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Slack / Private Message Drop, p.297 [SLACK_000511] · slack_pm:msg:03097

Page text: p.297 · original PDF

Date
2020-12-06 10:16
Type
chat message · slack
recipient
Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker
Kristian G. Andersen

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[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]

In context

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

  1. 2020-12-06 10:13 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]
  2. 2020-12-06 10:13 Kristian G. Andersen open
    WA1 has three differences to both WH04 and Hu-1 - all three ancestral.
  3. 2020-12-06 10:15 Kristian G. Andersen open
    Lemme check these human sequences against the larger pango/bat alignment I have - since I have all the assemblies for those too.
  4. 2020-12-06 10:16 Andrew Rambaut open
    Not sure that is the same WH04 - there are some confusing names
  5. 2020-12-06 10:16 Kristian G. Andersen
    [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]
  6. 2020-12-06 10:17 Kristian G. Andersen open
    Lemme get WH04 from GISAID (I have been using MT291829 from NCBI as WH04)
  7. 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...
  8. 2020-12-06 10:42 Andrew Rambaut open
    hCoV-19/Fujian/8/2020 I EPI_ISL_411060 -> seems to be identical to WA1 and sampled around the same time.
  9. 2020-12-06 10:51 Kristian G. Andersen open
    SARS splits the differences.

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