It's starting to look like pasteurization inactivates #H5N1 #birdflu viruses in milk. But people who drink raw milk are playing with fire right now. statnews.com/2024/04/29/bir…

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My colleagues and I have just posted a
'Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species' Virological Posts.

Consensus genomes and metadata.

virological.org/t/note-about-a…

We need to talk about that human case of H5N1 in Texas...

Here is a bootstrapped (NJ) tree showing how the closest realtive of H5N1 sampled in cattle is a virus the infected an male individual who reportedly worked on a farm with cattle (dairy, I believe).

Important update on metadata of H5N1 in cattle (and back to birds):

Thanks to the extraordinary detective skills of Flo Débarre, we are pleased to be able to share this table containing locations and dates for several H5N1 cases in cattle and birds:

github.com/andersen-lab/a…

Due to enormous and collaborative effort from the Nextstrain team, james hadfield Trevor Bedford and of course Dept. of Agriculture , we now have the USDA cattle sequences on Nextstrain: nextstrain.org/avian-flu/h5n1… visualized with new, 2-year builds.

The discovery of #H5N1 #birdflu in a significant portion of commercially purchased milk suggests the outbreak in cows is much larger than we know, scientists who've been doing this work tell Megan Molteni. statnews.com/2024/04/25/h5n…

So, *preliminary* molecular clock analyses indicate that the time of the most recent common ancestor (TMRCA) of the US cattle flu clade was late December.

TMRCA of that clade and the closest relatives in birds, mid-December.

If single intro, likely between those rough dates.

Interesting tidbits from a press conf today on #H5N1 #birdflu by US agencies
—NIAID-funded researchers found commercial milk that was PCR-pos for H5, but could not grow live virus from it. (Good)
—USDA & CDC admitted some farmers won't let them test.
statnews.com/2024/04/24/h5n…

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Here's a visual of the US H5N1 'Cattle clade', HA plus two internal genes.

Strongly suggests to me there was single origin, at least for these sequences.

Possibly in late 2023/early 2024.

Here is a link to 239 consensus genome sequences, assembled by 👾 Karthik, from sequencing reads of 2.3.4.4b H5N1 influenza A virus from cattle and other species.

github.com/andersen-lab/a…

A short distraction from MooFlu (© TompkinsLab) to BatFlu:

'The bat-borne influenza A virus H9N2 exhibits a set of unexpected pre-pandemic features'

from Schwemmle Lab and company

assets.researchsquare.com/files/rs-29375…