Slack / Private Message Drop — page 298

[2020-12-06 10:52:18] [Kristian Andersen] 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 10:53:10] [Kristian Andersen] 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 10:53:41] [Andrew Rambaut] Am I going mad - I just downloaded RmYN01 from GISAID and it is coming out as more divergent than RaTG13? [2020-12-06 10:53:49] [Kristian Andersen] Yes [2020-12-06 10:54:43] [Andrew Rambaut] Doh. I was thinking of RmYN02 [2020-12-06 10:55:22] [Kristian Andersen] 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 10:56:44] [Andrew Rambaut] We have always used WH04 as the root - [2020-12-06 10:57:19] [Kristian Andersen] WA1 may be a more appropriate one - firmly placing the start of the pandemic in the United States :wink: [2020-12-06 10:58:24] [Andrew Rambaut] Question is do we consider that WA1 (or more likely a Chinese genome such as hCoV-19/Fujian/8/2020) is basal to WH04? [2020-12-06 10:59:05] [Kristian Andersen] 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] [2020-12-06 10:59:33] [Kristian Andersen] I think considering WA1 basal to WH04 is appropriate based on that single difference [2020-12-06 10:59:51] [Kristian Andersen] (and I'd say ancestral here, since we have all the other genomes we can compare to) [2020-12-06 11:00:29] [Andrew Rambaut]