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Slack / Private Message Drop, p.325 [SLACK_000539] · slack_pm:msg:03423

Date: 2020-12-19 11:01
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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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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2020-12-19 09:55 Kristian G. Andersen open

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

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.
2020-12-19 11:02 Kristian G. Andersen open

(as in - probably not N501Y alone, but N501Y with some other 'contextual' mutations)
2020-12-19 11:06 Kristian G. Andersen open

@Andrew Rambaut - is this true? In Emma's build, yes, but if you include basal lineages, does this still hold? I was trying to look at this on Nextstrain, but it's a mess trying to identify individual events on their tree and I can't move stuff around. Also trying to look at the alignment, but I don't have all the relevant sequence. Lord, do I hate GISAID. [shared file(s): Screen Shot 2020-12-19 at 11.04.37 AM.png]

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