A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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"we had failed to realize the real importance of the pangolin RBD" That bit is pretty key.
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Yes - the 7th Feb version on google docs (basically the 'report') doesn't have pangolins in the alignment.
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No - we didn't use the pangolin genomes initially because they were so fragmented.
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OK. Good. More evidence of science being done
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2022-01-27 13:57
Andrew Rambaut
From the 8th Feb version on GoogleDocs: > Although RaTG13 remains the closest relative to 2019-nCoV across the genome as a whole, the Malayan pangolin CoVs are identical to 2019-nCoV at all six key RBD residues. Analyses of these pangolin viruses are ongoing, although they do not carry the furin cleavage site insertion.
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I think the key for me was when one of us pointed out that "if the RBD was natural, then the whole thing is natural." Also we were arguing all sides of this from the get go - the whole o-linked glycan thing which was discussed on theconf call was pointing to natural although I do agree with K that it's as likely as not that that's a common regulatory mechanism for FCS rather than immune evasive - still think that it could possibly have some role there though too -the FCS is a major epitope in other class I fusion proteins in SARS-CoV-2 it isn't AFAIK which is strange.
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And if it is used as a regulatory system there is no way a human designer would know how to do that
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Yeah, but notice our discussion of "passage". The Pangolin RBD _disproves_ that, but we didn't catch that until later- we use the RBD to say "not engineering" but we didn't yet use it to say "not passage". That only came after peer review
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And by disproving - I mean, it disproves that the specific RBD mutations seen in SC2 arose via culture passage, but,of course, it doesn't directly disprove passage itself.