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Slack / Private Message Drop, p.325 [SLACK_000539] · slack_pm:msg:03418

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Actually the earliest one is a pretty good one: `England/MILK-9E05B3/2020|2020-09-20`

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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

Actually the earliest one is a pretty good one: `England/MILK-9E05B3/2020|2020-09-20`
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