Private channel session 1110
18 messages over 1h 26m, 2021-03-15 – 2021-03-15.
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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Still eagerly awaiting the WHO report. Hard to believe but Eddie's email about the smoking raccoon dog was only March 9. "the drain grates that the raccoon dogs were sitting on top of in your pictures correspond to the places inthe market where they found the lowest CoV Ct values (all of this is still confidential but will be in the report I think). Seems reasonable that those guys were infected and shedding virus in their feces, as Koopmans thought it was highly unlikely that that level of CoV RNA would be in those grates from human sources." Coming to realize that the2nd part of the email also interesting: "The WHO team also found frozen raccoon dog/ferret badger (they're unsureand I think are waiting for barcoding) carcasses still at the market, so it's possible that *some of the frozen fooddetections they've had could have come from the same source farm or processing plant as the live animals*." The*bolded* part would be another bullet fired from the smoking gun, if true. I've still got more questions: 1. Cases - Ihad to confirm that I was remembering correctly - were linked to the Huanan Market for over a MONTH.https://www.nejm.org/doi/full/10.1056/NEJMoa2001316 Market closed and environmental samples from the Market taken 1Jan21.I don't think that high levels of virus would stick around on a grate for all that long a period of time. Does this mean based on when the the cases showed up that there were infected animals that market for several weeks? [shared file(s): image.png]
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Question 2: Given that the virus in the environmental samples most likely came from animals in the market [I agree with Koopmans on this key point], and that the environmental samples are in fact SARS-CoV-2 (lineage B) does this mean that SC2 already fully formed has been circulating in nature? I'm having a hard time coming to any other conclusion, but would like to talked down from that as a conclusion and hear other possibilities.
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I don't understand the frozen food hypothesis. How did it get from bats to frozen foods and then to animals at the market? Doesn't make sense to me...
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I'm not sure it has to come from bats to the frozen foods to the animals. In fact, looks to me like SC2 is already inthose animals. If I understand the EgoHealth email to Eddie and what Koopsmans had leaked to the press over the past few weeks - she thinks that some of the frozen animal samples that are positive came from the same supplieras the suppler for the raccoon dogs. Some of the frozen meat also being raccoon dogs. Koopmans said it was likely that the meat itself was positive not the outside of the package.
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Still seems very strange to me - a batch of, say, frozen raccoon dogs are positive, but so are live raccoon dogs atthe market? Coming from the same supplier?
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Exactly - that's what I think Koopmans is sitting on...
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Well, if they have actual evidence of that, then it's a done deal. Not impossible, I guess, but seems strange.
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I'm not sold on the frozen food thing either - far from it. But I think that the positive grate plus Eddie's raccoon dog pics are pretty nearly the same thing to actually have taken the swab directly from the animal's ass.
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The grates, totally - and yes, raccoon dogs, or whatever other animal for that matter. Makes perfect sense. But how that fits in with frozen foods, I don't understand. That said, Marion must have something good here, otherwise there's no way she'd go down that path - she's much, much too smart for that. There must be some actual evidence.
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Then there is the whole lineage A and B = the animals in the Huanan market are lineage B, so how did lineage A get started? The NEJM paper says other case werelinked to other markets, but which ones and which were sequenced Idon't know,.
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My read as well -on Marion.
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Yes, Marion is cautious so they must have something. Hope they release soon. I may have told you but I also heard that they had discounted the Dec 1 case and the earliest known one is now Dec 8. I also think I heard that while this patient had no link to the market his parents had some sort of link to another live animal market. Not sure is this issomething or not.
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Dec 8 is consistent with the graph from the CCDC NEJM paper.
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Lots of questions for Kristian: [shared file(s): image.png]
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Pathetic
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I think there's _a lot_ of early unsampled diversity, which can help explain the A vs B split. Much focus turned to the Huanan market, where super spreading might have occurred, so we end up having very biased sampling early on.
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That seems right. But is the diversity in unsampled humans, unsampled animals or perhaps both. Only A and B lineages made it through the bottleneck.
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Another way to ask the questions: B came from A as Andrew said in the NatMicro paper. But did the split happen inan animal or after the human to animal transfer? Maybe doesn't really matter.