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Slack / Private Message Drop, pp.645-646 [SLACK_000859] · slack_pm:msg:06764

Page text: p.645, p.646 · original PDF

Date
2021-03-27 17:04
Type
chat message · slack
recipient
Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker
Andrew Rambaut

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Test significance of being 1 base closer to RaTG13 - is it just chance? a reversion?

In context

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  1. 2021-03-27 16:58 Andrew Rambaut open
    OK - returning to this thread from Dec last year: https://andersenlab.slack.com/archives/GTGL6LY5C/p1607277127336700
  2. 2021-03-27 16:59 Andrew Rambaut open
    Do we want to pursue this a bit more? Perhaps have something ready for the WHO report drop?
  3. 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.
  4. 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.
  5. 2021-03-27 17:04 Andrew Rambaut
    Test significance of being 1 base closer to RaTG13 - is it just chance? a reversion?
  6. 2021-03-27 17:05 Kristian G. Andersen open
    Worth (possible?) to test if midpoint fits the early data best too?
  7. 2021-03-27 17:08 Andrew Rambaut open
    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?
  8. 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)
  9. 2021-03-27 17:58 Kristian G. Andersen open
    ... but it requires some proper phylogenetics - i might try some stuff.

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