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Slack / Private Message Drop, p.956 [SLACK_001170] · slack_pm:msg:09945

Page text: p.956 · original PDF

Date: 2021-06-21 17:26
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Andrew Rambaut
speaker: Edward C. Holmes

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Have you seen Sergei's Italian job?

In context

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2021-06-21 17:19 Kristian G. Andersen open

It seems to me that there are four main issues here with his / Rasmus' thinking: • They assume the sequence closest to RaTG13 must be the root - that is incorrect as we see _a lot_ of reversions.• They assume A > B and that that happened in the human population. We don't know that - A > B or B > A(former more parsimonious) and the MRCA may _very_ well be in animals, not humans.• They assume a single introduction into the human population.• They assume non-biased sampling from both the Huanan market and elsewhere - we know this definitely isn't true. There might _very_ well have been Lineage A circulating at the Huanan market, but we didn't capture it because ofbias - e.g., SSE of Lineage B at that market. The idea that _any_ of the recent data make Huanan a less likely place for a spill-over is hugely flawed IMO - totally wrong.
2021-06-21 17:19 Andrew Rambaut open

@Andrew Rambaut I have lazily put in a few 'REF's where it seem to need it. If they are still there tomorrow, I will gohunting.
2021-06-21 17:24 Edward C. Holmes open

Sure. I'm out of town this week and don't have much time to do much, but I'll take a look later. Is there anything about the rooting in the paper? I think we had probably add a line about this...I agree with Kristian's logic - I don't see why the sequence closest to RaTG13 is the root.
2021-06-21 17:25 Andrew Rambaut open

Be good to preempt them
2021-06-21 17:26 Edward C. Holmes

Have you seen Sergei's Italian job?
2021-06-21 17:27 Andrew Rambaut open

No?
2021-06-21 17:27 Kristian G. Andersen open

The problem with the rooting is that it's very complex so not sure we want to add it - working on a paper with Joel and Marc that should settle this. But it's just so frustrating to see their naiveté - especially since they know a lot more about rooting than I do. But this one is obvious...
2021-06-21 17:27 Edward C. Holmes open

Ok...I'll find it....definitely keep this to yourself...
2021-06-21 17:27 Kristian G. Andersen open

Oh boy.

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