From: rokimoto557@gmail.com   
      
   https://gisaid.org/fileadmin/c/gisaid/files/H5N1-HA-tree/H5N1_HA   
   subsampled_tree_US_20250302.pdf   
      
   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_P   
   2_subsampled_tree_US_20250302.pdf   
      
      
   Ron Okimoto   
      
   --- SoupGate-DOS v1.05   
    * Origin: you cannot sedate... all the things you hate (1:229/2)