Private channel session 1533
36 messages over 1h 28m, 2021-06-21 – 2021-06-21.
A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.
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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.`
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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.
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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).```
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@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.
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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.
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@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.
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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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Be good to preempt them
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Have you seen Sergei's Italian job?
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No?
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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...
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Ok...I'll find it....definitely keep this to yourself...
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Oh boy.
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Check out Figure 2 [shared file(s): 21-09335_Proof_hi.pdf]
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I cant read it now but they are mental
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They say D614G was there in September 2019
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@Kristian Andersen We talk about the 2 haplotypes (I think we should add the 3rd). We can just say that the 1100mutations to bat makes it impossible and cite Sergeis reply to the Forsters. I will come up with something in the morning
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OMG, he mentioned "early cases in Europe" on the call yesterday and how "all the timing may well change". Come on - this is dumb. I didn't want to get into an argument about it on the call, but come on guys. :face_with_rolling_eyes:
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I'm sure Chairman Xi will welcome this paper with open arms.
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@Kristian Andersen Awesome.
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It was sent to me by someone who was reviewing it for advice and I said it was almost certainly just contamination from the major Italian wave...notable that they are getting the sequences from the patients that are PCR negative.
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Why are they saying it came from Wuhan? Why not an Italian lab escape? Bonkers
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D614G is pretty much a dead giveaway...
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USAMRIID after all, huh? I hear there's an Italian working there.
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Knew it. It was Gus
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Yes, I love the way it goes from Wuhan and then to Italy :zany_face: For the rooting thing, I think it just needs one statement given that we have the 2 lineages x 2 markets story. It doesn't need to be definitive but just to say it iscomplex.
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Argentinian, I believe, but basically the same, so definitely. Just connecting dots here.
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There are a lot Italians in Argentina...
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Diego Maradona played for Napoli
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Nailed it! King of DRASTIC.
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Diego was a good mate of Castro!
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I mean - what are the chances? Maradona 100% the best player of all times, so clearly there's a connection here.
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@Kristian Andersen Yes, that's all I wanted. Perfect.
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:exploding_head:
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USAMRIID were developing the bioweapon and testing on prisoners at Guantanamo. Castro found out and wanted to know what it was. He got hold a sample and gave it to his mate Maradona to give to an Italian lab to be discretelytested. Their sloppy lab protocols allowed it to escape into Rome. Unfortunately, Maradona also took a sniff of thevial and died. Patient zero - 25th November 2020. If we had his sequence it would be another snp closer to RaTG13.Maradona's shirt number was 10, which only 3 away from the 13 in RaTG13. It all fits, apart from the Wuhan wet market.
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You might want to email that to Metzl - I suspect he might want to replace his current history of events that took place.