Slack / Private Message Drop — page 545

[Andrew Rambaut] [thread - ID: 2021-02-24 08:11:33] There are 2 subclades of B.1.526 - one has E484K, the other S477N. https://github.com/cov-lineages/pango-designation/issues/6 [2021-02-24 08:26:29] [Kristian Andersen] 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 of NYC. [2021-02-24 08:51:17] [Robert Garry] That's a really good point about all the pre-existing immunity in NYC. E484K doing double duty - ACE2 binding plus a neutralizing epitope. S477N likely the same/overlapping epitope, but NO interaction with ACE2 at least directly. [shared file(s): image.png] [2021-02-24 09:02:19] [Robert Garry] [thread - ID: 2021-02-24 08:11:33] @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, [2021-02-24 09:22:50] [Kristian Andersen] 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 [2021-02-24 09:27:32] [Robert Garry] [thread - ID: 2021-02-24 09:27:32] Speaking of the WSJ - they just requested an interview to discuss our Virological post. [2021-02-24 09:27:44] [Andrew Rambaut] It is weird the V701A reverting in the S477N lineage - maybe the tree is wrong [2021-02-24 09:29:14] [Robert Garry] HMMMM - that is interesting. [2021-02-24 09:29:17] [Kristian Andersen] 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 [2021-02-24 09:29:38] [Kristian Andersen] If this is from NYC, it's possible they used Illumina's DRAGEN pipeline [2021-02-24 09:29:55] [Kristian Andersen]