Slack / Private Message Drop — page 302

WA1 [2020-12-06 12:27:59] [Andrew Rambaut] And by WA1 we mean a haplotype identical to WA1 that was in Wuhan before the 15th January [2020-12-06 12:33:35] [Andrew Rambaut] Curious though that the Malaysian one is one SNP closer to RmYN02 than all the others. So possibly that one (but the January cases in Malaysia were Chinese nationals visiting) [2020-12-06 12:35:09] [Andrew Rambaut] So I think most parsimonious would be `Malaysia/MKAK-CL-2020-6430|EPI_ISL_416886|2020-02-04` -> `WA1` -> `WH04` -> `Wuhan-Hu-1` [2020-12-06 12:35:22] [Andrew Rambaut] (but all in Wuhan) [2020-12-06 12:36:07] [Kristian Andersen] Would it be worth trying to simulate a WA1 with a date in the beginning of December and run beast? [2020-12-06 12:38:23] [Andrew Rambaut] shared file(s): image.png [2020-12-06 12:39:39] [Andrew Rambaut] Given we see identical genomes spaced 6 weeks apart, I don't think we need to use imputed dates - just enforce WA1 to be an outgroup [2020-12-06 12:40:59] [Andrew Rambaut] By the way - the C16T in WH04 is probably wrong, it is the very first nucleotide of that sequence. Should find a better canonical lineage A [2020-12-06 12:44:25] [Kristian Andersen] Ah, yes - could be wrong. Let me see if I can pull the raw data [2020-12-06 12:52:50] [Andrew Rambaut] I will find a better one - it isn't full length. [2020-12-06 13:16:21] [Kristian Andersen] Some cleaner alignments here with better naming, etc. [shared file(s): 2020.12.06_SARS-CoV-2_RaTG13.geneious, 2020.12.06_SARS2_SARS_SARS-like.geneious] [2020-12-07 04:34:27] [Robert Garry] Maybe the NOLa data somewhat relevant? Limited sequence diversity - "clear" timing... [2020-12-08 09:58:27]