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Slack / Private Message Drop, p.646 [SLACK_000860] · slack_pm:msg:06766

Date: 2021-03-27 17:08
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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I can't see anything obvious in that Tanzanian one - just lots of convergent stuff as you say. I assume they are 3connected cases so probably some chronic case?

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-03-27 17:02 Kristian G. Andersen open

Yes, I think we do - because with the WHO report coming out, chances are well be hammering hard on the market. I'll play around with some stuff later too.
2021-03-27 17:02 Andrew Rambaut open

We have a number of haplotypes that are definitely in Wuhan in Jan 2020 but I think only 3 with multiple instances (there are ones with a few unique mutations) - A (WH04 etc), B (Wuhan-Hu-1) and WA1 - we could root on each ofthese and do a beast tree and see which fits best.
2021-03-27 17:04 Andrew Rambaut open

Test significance of being 1 base closer to RaTG13 - is it just chance? a reversion?
2021-03-27 17:05 Kristian G. Andersen open

Worth (possible?) to test if midpoint fits the early data best too?
2021-03-27 17:08 Andrew Rambaut

I can't see anything obvious in that Tanzanian one - just lots of convergent stuff as you say. I assume they are 3connected cases so probably some chronic case?
2021-03-27 17:56 Kristian G. Andersen open

It shares the early unique SNPs with e.g. WA1 and has a couple of additional 'ancestral' ones. Plus a bunch of private mutations. It looks to me like a very old lineage that turned into a chronic infection (in humans or possibly not)
2021-03-27 17:58 Kristian G. Andersen open

... but it requires some proper phylogenetics - i might try some stuff.

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