This isn't good, folks.
I'm not worried about H5N1 transmission to humans (yet) but the Dept. of Agriculture pathetic lack of transparency, how long it took for the genomes to be released, lack of testing asymptomatic cattle......
All detracts from 'confidence'

OK, I think we're close to decisive evidence that US bovine H5N1 had a single origin from birds, and that when related viruses from birds *have* been found, they are jumps from cattle back into birds.

Grackles, blackbirds, chickens all show mammalian adaptation like PB2 M631L.

USDA/CDC still heedless of what The Great Influenza author John Barry calls the *fundamental lesson* of the 1918 pandemic:

'Those in authority must retain the public’s trust. The way to do that is to distort nothing, to put the best face on nothing, to try to manipulate no one.'

Could it be any more obvious that the USDA is totally captured by industry?

Been following this for a while. It's the most remarkable, well-documented case of a long-term chronic infection on the record (excepting some of Marc Johnson's Cryptics), & we know about it thanks to Matthijs Welkers's dedicated efforts & the patient's selfless cooperation.

This intense thread from Ryan links mutation patterns during chronic SC2 infections to optimization of the complex inner workings of the micro-factories that coronaviruses use to both replicate their genomes and produce transcripts for gene expression. I learned so much from it.

This patient was treated w/molnupiravir in the 1st 5 days of infection. All 3 branches share a MOV mutational signature. Incredibly, there are *zero* shared private mutations btwn the four sequences. MOV likely created an enormous amount of genetic diversity, which...