Slack / Private Message Drop — page 388

That is interesting, Bob! [2021-01-12 14:38:06] [Robert Garry] Yeah Align SC1 with SC2 (and RatG13) just for completeness. The deletions that you see in the UK and ZA variants are EXACT deletions comparing SC1 to the others. Also note the deletion near 484 - these are hotspots! [2021-01-12 14:38:59] [Andrew Rambaut] Are they in the civet versions of SC1? [2021-01-12 14:39:28] [Andrew Rambaut] Or the closest bats to SC1 (could check this myself of course). [2021-01-12 14:39:52] [Robert Garry] Good question - that would be interesting... [2021-01-12 14:42:42] [Andrew Rambaut] [thread - ID: 2021-01-12 14:42:42] It is a bit tricky - my alignment is a bit different (I did a nucleotide alignment) [2021-01-12 14:44:00] [Robert Garry] THey are the same in the civet.. [2021-01-12 14:44:08] [Andrew Rambaut] Yes. [2021-01-12 14:44:21] [Andrew Rambaut] And in some of the bats it looks [2021-01-12 14:49:59] [Robert 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 14:52:25] [Robert 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 14:56:15] [Robert Garry] [thread - ID: 2021-01-12 14:42:42] @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 15:02:05] [Eddie Holmes]