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Slack / Private Message Drop, p.388 [SLACK_000602] · slack_pm:msg:04043

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Yes - lots of possibilities, but it looks like SC2 and RaTG13 spikes mostly diverging from SC1 by insertions - including the obvious PRRA.

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2021-01-12 14:42 Andrew Rambaut open

It is a bit tricky - my alignment is a bit different (I did a nucleotide alignment)
2021-01-12 14:44 Robert F. Garry open

THey are the same in the civet..
2021-01-12 14:44 Andrew Rambaut open

Yes.
2021-01-12 14:44 Andrew Rambaut open

And in some of the bats it looks
2021-01-12 14:49 Robert F. Garry

Yes - lots of possibilities, but it looks like SC2 and RaTG13 spikes mostly diverging from SC1 by insertions - including the obvious PRRA.
2021-01-12 14:52 Robert F. Garry open

The insertions not needed so put SC2 under the right situation and it starts to delete. Just like im cell culture the FCS and the QTQTN can be deleted.
2021-01-12 14:56 Robert F. Garry open

@Andrew Rambaut yes indeed - may get a somewhat different alignment with the nucleotides but the point remains that these are hotspots for deletions. Mechanism TBD but could be swapping out a shorter sequence with end homologiesy via copy-choice.
2021-01-12 15:02 Edward C. Holmes open

Wow Bob, that's amazing.
2021-01-12 15:14 Robert F. Garry open

Important for the origins argument as well - if these indels between SC1 and SC2 are natural and in play for variation, then the PRRA insert is natural as well.