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Slack / Private Message Drop, p.510 [SLACK_000724] · slack_pm:msg:05336

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What is up with that nsp6 deletion? Curious.... @Andrew Rambaut how's L452R growing in the UK?

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2021-02-12 08:02 Kristian G. Andersen

What is up with that nsp6 deletion? Curious.... @Andrew Rambaut how's L452R growing in the UK?
2021-02-12 08:10 Andrew Rambaut open

That nsp6 is cropping up a lot, isn't it. The B.1.525 I posted this morning has E484K and all three of the lineage defining B.1.1.7 deletions (plus Q677H - i.e. adjacent to FCS - possibly affects the O-linked glycs?).
2021-02-12 08:15 Kristian G. Andersen open

No coincidence that's for sure
2021-02-12 08:17 Andrew Rambaut open

No. We are working on a project trying to define the convergent peak for all this. I would love you all's input once wehave put the guts together.
2021-02-12 08:22 Kristian G. Andersen open

It's definitely interesting - and I can't quite figure out what's going on here. Is it selection driving the same deletions?Or do we have some homology among these sites in general, and then during a chronic infection they're more likelyto be cut out because of polymerase slippage, recombination, etc? When not deleted, how conserved are these sites in nucleotide space? Lots of interesting questions here - I definitely think they warrant a very close look since something is definitely goingon.