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1. 2021-01-11 15:09 Kristian G. Andersen open
   Yup
2. 2021-01-11 15:09 Edward C. Holmes open
   I'm really not sure I believe the chronic theory any more...once may be, but three times? Chronic infections are a tiny fraction of the overall population.
3. 2021-01-11 15:10 Kristian G. Andersen open
   Epizootic? Chronic infections? Immune escape? I think all in play.
4. 2021-01-11 15:11 Kristian G. Andersen open
   > 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/S0092-8674(17)30292-1?_returnURL=https%3A%2F%2Fl[...]vier.com%2Fretrieve%2Fpii%2FS0092867417302921%3Fshowall%3Dtrue
5. 2021-01-11 15:12 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
6. 2021-01-11 15:12 Kristian G. Andersen open
   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.
7. 2021-01-11 15:13 Andrew Rambaut open
   3 very strange events with similar sets of mutations come up.
8. 2021-01-11 15:13 Kristian G. Andersen open
   Yeah.
9. 2021-01-11 15:13 Kristian G. Andersen open
   And in different parts of the world - with different climates, so not e.g., a "cold" adaptation.

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