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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: California dairies infected in Jan. 2024?
Date: Sat, 22 Mar 2025 17:35:23 -0500
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On 3/22/2025 1:56 PM, RonO wrote:
> On 3/21/2025 2:38 PM, RonO wrote:
>> On 3/20/2025 2:59 PM, RonO wrote:
>>> https://gisaid.org/fileadmin/c/gisaid/files/H5N1-HA-tree/ 
>>> H5N1_HA_subsampled_tree_US_20250302.pdf
>>
>> https://gisaid.org/fileadmin/c/gisaid/files/H5N1-HA-tree/ 
>> H5N1_HA_subsampled_tree_US_20250320.pdf
>>
>> The old links get discontinued and new ones get put up.
>>
>> https://gisaid.org/resources/gisaid-in-the-news/highly-pathogenic- 
>> avian- influenza-outbreak-in-the-united-states/
>>
>> This page is stable and you can access the 3 gene phylogenies from here.
>>
>> The new H5 tree seems to have had only one D1.1 sequence added and it 
>> pulled the outlier (A/Texas/37/2024) onto its own branch this differs 
>> from the previous tree.  My take is that they should remove the A/ 
>> Texas/37/2024 sample from the analysis and see where the node actually 
>> is that separates the wild bird B3.13 genotype from the dairy 
>> infection.   Just going by relative sequence divergence it looks like 
>> the node may fall within or closer to the California sequences.  The 
>> amount of divergence of the California sequences indicated that the 
>> virus was circulating within the California herds before Texas and the 
>> other states got infected.  The early 2024 Idaho infections are much 
>> closer to the Michigan, Minnesota and Colorado sequences (all likely 
>> infected by Michigan strains) than they are to the California 
>> sequences.  The herd that they tracked to Idaho from California and 
>> claimed that the virus was similar to California (that October Idaho 
>> sequence is not included in the phylogeny) were likely infected by the 
>> California herd, and the Idaho cattle likely did not infect the 
>> California cows that returned to California.  The Idaho herds 
>> confirmed to be infected from May to July 2024 are a very different 
>> sequence than the California H5 sequence, and the Idaho infection 
>> would likely not have changed as much by Sept. to infect California 
>> with it's own clade so different from the Texas sequences that the 
>> previous Idaho sequences evolved from.
>>
>> My prediction is that California may have been the first state 
>> infected by the dairy virus, but they were just in denial and never 
>> self reported the disease until the cows started dying in the summer 
>> heat.
>>
>> Ron Okimoto
>>
>>>
>>> This is a phylogeny of the HA gene segment.  It is for the H5 Asian 
>>> allele that is found in both the B3.13 dairy genotype and the D1.1 
>>> wild bird genotype that has started to be found in dairy cattle.
>>>
>>> The B3.13 H5 sequence is at the top of the phylogeny and the D1.1 H5 
>>> sequence is below and includes the Washington poultry worker (A/ 
>>> Washington/240/2024|2024-10-18).  A/Nevada/10/2025|2025-02-04 is a 
>>> recent D1.1 dairy infection.  The H5 sequence came into the US in 
>>> 2022, but the D1.1 and B3.13 alleles of the H5 gene may have 
>>> separated before getting to the US.  They don't have any sequences 
>>> from 2022 so I can't tell.
>>>
>>> The bogus way that the USDA labels their sequences inhibits 
>>> interpretation of the phylogeny.  The USDA only gives the collection 
>>> date and sequencing date, and lists the location as USA.  GISAID 
>>> seems to try to infer the location by the date of sequencing and 
>>> press releases about those dates.  If they can't infer the location 
>>> they leave it as USA which is useless for epidemiology within the US.
>>>
>>> It looks like the Iowa and Wisconsin patients were infected with a 
>>> D1.3 genotype closely related to D1.1.  The Washington, Oregon, 
>>> Wyoming, and Louisiana patients seem to have been infected with 
>>> different strains of D1.1.  But all the D1.1 and D1.3 H5 alleles seem 
>>> to come from a clade that may have branched off in 2022-2023.
>>>
>>> Something is strange about the B3.13 genotype H5 alleles.  It has 
>>> been known that the first human patient in Texas with the B3.13 
>>> genotype was a sequence outlier compared to all the other dairy 
>>> sequences. A/ Texas/37/2024|2024-03-28 still falls outside of all the 
>>> other dairy sequences, but it now groups with a mountain lion from 
>>> Montana, and a wild bird from Wyoming.  For the NA gene sequence the 
>>> Texas patient is within the dairy clade instead of out side of it and 
>>> is most closely related to the Missouri and Michigan human patients.  
>>> The Texas H5 sequence may just have multiple mutations that occurred 
>>> during the infection of that individual.  The mountain lion and wild 
>>> bird N1 sequences continue to fall outside of the dairy clade.  My 
>>> take is that this means that the Texas patient H5 sequence should not 
>>> be trusted in trying to figure out the source of the dairy infection.
>>>
>>> One thing to note is that all the California H5 sequence dairy 
>>> infections are a separate clade that looks significantly different 
>>> from other dairy infections.  Their sequences are also more variable 
>>> than those more closely related to the Texas B3.13 H5 sequences.  It 
>>> looks like the infection has been in California for a lot longer than 
>>> when it was first detected late last year.  For some reason there 
>>> seems to have been sequence evolution before California was infected 
>>> or after the first few herds were infected, possibly, before Texas 
>>> was detected in March 2024.  They need to redo their estimated time 
>>> of divergence for the dairy B3.13 genotype.  A full genome sequence 
>>> comparison is likely needed to figure out how California fits in with 
>>> the spread of the dairy virus.  California commercial poultry farms 
>>> started to go down in the central valley in October/November 2023 
>>> when it was estimated that the dairy virus entered into dairy cattle. 
>>> Because of the stupid way that the USDA labels their sequences I 
>>> could not tell which ones came from California last year, and I was 
>>> told that the USDA did not give out the names of the researchers 
>>> involved in the sequencing so that I could ask them to identify the 
>>> California samples from 2023.
>>>
>>> The PB2 data may have some sample labeling issues or sample mix up 
>>> because a sequence from one of the California human patients 
>>> (California/192/2024) definitely groups with the D1.1 clade for the 
>>> PB2 gene sequence, but the NA and H5 gene sequences group with the 
>>> B3.13 genotype.
>>>
>>> NA phylogeny:
>>> https://gisaid.org/fileadmin/c/gisaid/files/H5N1-NA-tree/ 
>>> H5N1_NA_subsampled_tree_US_20250302.pdf
>>> PB2 phylogeny:
>>> https://gisaid.org/fileadmin/c/gisaid/files/H5N1-PB2-tree/ 
>>> H5N1_PB2_subsampled_tree_US_20250302.pdf
>>>
>>>
>>> Ron Okimoto
>>>
>>
> https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/
> 
> GISAID has a full genome phylogeny that indicates that A/Texas/37/2024 
> is likely causing incorrect rooting of the dairy virus.  They should 
> likely take that sequence out of the phylogentic analysis.  As crazy as 
> it may seem the GISAID has evidence that California dairies and poultry 
> farms were infected by the B3.13 genotype before Texas.  I do not know 
> the reason for them not to have disclosed this by now.  There are 4 
> dairy samples and 3 chicken samples collected in California Jan. 2024. 
> They would precede the Texas infections by a couple months.  The Jan 
> 2024 samples have much shorter branch lengths than the other California 
> genomes.  This would be expected if they had been collected before the 
> other California samples that were all collected after August 2024. Even 
> though they have shorter branch lengths they all nest within the other 
> California B3.13 sequences which form their own clade with more sequence 
> variation than is found in the virus that infected Texas and Michigan.  
> The phylogeny indicates that the virus has been evolving in California 
> for longer than it has in the dairies infected with the Texas strain.
> 
> Ron Okimoto
> 
> I do not know how long they have known that California had been infected 
> by Jan 2024.

I have tried to find the sequences claimed to be collected Jan 2024, but 
nothing comes up when I search for the claimed USDA name.  I did find a 
sequence using only the number 037824-003.  It may be a sample labeling 
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