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Slack / Private Message Drop, p.302 [SLACK_000516] · slack_pm:msg:03156

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Would it be worth trying to simulate a WA1 with a date in the beginning of December and run beast?

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2020-12-06 12:27 Andrew Rambaut open

And by WA1 we mean a haplotype identical to WA1 that was in Wuhan before the 15th January
2020-12-06 12:33 Andrew Rambaut open

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 Andrew Rambaut open

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 Andrew Rambaut open

(but all in Wuhan)
2020-12-06 12:36 Kristian G. 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 Andrew Rambaut open

shared file(s): image.png
2020-12-06 12:39 Andrew Rambaut open

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 Andrew Rambaut open

By the way - the C16T in WH04 is probably wrong, it is the very first nucleotide of that sequence. Should find abetter canonical lineage A
2020-12-06 12:44 Kristian G. Andersen open

Ah, yes - could be wrong. Let me see if I can pull the raw data