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https://www.cidrap.umn.edu/avian-influenza-bird-flu/h5n1-avian-flu- strikes-south-dakota-turkey-farm
They aren't releasing the genotype information on the virus infecting
these animals.
No new herds have been infected since August 1st, but the USDA is not releasing information on reinfected herds and California admitted that
43 herds have been reinfected by August 21 since May.-a States like Colorado, Minnesota, and Iowa supposedly have reinfected herds that are
not being reported by the USDA.-a Those states were infected early and
had likely cleared the the virus (went through the entire state) before being reinfected.
GISAID phylogeny indicates that Idaho was reinfected with the California strain of the virus.-a Idaho had initially been infected by the Texas lineage in 2024, but starting in April 2025 they had been infected with
the California lineage.-a So the virus seems to have made it out of California, and they likely need to see if the reinfected herds in other states are being infected with the California lineage.-a The California virus is significantly different and more divergent than the Texas
virus.-a It looks like the phylogeny is incorrect.-a It may be that The Texas human infection is messing up the analysis and the root node is misplaced.-a The Texas sample has always been known to be a sequence
outlier and possible recombinant.-a It looks like using this sequence is making the Texas lineage look more closely related to the outgroup wild
bird lineages.-a If they remove A/Texas/37/2024 the actual root of the
dairy virus sequences may shift to be closer to the California sequences.
https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/
Ron Okimoto
On 9/3/2025 10:02 AM, RonO wrote:
https://www.cidrap.umn.edu/avian-influenza-bird-flu/h5n1-avian-flu-
strikes-south-dakota-turkey-farm
They aren't releasing the genotype information on the virus infecting
these animals.
No new herds have been infected since August 1st, but the USDA is not
releasing information on reinfected herds and California admitted that
43 herds have been reinfected by August 21 since May.-a States like
Colorado, Minnesota, and Iowa supposedly have reinfected herds that
are not being reported by the USDA.-a Those states were infected early
and had likely cleared the the virus (went through the entire state)
before being reinfected.
GISAID phylogeny indicates that Idaho was reinfected with the
California strain of the virus.-a Idaho had initially been infected by
the Texas lineage in 2024, but starting in April 2025 they had been
infected with the California lineage.-a So the virus seems to have made
it out of California, and they likely need to see if the reinfected
herds in other states are being infected with the California lineage.
The California virus is significantly different and more divergent
than the Texas virus.-a It looks like the phylogeny is incorrect.-a It
may be that The Texas human infection is messing up the analysis and
the root node is misplaced.-a The Texas sample has always been known to
be a sequence outlier and possible recombinant.-a It looks like using
this sequence is making the Texas lineage look more closely related to
the outgroup wild bird lineages.-a If they remove A/Texas/37/2024 the
actual root of the dairy virus sequences may shift to be closer to the
California sequences.
https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/
Ron Okimoto
https://www.nbcnews.com/news/us-news/california-cat-euthanized-getting- bird-flu-raw-cat-food-rcna229349
https://www.fda.gov/animal-veterinary/cvm-updates/fda-notifies-pet- owners-tests-show-h5n1-contamination-certain-lots-rawr-raw-cat-food- chicken-eats
The raw cat food that the cat ate was contaminated with the dairy
influenza genotype B3.13.-a The FDA claims that the virus isolated from
the cat food and the cat are similar to virus circulating Nov. Dec.
2024.-a They seem to think that the frozen ingredients were collected in late 2024.-a The food was labeled as containing raw chicken meat.-a The company has removed the contaminated lots from distribution, but the FDA
has not issued a recall.
Ron Okimoto
On 9/5/2025 1:11 PM, RonO wrote:
On 9/3/2025 10:02 AM, RonO wrote:https://www.cidrap.umn.edu/avian-influenza-bird-flu/h5n1-detected-texas- dairy-herd-researchers-cant-pinpoint-source-california
https://www.cidrap.umn.edu/avian-influenza-bird-flu/h5n1-avian-flu-
strikes-south-dakota-turkey-farm
They aren't releasing the genotype information on the virus infecting
these animals.
No new herds have been infected since August 1st, but the USDA is not
releasing information on reinfected herds and California admitted
that 43 herds have been reinfected by August 21 since May.-a States
like Colorado, Minnesota, and Iowa supposedly have reinfected herds
that are not being reported by the USDA.-a Those states were infected
early and had likely cleared the the virus (went through the entire
state) before being reinfected.
GISAID phylogeny indicates that Idaho was reinfected with the
California strain of the virus.-a Idaho had initially been infected by
the Texas lineage in 2024, but starting in April 2025 they had been
infected with the California lineage.-a So the virus seems to have
made it out of California, and they likely need to see if the
reinfected herds in other states are being infected with the
California lineage. The California virus is significantly different
and more divergent than the Texas virus.-a It looks like the phylogeny
is incorrect.-a It may be that The Texas human infection is messing up
the analysis and the root node is misplaced.-a The Texas sample has
always been known to be a sequence outlier and possible recombinant.
It looks like using this sequence is making the Texas lineage look
more closely related to the outgroup wild bird lineages.-a If they
remove A/Texas/37/2024 the actual root of the dairy virus sequences
may shift to be closer to the California sequences.
https://gisaid.org/phylogeny-influenza/hpai-h5n1-usa/
Ron Okimoto
https://www.nbcnews.com/news/us-news/california-cat-euthanized-
getting- bird-flu-raw-cat-food-rcna229349
https://www.fda.gov/animal-veterinary/cvm-updates/fda-notifies-pet-
owners-tests-show-h5n1-contamination-certain-lots-rawr-raw-cat-food-
chicken-eats
The raw cat food that the cat ate was contaminated with the dairy
influenza genotype B3.13.-a The FDA claims that the virus isolated from
the cat food and the cat are similar to virus circulating Nov. Dec.
2024.-a They seem to think that the frozen ingredients were collected
in late 2024.-a The food was labeled as containing raw chicken meat.
The company has removed the contaminated lots from distribution, but
the FDA has not issued a recall.
Ron Okimoto
A new dairy has been infected in Texas.-a They are not releasing the genotype, but Nevada and Arizona have D1.1 infected dairy herds.-a This
is the first new infection since May, but they aren't saying where it occurred.-a Herds clear the virus in around 3 months so they need to
figure out where this virus came from.
They claim to have not been able to identify how the California child
was infected in Dec. 2024.-a The child had an abdominal flu infection,
and they will not even consider that it might have been the milk that
the child drank.-a The child did not drink raw milk, but in Oct. 2024 the CDC published a report of their work indicating that infective virus
might survive the most common method of pastuerization and survive in refrigerated milk for at least 4 days.-a The FDA claimed that they were going to check that out at that time, but nothing ever was tested.-a They claimed that they were asking for volunteer processing plants to be
tested, apparently, they did not get anyone that was willing to find out that they were producing infective dairy products so the study was never started.-a No results have ever been published.-a The California investigators claim to have checked out all ways that the child may have been infected, but they left dairy products off their list of things
that they checked.
The USDA is still not announcing reinfected herds and California has not updated their reinfection numbers since Aug 1.-a At that time they
claimed to have 43 reinfected herds since May, and that they were
continuing their herd isolation policies.-a As crazy as it may seem these policies do not require the restriction of dairy worker movements.-a You
can go to the GISAID H5N1 influenza phylogeny and see that Idaho dairies began to be infected with the California strain of the B3.13 genotype in May.-a The 2024 infections of Idaho herds was with the Texas strain of
the virus that is a very different sequence from the California variant.
-aThere has never been an effort to try to figure out where the
California virus came from.-a It is obviously not very related to the
Texas lineages.-a You can check out the GISAID phylogeny and it looks
like the California strain came from outer space.-a The GISAID phylogeny
is likely wrong.-a 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.-a What they need to do is redo the phylogenetic analysis without the A/Texas/37/2024 sequence.-a 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.-a 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.-a They obviously need to keep the virus from spreading from California when the movement of animals is already restricted.-a 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.-a All
three had been infected with the same lineage of the D1.1 virus.-a 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.-a Those sequence were removed for some reason and GISAID is not giving any explanation.-a The epidemiological analysis has never been done, and the Nevada dairy workers movements were not
restricted and Arizona got infected with the Nevada virus.-a 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.-a 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.-a They aren't
even counting them as infected herds.
Ron Okimoto