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Slack / Private Message Drop, p.297 [SLACK_000511] · slack_pm:msg:03100

Page text: p.297 · original PDF

Date
2020-12-06 10:42
Type
chat message · slack
recipient
Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker
Andrew Rambaut

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hCoV-19/Fujian/8/2020 I EPI_ISL_411060 -> seems to be identical to WA1 and sampled around the same time.

In context

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  1. 2020-12-06 10:16 Andrew Rambaut open
    Not sure that is the same WH04 - there are some confusing names
  2. 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]
  3. 2020-12-06 10:17 Kristian G. Andersen open
    Lemme get WH04 from GISAID (I have been using MT291829 from NCBI as WH04)
  4. 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...
  5. 2020-12-06 10:42 Andrew Rambaut
    hCoV-19/Fujian/8/2020 I EPI_ISL_411060 -> seems to be identical to WA1 and sampled around the same time.
  6. 2020-12-06 10:51 Kristian G. Andersen open
    SARS splits the differences.
  7. 2020-12-06 10:52 Kristian G. Andersen open
    Compared to all the pango/bat genomes, those positions appear ancestral to me - Hu-1 and RmYN01 have derived residues in those positions.
  8. 2020-12-06 10:53 Kristian G. Andersen open
    Here's an alignment - it's pretty messy and some duplicates... [shared file(s): 2020.12.06_pango-bat-sars2_alignment.geneious]
  9. 2020-12-06 10:53 Andrew Rambaut open
    Am I going mad - I just downloaded RmYN01 from GISAID and it is coming out as more divergent than RaTG13?

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