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1. 2021-02-21 15:12 Kristian G. Andersen open
   Yeah, just saw it too - pretty interesting. And yes, "A" is totally unique to SC2 there
2. 2021-02-21 15:13 Edward C. Holmes open
   I'm in...sorry, just catching up this thread now.
3. 2021-02-21 15:14 Kristian G. Andersen open
   it's nicely spotted, since it's the only mutation unique to SC2 in the RBD - we should have picked this up earlier. Iwonder if H519 does something interesting too.
4. 2021-02-21 15:16 Kristian G. Andersen open
   519 is "H" in SC2, but N in almost all other sequences - the only other deviation is K in the P378 pangolin, although that is a pretty bad sequence, so might not be real.
5. 2021-02-21 15:16 Edward C. Holmes
   No one thinks about fixed changes: nicely blows-up the idea that SARS-CoV-2 was perfectly adapted to humans at the outset.
6. 2021-02-21 15:18 Kristian G. Andersen open
   Well, actually, this supports being perfectly adapted to humans :wink:. A in that position was fixed from the get go.
7. 2021-02-21 15:20 Kristian G. Andersen open
   (and yeah - dN/dS is shit. Just no point).
8. 2021-02-21 15:23 Edward C. Holmes open
   I can certainly see that Doug & Phil increased transmissibility, but that does not explain why B.1.1.7 et al.,which arose later, are doing so well. That may have arisen through an intra-host advantage, but it's obvious that they have an epidemiological scale advantage as well. Clearly they have increased fitness which can only be due to (i)increased transmissibilty in itself....which suggests that there should other key mutations in ORF1ab (?) and/or (ii)immune evasion that enables more refection and hence increases R. Perhaps that deletion in nsp6 is the key?
9. 2021-02-21 15:24 Edward C. Holmes open
   Are there *proportionately* more chronic infections? Do we know their overall frequency?

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