ryhisner
commented
1 year ago I used to look for changes to the various Omicron S2/near-S2 mutations, but I've stopped looking. It's become clear that those mutations—H655Y, N679K, N764K, D796Y, Q954H, & N969K—aren't going anywhere and that changes to any one of them are clearly deleterious. I don't know enough to say how these S2 mutations are connected or function together, but it seems to me like the only way they are going to change—if they ever change—is via wholesale replacement, which is probably only possible through either emergence of an orthogonal variant from a chronic infection or recombination with such a variant. The fact that all the Omicron-Delta recombinants retain the entire Omicron S2 has to mean something, maybe that there are allosteric interactions between some of the Omicron S2 and NTD/RBD mutations that are an essential part of its S2 machinery?
There was that Gupta Lab study that showed Delta and Kappa's NTDs had a large effect on S2 function, and also an earlier one positing a mechanism whereby the NTD could affect S2. If I remember right, the latter involved residues around 735-737, and its interesting to note that a few of the most highly mutated chronic Delta sequences have had mutations at S:735 and S:737. https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01037-3 https://www.sciencedirect.com/science/article/pii/S2211124722005538
oobb45729
Will it be the next R346T? Not sure. It appeared in many highly mutated sequences recently.
V642G is just beside F643, which forms π–π interaction with H655/Y655.
FedeGueli
HynnSpylor
Memorablea
RajLABN
corneliusroemer
@corneliusroemer , happy new year first!, then here the new XBB.1.5 Spike Diversity Issue: (last update 12/03/23)
XBB.1.5 query : T17124C,T23018C +
Legenda: N or n= not growing = zero new sequences blank = growing little but different from 0seqs y= growing around 15% since last update yy = growing more than 20% since last update yyy = growing more than 50% since last update (Designated lineages are out of the game , no updates for them) Lineages with less than 10 sequences now will not be updated.