Private channel session 1163

9 messages over 1h 0m, 2021-03-27 – 2021-03-27.

A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.

1. 2021-03-27 16:58 Andrew Rambaut open PDF p.645
   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 PDF p.645
   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 PDF p.645
   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 PDF p.645
   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 open PDF p.645
   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 PDF p.646
   Worth (possible?) to test if midpoint fits the early data best too?
7. 2021-03-27 17:08 Andrew Rambaut open PDF p.646
   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 PDF p.646
   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 PDF p.646
   ... but it requires some proper phylogenetics - i might try some stuff.