Slack / Private Message Drop — page 1025

[Kristian Andersen] Holy shit - that is quite something. The length of that branch... :scream:. What's the N/S on the branch? [2021-11-24 07:41:47] [Kristian Andersen] Just had a look at the list of mutations - so nuts. Getting rid of a lot of serines (although also adding some new ones...) and adding in lysine - the friggin' genome is going to be made out of lysines at some point! Just nuts. [2021-11-24 08:22:15] [Robert Garry] Oh boy - it's getting more polybasic - that's not good.... [2021-11-24 08:23:59] [Andrew Rambaut] It must surely be from a immunocompromised chronic infection. Possibly a dual infection with recombination and heavy mutation. But the random traveller in HK has me very worried [2021-11-24 08:24:34] [Andrew Rambaut] Visited South Africa for 20 days - must be a much more prevalent virus than the sequencing suggests [2021-11-24 08:24:56] [Andrew Rambaut] Will cause S gene dropout and I think SA is seeing some signal of that apparently [2021-11-24 08:29:58] [Kristian Andersen] HIV patient or animal reservoir - I'll say 70/30 odds. [2021-11-24 08:32:43] [Kristian Andersen] Bob, presumably the N679K combined with P681H makes this a better FCS, correct? It's interesting to see E484A in there too - presumably E484K was a bit too much. [2021-11-24 08:33:44] [Kristian Andersen] I swear to god - if we see another monster variant gain territory here in November/December, something is driving the emergence. What, I don't know, but "something". [2021-11-24 08:35:31] [Robert Garry] Yes definitely better FCS - the RXXR site really is minimal. Any changes that put postive charges, K, R, H nearby are going to up the efficacy. It already as discussed has an effective furin landing site in QTQT [2021-11-24 08:37:21] [Robert Garry] LPAI goes from a minimal site to multiple basic residues in HPAI... [shared file(s): image.png] [2021-11-24 08:37:47] [Kristian Andersen] Yup. QTQT is a landing site? [2021-11-24 08:40:50] [Robert Garry] yes both are neutral polar animo acids