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Slack / Private Message Drop, pp.298-299 [SLACK_000512] · slack_pm:msg:03114

Page text: p.298, p.299 · original PDF

Date
2020-12-06 11:00
Type
chat message · slack
recipient
Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker
Andrew Rambaut

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I think we know that WA1 travelled from Hubei (need to check) so that places the WA1 haplotype in Hubei

In context

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  1. 2020-12-06 10:58 Andrew Rambaut open
    Question is do we consider that WA1 (or more likely a Chinese genome such as hCoV-19/Fujian/8/2020) is basal to WH04?
  2. 2020-12-06 10:59 Kristian G. Andersen open
    Out of curiosity, I also checked WH1-4 since they had those super funky ENA entries (still do.... SAMEA6507890 -SAMEA6507893) - WA1/WH04 basal to those as well. [shared file(s): 2020.12.06_early-genomes.geneious]
  3. 2020-12-06 10:59 Kristian G. Andersen open
    I think considering WA1 basal to WH04 is appropriate based on that single difference
  4. 2020-12-06 10:59 Kristian G. Andersen open
    (and I'd say ancestral here, since we have all the other genomes we can compare to)
  5. 2020-12-06 11:00 Andrew Rambaut
    I think we know that WA1 travelled from Hubei (need to check) so that places the WA1 haplotype in Hubei
  6. 2020-12-06 11:02 Kristian G. Andersen open
    Yup.
  7. 2020-12-06 11:03 Andrew Rambaut open
    Sampled in WA on 19-Jan
  8. 2020-12-06 11:04 Kristian G. Andersen open
    I don't have my annotations right - which one is the non-synonymous change? Position 18060, which is the one thatdistinguishes WA1 from WH04 is the same in SARS as it is in WA1/RaTG13 (T)
  9. 2020-12-06 11:04 Andrew Rambaut open
    One other possibility - hCoV-19/Malaysia/MKAK-CL-2020-6430/2020|EPI_ISL_416886|2020-02-04 is one SNP from WA1. Pangolin connection?

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