Slack / Private Message Drop — page 328

[Robert Garry] [thread - ID: 2020-12-20 07:28:32] @Robert Garry It's N501T [2020-12-20 08:15:46] [Robert Garry] [thread - ID: 2020-12-20 07:28:32] @Robert Garry Same residue changes to two diff amino acids when SC2 "adapts" to two diff animals. [2020-12-20 08:27:39] [Robert Garry] [thread - ID: 2020-12-20 07:28:32] @Robert Garry In SC1 it's T501 fwiw. [2020-12-20 08:33:25] [Robert Garry] Note to self that the Benton structures are "stabilized" with two proline substitutions - this is what we did to ultimately get the Lassa GP structure. [2020-12-20 12:31:18] [Eddie Holmes] Thanks Bob, a lot to think about. [2020-12-20 13:10:00] [Kristian Andersen] Thanks Bob - this is very helpful. One nagging question I have is that it doesn't seem to me that N501Y _alone_ can explain the 'spreader' phenotype, yet, the lineages in the UK and SA are quite distinct - and as far as I can tell, only share N501Y. However, it's entirely plausible that different mutations can lead to similar conformational changes, that might give the virus a 'spreader' phenotype if N501Y pops up on that genetic backbone. We have seen N501Y before (e.g., Australia), but I don't know that any of those are associated with increased spread? With that said, Australia isn't exactly representative when it comes to the question of spread, and I don't believe N501Y has been observed in that many places (I think just random stray sequences here and there) [2020-12-20 13:16:45] [Andrew Rambaut] There are actually 2 501Y lineages in the UK - the other one in South Wales (now up to about 500 genomes but associated with a hospital outbreak as well). Again only N501Y in common. As you say - there was a cluster in Australia - 37 genomes from beginning of June to beginning of July. [2020-12-20 13:18:32] [Kristian Andersen] I missed that - I thought same lineage, but two separate emergence events (from a common source, I assumed). But I see the differences on Emma's Nextstrain build - very interesting. [2020-12-20 13:19:10] [Andrew Rambaut] There are 5 from Massachusetts with a shit load of mutations [2020-12-20 13:19:20] [Andrew Rambaut] Spike A1020S, Spike C15del, Spike D614G, Spike G142del, Spike I870V, Spike L18del, Spike L141del, Spike N17del, Spike N440D, Spike N501Y, Spike Q14del, Spike Q183H, Spike Q493K, Spike S12del, Spike S13del, Spike S494P, Spike T478K, Spike V16del, Spike V143del, Spike Y144F, E T30I, M A2V, N A208S, NS3 Q57H, NS7a S83L, NSP2 I21V, NSP2 T85I, NSP4 A307V, NSP12 P323L, NSP13 T115I