A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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R681S - That is interesting - hard to predict the effect on cleavage. The fsc is still there of course, but cleavage could be improved (the S might be a better landing site than the R) or decreased. And, the wild-card of the O-glycans not being there.
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These are the mutations we are seeing (we are not sure how they are linked as they are environmental samples). The last column is me looking outside the SARS-CoV-2 to the bats/pangolins ```S:R102T (21867:G>C) conserved S:D442N (22886:G>A) conserved S:Y449H (22907:T>C) 449F 449G S:N450T (22911:A>C) 450S (RaTG13), 450G S:P499S (23057:C>T) 499S (Cambodian bats) S:N501D (23063:A>G) 501D (RaTG13), 501T, 501V S:N501S (23064:A>G) S:Q506P (23079:A>C) conserved S:P681S (23603:C>T) missing S:V772A (23877:T>C) conserved S:Q779L (23898:A>T) conserved S:L828I (24044:C>A) conserved S:G932D (24357:G>A) conserved S:S937A (24371:T>G) conserved```
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question is - does any of this spike profile make you think it might be in a non-human host?
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501D is interesting as it is in RaTG13 (i.e., one of the residues SC2 ancestors lost)
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2021-09-14 06:36
Robert F. Garry
For completeness - here's P681R - as discussed previously it changes one of the O-linked glycans [shared file(s): image.png]
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The loss of furin cleavage and some RBD mutations seems like it might be non-human
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There are about 100 681S human genomes on GISAID and some evidence of transmission clusters so can't be a totally unfit virus in humans
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THe FCS will still be there but most likely not as good as P681R. Totally agree about the N501 S or D maybe non-human. That could be spillback followed I guess by another spillover..
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That is a weirdly mutates spike... Often we see charge reversions, but that's not what's going on here - instead we see several hydroxyl groups? There are more S/T mutations in that spike than the two you mentioned. Novel receptor?