COVID-19 Records

Chat message

Slack / Private Message Drop, p.443 [SLACK_000657] · slack_pm:msg:04586

Page text: p.443 · original PDF

Date
2021-01-23 17:19
Type
chat message · slack
recipient
Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker
Andrew Rambaut

Recipients on this medium are inferred from channel membership, not per-message addressing.

Trevor has been going around saying the RSA lineage arose in sequence based on some genomes with only some of the mutations but they are not old sequences and I have heard that Tulio uses some weird homebrew bioinformatics that may call for reference occasionally.

In context

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

  1. 2021-01-23 17:16 Kristian G. Andersen open
    I thought the mutations observed in P.1 / B.1.351 were likely fixed in a single individual and then took off in the population. But seeing them pop up here suggest to me that that likely wasn't the case. Maybe immune selection in_the population_, not _intrahost_, actually fixed them in the first place.
  2. 2021-01-23 17:17 Kristian G. Andersen open
    I think the UK lineage is likely a weird example of a chronic infection that took off, while the BRA/RSA lineages are just a result of selection on the population.
  3. 2021-01-23 17:17 Andrew Rambaut open
    The plastic ones could have just been hitchhiking in the generating individual
  4. 2021-01-23 17:17 Kristian G. Andersen open
    True
  5. 2021-01-23 17:19 Andrew Rambaut
    Trevor has been going around saying the RSA lineage arose in sequence based on some genomes with only some of the mutations but they are not old sequences and I have heard that Tulio uses some weird homebrew bioinformatics that may call for reference occasionally.
  6. 2021-01-23 17:20 Kristian G. Andersen open
    Eh?
  7. 2021-01-23 17:20 Andrew Rambaut open
    Exactly
  8. 2021-01-23 17:21 Kristian G. Andersen open
    That's weird. I mean, P.1. has many overlapping mutations so surely those at least must be right?
  9. 2021-01-23 17:21 Andrew Rambaut open
    I thought they were more likely reversions than intermediates (still unlikely) but when I pointed them out to Tulio hesaid he thought they weren't real and they were fixing them.

Full conversation →