Slack / Private Message Drop — page 956

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 of bias - 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 17:19:31] [Andrew Rambaut] [thread - ID: 2021-06-21 17:18:54] @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 go hunting. [2021-06-21 17:24:50] [Eddie Holmes] 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 17:25:54] [Andrew Rambaut] Be good to preempt them [2021-06-21 17:26:42] [Eddie Holmes] Have you seen Sergei's Italian job? [2021-06-21 17:27:09] [Andrew Rambaut] No? [2021-06-21 17:27:15] [Kristian Andersen] [thread - ID: 2021-06-21 17:27:15] 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 17:27:39] [Eddie Holmes] Ok...I'll find it....definitely keep this to yourself... [2021-06-21 17:27:56] [Kristian Andersen] Oh boy. [2021-06-21 17:29:09] [Eddie Holmes] Check out Figure 2 [shared file(s): 21-09335_Proof_hi.pdf] [2021-06-21 17:30:02] [Andrew Rambaut]