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Slack / Private Message Drop, p.388 [SLACK_000602] · slack_pm:msg:04044

Date: 2021-01-12 14:52
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry

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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.

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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 open

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

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.
2021-01-12 15:26 Andrew Rambaut open

Of course the nefarious supervillain making this virus spent all that time putting those insertions in (from HIV or fish presumably) and all it does is delete them.

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