Chat message

Slack / Private Message Drop, p.955 [SLACK_001169] · slack_pm:msg:09939

Date: 2021-06-21 17:14
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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My reply about the rooting: ```But I don't really see any of this as relevant other than some interesting epi and timing - it looks to me that the ideas we had right at the beginning that this was live animal population in markets, starting multiple chains ofinfection until 3 of them really kicked off. The evidence of live animals in these markets seem conclusive that here isa hugely explanatory hypothesis. The lab-escape idea is a non starter unless there was actually evidence of 'lab-capture'. Anyone can see that escape has prior. The problem is without evidence that SC2 was in the lab in the first place just asserting it was is anon-starter. There are vastly more ways that live viruses can reach markets in Wuhan over nearly 2 decades than the chance that a few scientists found one in a bat (let alone cultured and stored in secret without sequencing it).Jesse, Fred and the others are going to make a huge fuss but there will never be anyway of scientifically getting evidence to support their idea - it basically requires documentary evidence which will not exist either way (either itdoesn't exist or it was destroyed).```

In context

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2021-06-21 17:12 Andrew Rambaut open

Uggh.... ```Thanks for the note Andrew. Public discourse and Twitter in particular surrounding "lab leak" has become increasingly toxic. I hope you're surviving the Fauci FOIA sniping. I wrote today's message to the group imagining it will get FOIAed. I do see this rooting issue as pretty critical. If root is parsimonious with RaTG13 or other outgroups it would suggest market as Huanan market outbreak as secondary foci. Or at least that's my take. But would be good to have a fullyrigorous assessment of root and on top of this epi implications of different rootings. (edited)10:12 I've had a sparsely running DM with Kristian about origins since last summer, though I largely hadn't been paying much attention to it until things blew up recently.````I wrote today's message to the group imagining it will get FOIAed.`
2021-06-21 17:14 Kristian G. Andersen open

I don't think Trevor is thinking right... Does he understand the _actual_ issues with the type of rooting he mentions? We have come a long way since the days of parsimony and I don't necessarily think this needs to go to Cladistics.
2021-06-21 17:14 Andrew Rambaut

My reply about the rooting: ```But I don't really see any of this as relevant other than some interesting epi and timing - it looks to me that the ideas we had right at the beginning that this was live animal population in markets, starting multiple chains ofinfection until 3 of them really kicked off. The evidence of live animals in these markets seem conclusive that here isa hugely explanatory hypothesis. The lab-escape idea is a non starter unless there was actually evidence of 'lab-capture'. Anyone can see that escape has prior. The problem is without evidence that SC2 was in the lab in the first place just asserting it was is anon-starter. There are vastly more ways that live viruses can reach markets in Wuhan over nearly 2 decades than the chance that a few scientists found one in a bat (let alone cultured and stored in secret without sequencing it).Jesse, Fred and the others are going to make a huge fuss but there will never be anyway of scientifically getting evidence to support their idea - it basically requires documentary evidence which will not exist either way (either itdoesn't exist or it was destroyed).```
2021-06-21 17:18 Andrew Rambaut open

@Eddie Holmes Eddie - will you take control of the document again? I have been over it and removed some of the added waffle, tried to tighten it up a bit. Need to stop it wandering again. But I think it is looking really good.
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.

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