Chat message

Slack / Private Message Drop, p.302 [SLACK_000516] · slack_pm:msg:03158

Recipients on this medium are inferred from channel membership, not per-message addressing.

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

In context

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

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 open

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

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
2020-12-06 12:52 Andrew Rambaut open

I will find a better one - it isn't full length.
2020-12-06 13:16 Kristian G. Andersen open

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]