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Slack / Private Message Drop, p.298 [SLACK_000512] · slack_pm:msg:03106

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Doh. I was thinking of RmYN02

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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.
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]
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?
2020-12-06 10:53 Kristian G. Andersen open

Yes
2020-12-06 10:54 Andrew Rambaut

Doh. I was thinking of RmYN02
2020-12-06 10:55 Kristian G. Andersen open

I think it's fair to say that the lineage that led to WA1 > WH04 is probably older than the lineage that led to Hu-1.And yeah - RmYN02.. :wink: That one is ancestral in those positions too
2020-12-06 10:56 Andrew Rambaut open

We have always used WH04 as the root -
2020-12-06 10:57 Kristian G. Andersen open

WA1 may be a more appropriate one - firmly placing the start of the pandemic in the United States :wink:
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?