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Slack / Private Message Drop, p.296 [SLACK_000510] · slack_pm:msg:03085

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What do you use as prototypical Lineage A?

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

2020-12-06 09:52 Andrew Rambaut open

I was just taking a closer look at the rooting of the pandemic. Our lineage A is definitely 2 nucleotides (1 amino acid) closer to RaTG13 than lineage B (Wuhan-Hu-1). But interestingly WA1 is one nucleotide closer still (out of a1150-odd, of course). It looks like the some of lineage A had a chance reversion (synonymous). But may be the cause of mis-rooting.
2020-12-06 09:54 Kristian G. Andersen open

In what sites? Lemme check the bam file to see how confident those RaTG13 calls are in those positions
2020-12-06 09:55 Kristian G. Andersen open

There are some low-coverage regions in that genome where you have ambiguous calls
2020-12-06 10:02 Kristian G. Andersen open

Just compared WA1 to Hu-1 and RaTG13. Only three differences between the two, all of them ancestral in WA1 - not Hu-1.
2020-12-06 10:02 Kristian G. Andersen

What do you use as prototypical Lineage A?
2020-12-06 10:03 Andrew Rambaut open

WH04
2020-12-06 10:03 Kristian G. Andersen open

Lemme include that too - and I should say, all those calls are fully supported in the RaTG13 assembly, so they're good
2020-12-06 10:04 Kristian G. Andersen open

It's that midpoint root.... Some early emergence funkiness.
2020-12-06 10:06 Kristian G. Andersen open

I have WH04 being identical to Hu-1, except the ends - do you have a different sequence?