A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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I've not read it carefully yet, but interesting to see the adaptive changes in ORF1ab as well. They are dead right thatdN/dS is pretty rubbish when you have fixed mutations.
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Yeah, just saw it too - pretty interesting. And yes, "A" is totally unique to SC2 there
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I'm in...sorry, just catching up this thread now.
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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.
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2021-02-21 15:16
Kristian G. Andersen
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.
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No one thinks about fixed changes: nicely blows-up the idea that SARS-CoV-2 was perfectly adapted to humans at the outset.
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Well, actually, this supports being perfectly adapted to humans :wink:. A in that position was fixed from the get go.
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(and yeah - dN/dS is shit. Just no point).
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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?