Slack / Private Message Drop — page 382

[2021-01-11 15:10:19] [Kristian Andersen] Epizootic? Chronic infections? Immune escape? I think all in play. [2021-01-11 15:11:14] [Kristian Andersen] > It seems like all of these lineages are converging to the same set of mutations And just to this part - it's strongly suggestive of some very pervasive selections pressure that's in common in all these places. Or, alternatively (but I think less likely) something like this: https://www.cell.com/cell/fulltext/S0092-86 74(17)30292-1?_returnURL=https%3A%2F%2Fl[...]vier.com%2Fretrieve%2Fpii%2FS0092867417302921%3Fshow all%3Dtrue [2021-01-11 15:12:38] [Andrew Rambaut] Except that these 3 cases have a shit load of other stuff. Masses of spike mutations (and no synonymous in spike). Orf8 mutations and that nsp6 deletion [2021-01-11 15:12:47] [Kristian Andersen] Why're we seeing it now and not earlier? More widespread transmission, vaccines being deployed in some places, more standing immunity. But I do feel something's up here - doesn't seem normal to find so many clearly unrelated lineages ending up with a subset of the same mutations. That's just weird. [2021-01-11 15:13:11] [Andrew Rambaut] 3 very strange events with similar sets of mutations come up. [2021-01-11 15:13:30] [Kristian Andersen] Yeah. [2021-01-11 15:13:53] [Kristian Andersen] And in different parts of the world - with different climates, so not e.g., a "cold" adaptation. [2021-01-11 15:14:17] [Andrew Rambaut] Yup. Manaus is not chilly this time of year! [2021-01-11 15:15:39] [Kristian Andersen] They DID have a fuck ton of infections in the spring though. Same for UK. Same for RSA. [2021-01-11 15:15:50] [Andrew Rambaut] Rare chronic infections could just be a ready source of these mutations in combination (because they can all be selected for in the very large population sizes). When you get the combination it takes off [2021-01-11 15:16:13] [Andrew Rambaut] You just don't get them step by step in normal transmission with bottle necks [2021-01-11 15:16:26] [Kristian Andersen] Does Oli/Nuno have any data on reinfections? You mentioned a Virological study yesterday, but not sure if they're looking at that?