consistently refused to do the epidemiological analysis.  They do not want to do contact tracing nor detect the human to animal and human to human infections that have likely been occurring.
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Idaho is having a major second round of infection of their herds. They were one of the first states to have infected herds, but they stopped testing their herds early on and just let the infection run through the state.  They are not stating if this round is the D1 virus or continues to be the B3.13 genotype.  The initial Idaho infection were infected by a lineage that came from Texas, but the infection detected by contact tracing from California half a year later was infected by the California lineage.  This lineage is significantly different from the Texas lineages, and it is likely that those herds were infected by the California cattle, and not the other way around as California was claiming.  The California strain may be infecting all the recent Idaho herds or it could be the D1 genotype from Arizona and Nevada.
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Since I went on the road, herds in Arizona, Idaho, and California have continued to be confirmed to be infected, but they are not saying what genotype is responsible for the infections.
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Ron Okimoto
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