Slack / Private Message Drop — page 518

[2021-02-16 17:27:55] [Robert Garry] Thanks - still severl bits that can be fine-tuned for sure. [2021-02-16 20:13:28] [Kristian Andersen] "Scariants" - pretty good term by Topol. (I don't know what the hell is up with that "7 strains" study...) [shared file(s): Screen Shot 2021-02-16 at 8.12.36 PM.png] [2021-02-16 20:16:14] [Kristian Andersen] Although, Eddie, that last part of the last sentence didn't age too well :wink:. (I maintain pretty much everything in that paper remains true, however). [shared file(s): Screen Shot 2021-02-16 at 8.15.08 PM.png] [2021-02-16 20:17:24] [Eddie Holmes] [thread - ID: 2021-02-16 20:17:24] Unless, of course, they are not 'natural'.... [2021-02-16 20:18:37] [Kristian Andersen] Well, then that other paper you wrote didn't age well... [2021-02-16 23:22:23] [Andrew Rambaut] I think the '7' variant one are 7 independent instances of 677H which Emma Hodcroft has named after birds in a preprint. [2021-02-17 01:21:19] [Eddie Holmes] https://www.theguardian.com/world/2021/feb/17/nicknames-emerge-for-growing-list-of-covid-variants?utm_source= dlvr.it&utm_medium=twitter [2021-02-17 02:09:12] [Robert Garry] Q677H in 6 lineages and Q677P is the 7th. Q677P is mostly in New Mexico and Louisiana. Histidine at 677 "removes" one of the o-linked glycan predictions and decreases the "scores" of the other two. OTOH, the proline in Q677P puts in another kink near the FCS to join P681 and increases the O-linked glycan "score." [2021-02-17 02:11:49] [Andrew Rambaut] Would the glycan's affect the accessibility of the cleavage site to furin and thus these 677 mutations be moderating/enhancing cleavage? [2021-02-17 02:25:47] [Robert Garry] [thread - ID: 2021-02-17 02:25:47] The O-linked glycan would probably inhibit cleavage, but the extra proline kink might enhance. Either could actually be advantageous under certain circumstances. Example: Cleaving the FCS too soon would active the fusion process which could be "bad" for the virus in the wrong tissue or depending on timing. It's thought that viruses may have evolved the whole cleavage scheme to keep from triggering fusion during synthesis/assembly, which would obviously be "bad." [2021-02-17 02:41:35] [Robert Garry]