Private channel session 1023
23 messages over 2h 30m, 2021-02-24 – 2021-02-24.
A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.
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Pompeo [shared file(s): China's Reckless Labs Put the World at Risk - WSJ.pdf]
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So much insinuation without actually accusing them of anything
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Hah, this is sooooo terrible. I'm pretty sure that Pompy looked up "Biosafety Level", thought, "That's some scary shit- let's blame China", and grabbed the keyboard.US politicians (and intelligence) actually used to be widely respected in the world. Boy, has that gone downhill.
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We now have an "NYC" variant... Sigh. Any concerns about any of these mutations - especially the ORF1s? [shared file(s): Screen Shot 2021-02-24 at 7.38.07 AM.png]
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Here's the report on it - rising in NYC (yes, of course there's a preprint...) https://outbreak.info/situation-reports?country=United%20States&division=California[...]20York&pango=B .1.526&selected=New%20York&selectedType=division
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There are 2 subclades of B.1.526 - one has E484K, the other S477N. https://github.com/cov-lineages/pango-designation/issues/6
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Ah, interesting - need to dig a little further then (we can now do pango lineage + mutation on outbreak.info, so that's pretty nifty). If this is the one with, especially, eek, then that's interesting - a lot of standing immunity in large parts ofNYC.
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That's a really good point about all the pre-existing immunity in NYC. E484K doing double duty - ACE2 binding plusa neutralizing epitope. S477N likely the same/overlapping epitope, but NO interaction with ACE2 at least directly. [shared file(s): image.png]
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@Andrew Rambaut Q957R is interesting - Q957 probably forms a salt bridge with K304. Put another positive charge there make clash and likely "loosens up" the monomer more than a bit. Like Eddies corridor analogy though - variants finding their way down to a common path,
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Yeah, B.1.526 with eek is definitely rising in New York. This might be real. https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3 AE484K&selected=New%20York&selectedType=division
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Speaking of the WSJ - they just requested an interview to discuss our Virological post.
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It is weird the V701A reverting in the S477N lineage - maybe the tree is wrong
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HMMMM - that is interesting.
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Oh... We have identified a MAJOR issue with Illumina's consensus caller - it's calling reference calls if there are _any_ mismatching reads at a variant site. That might be why
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If this is from NYC, it's possible they used Illumina's DRAGEN pipeline
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(I have reached out to them - crickets).
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shared file(s): image (1).png, Screen Shot 2021-02-24 at 09.30.29.png
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Interesting - we have seen quite a lot of 'reversions' in some of the VOCs. Who would be using this consensus caller? Is there a way to find out?
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Preprint on the NYC sequences - pretty interesting. https://www.biorxiv.org/content/10.1101/2021.02.14.431043v2.full.pdf
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I'm worried A LOT of people are using the Illumina pipeline - and there's no way to find out in most cases
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Any lab that hasn't previously been involved in virus sequencing and isn't as comfortable with command line tools would likely use this caller. It's a big big problem.
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B.1.526 with S477N: https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3AS477N&selected=New%20York&selectedType=division
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Interestingly, none with both (kinda supporting this is a real effect - since they're independent events): https://outbreak.info/situation-reports?pango=B.1.526&muts=S%3AE484K&muts=S%3AS477N