Slack / Private Message Drop — page 460

Oh and @Kristian Andersen correcting one mistake - THe cysteines in the sarbecos are very conserved but not 100%. RmYN02, (and noe the Thaibat and japan bat "deletes" or is missing a pair - Japan Bat essentially just excises the cysteine loop - of course it could will be the other way around with SC1 etc adding the new cysteine loop kinda like your "fake reinfection patient" just in the CTD instead of the NTD. [2021-01-27 13:58:27] [Eddie Holmes] As ever, great job Bob. The gaps are slowly filling... [2021-01-27 19:30:42] [Kristian Andersen] Pretty scary reading this - how much do we think Nuno and Oli over-estimated prevalence? https://www.washingtonpost.com/world/2021/01/27/coronavirus-brazil-variant-manaus/ [2021-01-27 19:54:46] [Kristian Andersen] I missed this paper on NTD neuts. Explains why P.1. and B.1.351 have the NTD mutations. https://www.biorxiv.org/content/10.1101/2021.01.14.426475v1 [2021-01-28 05:22:16] [Robert Garry] The money quote: "S2L28, S2M28 and S2X333 contact the N-terminal region (residues 14-20, NTD N-terminus), a
-hairpin formed by residues 140-158 (supersite
-hairpin), and a loop spanning residues 245-264 (supersite loop). These three regions collectively form an antigenic supersite on the pinnacle of the NTD on the side distal to the viral membrane (Figure 2A-I)." [2021-01-28 10:37:19] [Robert Garry] [thread - ID: 2021-01-28 10:37:19] Here's another look at the spike amino acid alignment. I've highlighted the RBD residues that make RBD contact according to PO1 and the Bloom mutagenesis paper. Somehow I think that Bloom2020 left out E484, but I'll double check that. PO1 predicted residues in green and Bloom contacts in blue highlights. One of the PO1 residues S494 is not considered a contact residue in Bloom2020 but again needs double checking. GDpango leads with 17/19 similar to SC2 followed by Cambobatcov at a respectable 13/19 and RaTG13 12/19. There are some interesting things going on in the indels particularly tracking GX pango and RatG13 in the NTD. THaibatcov VERY similar to RmYN02. Japan batcov adds a bit more variability in the S1/S2 junction. [shared file(s): image.png] [2021-01-28 14:02:31] [Kristian Andersen] Fuck. <50% efficacy - worse than I had hoped for (I expected something in the ~70% range) https://www.nytimes.com/live/2021/01/28/world/covid-19-coronavirus?type=styln-live-updates&label=coronavir us%20updates&index=0#novavaxs-[...]th-africa [2021-01-28 14:05:27] [Eddie Holmes] I know! Fuck!! [2021-01-28 14:14:12] [Andrew Rambaut] Question is whether it is all down to 484K? [2021-01-28 14:27:40] [Kristian Andersen] I bloody hope not. I think the other mutations play a role too - for sure 417, but probably also 18 [2021-01-28 14:27:57]