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Slack / Private Message Drop, p.297 [SLACK_000511] · slack_pm:msg:03095

Page text: p.297 · original PDF

Date
2020-12-06 10:15
Type
chat message · slack
recipient
Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker
Kristian G. Andersen

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

Lemme check these human sequences against the larger pango/bat alignment I have - since I have all the assemblies for those too.

In context

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

  1. 2020-12-06 10:11 Andrew Rambaut open
    Wuhan-Hu-1: T:8781:C|T:18059:C|C:28143:T WH04: T:18059:C WA1: 0:
  2. 2020-12-06 10:11 Kristian G. Andersen open
    The version I have of Hu-1 (MN908947) is identical - weird... Lemme check again
  3. 2020-12-06 10:13 Kristian G. Andersen open
    Yup, identical based on NCBI records (except the ends). Here's the Geneious alignment [shared file(s): 2020.12.06_alignment.geneious]
  4. 2020-12-06 10:13 Kristian G. Andersen open
    WA1 has three differences to both WH04 and Hu-1 - all three ancestral.
  5. 2020-12-06 10:15 Kristian G. Andersen
    Lemme check these human sequences against the larger pango/bat alignment I have - since I have all the assemblies for those too.
  6. 2020-12-06 10:16 Andrew Rambaut open
    Not sure that is the same WH04 - there are some confusing names
  7. 2020-12-06 10:16 Kristian G. Andersen open
    [and I'll see if I can get the raw data for WA1 so I can check the assembly for that one too - although it's been sequenced multiple times, so I assume it's correct]
  8. 2020-12-06 10:17 Kristian G. Andersen open
    Lemme get WH04 from GISAID (I have been using MT291829 from NCBI as WH04)
  9. 2020-12-06 10:32 Kristian G. Andersen open
    Comparing to all the pango/bat sequences here is interesting - in two out of the three positions (8782 (C/T) and(18060 C/T) where WA1 is ancestral compared to RaTG13, all the other pango/bat genomes have the same asRaTG13 - so definitely ancestral. HOWEVER, RmYN01 has the same derived residues in those positions as WA1. (Ican't check the third position - RmYN01 has bad sequencing around that position). Checking SARS...

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