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Slack / Private Message Drop, p.299 [SLACK_000513] · slack_pm:msg:03115

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Yup.

In context

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

2020-12-06 10:59 Kristian G. Andersen open

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 Kristian G. Andersen open

I think considering WA1 basal to WH04 is appropriate based on that single difference
2020-12-06 10:59 Kristian G. Andersen open

(and I'd say ancestral here, since we have all the other genomes we can compare to)
2020-12-06 11:00 Andrew Rambaut open

I think we know that WA1 travelled from Hubei (need to check) so that places the WA1 haplotype in Hubei
2020-12-06 11:02 Kristian G. Andersen

Yup.
2020-12-06 11:03 Andrew Rambaut open

Sampled in WA on 19-Jan
2020-12-06 11:04 Kristian G. Andersen open

I don't have my annotations right - which one is the non-synonymous change? Position 18060, which is the one thatdistinguishes WA1 from WH04 is the same in SARS as it is in WA1/RaTG13 (T)
2020-12-06 11:04 Andrew Rambaut open

One other possibility - hCoV-19/Malaysia/MKAK-CL-2020-6430/2020|EPI_ISL_416886|2020-02-04 is one SNP from WA1. Pangolin connection?
2020-12-06 11:07 Andrew Rambaut open

18060 is synon.