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Slack / Private Message Drop, p.325 [SLACK_000539] · slack_pm:msg:03419

Date: 2020-12-19 09:55
Type: chat message · slack
mentioned: Robert F. Garry
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen
Topics: Furin cleavage site and molecular features

Recipients on this medium are inferred from channel membership, not per-message addressing.

That additional mutation in the South African lineage is quite interesting - E484K is a flip of charge and K is novel inthis position across all the CoVs. @Robert Garry - any chance you can please take a look at that mutation to see ifyou might have any insights? The mutation has popped up a few times independently across the tree.

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2020-12-19 08:04 Andrew Rambaut open

South African N501Y lineage also has E484K but not much else I think. It has a very long unsampled branch with some USA ones as an outgroup. So no real evidence of a big bunch of mutations happening together.
2020-12-19 08:50 Kristian G. Andersen open

Andrew, what's the best representative sequence for the UK lineage? All on GISAID?
2020-12-19 09:20 Andrew Rambaut open

Actually the earliest one is a pretty good one: `England/MILK-9E05B3/2020|2020-09-20`
2020-12-19 09:55 Kristian G. Andersen

That additional mutation in the South African lineage is quite interesting - E484K is a flip of charge and K is novel inthis position across all the CoVs. @Robert Garry - any chance you can please take a look at that mutation to see ifyou might have any insights? The mutation has popped up a few times independently across the tree.
2020-12-19 10:45 Andrew Rambaut open

486 is a contact residue, right? Crops up in the Dutch mink.
2020-12-19 10:52 Kristian G. Andersen open

Yup - it's F in SC2, but L in SC1 and many of the bat viruses (I believe also L in the mink?)
2020-12-19 10:58 Andrew Rambaut open

yup
2020-12-19 11:01 Kristian G. Andersen open

I pinged Andrew Ward this morning to see if he could get one of his structural guys to take a close look at all of this -I'm sure you're already doing it too, but good to get a bunch of eyes on this. What's interesting about the SA link is that if we're really seeing this explosive growth, then it's down to N501Y and not all the other mutations. Which seems a little strange to me.

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