[continued from previous message]   
      
   like the California strain came from outer space.  The GISAID phylogeny   
   is likely wrong.  The root node associating the dairy virus with the   
   B3.13 genotype is associated with the texas dairy lineage, but that may   
   be due to the use of the human infection A/Texas/37/2024 that has always   
   been known to be a sequence outlier and possible recombinant.  What they   
   need to do is redo the phylogenetic analysis without the A/Texas/37/2024   
   sequence.  From the branch lengths of the divergence phylogeny it looks   
   like the root may be closer to or within the California sequences.   
      
   The USDA has to start doing the epidemiological analysis of their   
   sequences that they should have been doing from day one.  They need to   
   inform the states that have reinfected herds of what Genotype of the   
   virus is infecting their herds and they have to start determining where   
   that virus is coming from.  They obviously need to keep the virus from   
   spreading from California when the movement of animals is already   
   restricted.  They have to restrict dairy worker movements unless they   
   have tested negative for the virus.   
      
   https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/   
      
   The GISAID have removed the Washington poultry worker, the Wyoming farm   
   worker, and the Nevada dairy worker from their D1.1 phylogeny.  All   
   three had been infected with the same lineage of the D1.1 virus.  The   
   Washington poultry worker had been infected in Oct and was likely part   
   of the second group of poultry workers 3 of whom were detected after   
   they left the state and were in Oregon, so infected workers had   
   obviously left the state, and it looks like one or more of them went to   
   Wyoming and/or Nevada.  Those sequence were removed for some reason and   
   GISAID is not giving any explanation.  The epidemiological analysis has   
   never been done, and the Nevada dairy workers movements were not   
   restricted and Arizona got infected with the Nevada virus.  They did not   
   restrict dairy worker movements even though they knew that at least one   
   Nevada dairy worker had been infected that worked at an infected dairy.   
   The CDC and USDA has always only recommended that dairy workers on   
   infected farms not go to other farms, and that recommendation obviously   
   does not apply to herds that are not yet known to be infected. It sounds   
   like 23 states are no longer testing their herds even though some states   
   are being reinfected.   
      
   The epidemic is supposed to be winding down, but it looks like another   
   round of reinfections is starting.  Colorado, Minn. and Iowa are   
   supposed to have reinfected herds, but they aren't doing the   
   epidemiology to find out where the virus is coming from.  They aren't   
   even counting them as infected herds.   
      
   Ron Okimoto   
      
   --- SoupGate-Win32 v1.05   
    * Origin: you cannot sedate... all the things you hate (1:229/2)