A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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Yeah. Just some phylogenies, recombination and date estimates of SARS related coronaviruses. Nothing you haven't heard already.
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Cool! One interesting thing I got from Trevor though - if he tries to date SARS2 via the related viruses (of which we now have a few), he gets a relatively nice signal for 2014/2015. Doesn't mean anything in isolation, but I still keepcontemplating that 'pre' circulation scenario for emergence. They need to go hunt some more viruses in those Yunnan caves!
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It is meaningless to date SARS2 with related viruses - makes no sense.
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I thought so too, but honing in on specific parts of the genomes that were homologous it seemed like it could bedone - no idea about the details though.
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2020-07-27 14:43
Andrew Rambaut
It also makes no sense that the SARS2 diversity circulating now was part of the pre-circulating scenario. The Wuhanhaplotype may have been around for a month or two prior to Dec 2019 but not much longer given the transmissibilityof the virus. This virus doesn't lurk unobserved.
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Has Trevor found his next thing to go off on Twitter about?
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"This virus doesn't lurk unobserved" - as is, definitely true - but I _do_ wonder if a pre-furin site virus could. But Iagree with you - I'm not sure such an analysis makes sense given our limited sampling. Assuming SARS2 came outof Yunnan diversity (which seems likely), it would be cool to go do some in-depth sampling from there. And yes, maybe we'll get the big reveal on Twitter :wink:
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But if the acquisition of the furin site is the point at which it becomes epidemic then once again we are back to the common ancestor of the current diversity being in late 2019. We don't have any other nodes to date.
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.... ehm, yes. That is, of course, true... Unless it's been in a freezer since that outbreak in the Mojiang mine...:parrot: