Private channel session 183
61 messages over 4h 19m, 2020-06-18 – 2020-06-18.
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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In basements all over the world people will be looking at Google Maps and drawing straight lines between the fish market and the China CDC head office in Beijing.
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Haha
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I don't really know. I think they all come from the market (1 environmental and 2 people) on the same day so it seems unlikely. Unless this is much bigger than they think.
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You probably saw it but here is the ML tree (with an outgroup root): [shared file(s): beijing_11.ml.tree.png]
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Weird that the one of them is at the base of that polytomy.
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Yeah, it's very interesting. Is it really possibly Beijing has had an outbreak for quite some time? As in at least a few weeks?I have been trying to create an alignment to look at the individual mutation for the last few hours - I can't deal with how big the data is these days... :wink:
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Plausible: https://www.theguardian.com/world/2020/jun/18/global-report-beijing-covid-19-cluster-may-have-begun-amonth-earlier-china-health-chief
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Yup. Bloody exponential growth!
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Could have been a single hit and then slow fuse, boom.
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This whole group has that triple mutation in N. I was trying to work out where that arose (first seen in a German sequence but there might be an earlier one now).
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The other day the narrative was that the Wuhan market was a hot spot because it was 'hot and sweaty' now these markets are hot spots because they are 'cold and wet'. Obviously dry and temperate is the best place to live. Does sound like this cluster has been around for a while though.
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I think the markets are probably just super spreading events + increased surveillance.
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I bet they have a flashing red light on the hospital computer which goes on whenever there is a pneumonia case associated with a live animal market.
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Hah.
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Still curious about the diversity in the 3 genomes.
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One main question I have here - were they wearing masks? There's this (likely wrong) belief now that if we all just put on masks, we'll be fine.
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> Still curious about the diversity in the 3 genomes Between them, or compared to others?
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But there was no coronavirus in Beijing so why would you need to wear masks?
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Between them.
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> But there was no coronavirus in Beijing so why would you need to wear masks? Yup - but question is - did they do anyway? I'm not sure what the current regulations are.
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But we are surely not going to be expecting people to wear masks when there are apparently no cases just in case.
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If the whole of China was wearing masks all the time?
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That is a lot of masks.
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I guess is that masks will still be effectively compulsory in China. In a similar bipolar world, I've screened lots ofpapers on bioRxiv that basically fall into two camps: (i) SARS-CoV-2 is able to bind to ACE2 from a broad range ofspecies; (ii) SARS-CoV-2 is able to bind to ACE2 from a narrow range of species.
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Just saw a paper that showed it infects guinea pigs (and transmits). So we have primates, rodents, carnivores andpholidotes so far.
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Forgot bats.
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I am not sure there is any evidence for bats.
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Mink.
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Human - mink - human - mink - human - human - human - human.
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Somewhere there's a bat.
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Speaking of animals and such - I don't know if some of you might want to chime in on this... https://twitter.com/Ayjchan/status/1273632816983683079?s=20
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Not doing Twitter at the moment
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Had a quick look...if Alina is suggesting that the pangolin RBD came from humans she's totally mad (look at the synonymous diversity). 100% clear that that RBD is out there in nature. Not sure what hosts, but definitely in nature.
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Yeah, I'm not sure what she's suggesting... Either from human or somebody invented the sequence. Hasn't that sequence been seen from multiple animals by multiple labs?
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Yes, it has. The two pangolin papers in Nature (different groups) both show the same RBD in the animals from Guangdong.
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Thought so...
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This is pretty interesting... [shared file(s): Screen Shot 2020-06-18 at 5.27.34 PM.png]
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But the pangolin sequence is only 'highly identical' at the amino acid level. Not synonymous sites...falls in the expected place at those sites.
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Yeah, agreed - but if what she's saying is actually true, then that's definitely strange - that is *not* how the authors describe their data and samples
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I'll get the manuscript from her
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Let me see what I can do on this. I'm working with both groups.
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Still makes no sense because the Liu et al. paper come out before the pandemic.
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"Liu et al. paper come out before the pandemic" > Yup.
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Published online October 24th 2019 if I remember.
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Yup - definitely well before the outbreak began (ohhhh, but what about all those parked cars, huh...?)
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I can easily imagine that the Liu et al. data has influenced the assembly in the later papers but (i) why would this only impact nonsynonymous sites and (ii) how could it possibly have produced the human sequence when no one knew what that was? Liu et al. is clearly a 'blind' study. I've just emailed Tommy if he can assemble the same RBD without the Liu et al. data and/or if it has been Sanger sequenced. The other group have a second paper on the clinicalmanifestations that I am helping them with. They've sequenced the virus again. I've also asked if they can assemble the same RBD without the Liu et al. data and/or if it has been Sanger sequenced.
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The similarity between the RBD and the Guangdong pangolins from the Liu et al. study alone was noted on Virological in late January. How can Liu et al. have possibly known what the human RBD would have looked like? https://virological.org/t/ncov-2019-spike-protein-receptor-binding-domain-shares-high-amino-acid-identity-with-a-coronavirus-recovered-from-a-pangolin-viral-metagenomic-dataset/362
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Here's the manuscript from her - please keep confidential. I haven't read it yet. [shared file(s): Matters Arising ChanZhan 2020.pdf]
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I think the main problem here is not really how that pangolin sequence ended up having that RBD, but rather whether there's anything sketchy here from a scientific standpoint. These studies are presented each as independent evidence of the pangolin virus RBD, but if all those papers are relying on a third data set - and don't actually have _any_ data from this very critical CoV RBD, then that's an issue.
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I don't really see how this changes anything from the evolutionary perspective - because seeing it even once is very strong evidence. But there's no denying that if these studies have to be modified (or possibly even retracted), then that is going to send a nuke into the whole evolution conversation - whether justified or not.
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Can we do a quick Zoom now.
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Tommy's paper very clearly stated the provenance. Can't speak for the others.
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https://us02web.zoom.us/j/9673242666
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Hi Eddie, Although the pangolins used in Liu's study overlap with ous, we did not used Liu's data in this new paper,and assemble four new virus genomes. In addition, we amplied and sequenced (Sanger sequencing) the complete S genes from lung tissues and virus isolate independently, and comfirm the high-throughput sequencing. As showed inFigure S2, the new genomes almost the same as our previous genome and Lam's. Therefore, i am sure that the previous data is correct.I have discussed with Liu several days ago, he also used Sanger sequencing to attain a nearly complete genome, and confirm his high-throughput result. The latest data in this new article will reassure everyone.Sincerely,Yongyi Shen [shared file(s): image.png]
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Just to spice things up, Australia is currently experiencing a state-sponsored cyber-attack that is widely believed tobe from China.
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.... this won't end well.
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Oh no.
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For the last month, I have been feeling like I'm one of these guys: https://en.wikipedia.org/wiki/Musicians_of_the_RMS_Titanic
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I had better buy a top-hat.
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I keep thinking of Hugh Trevor-Roper and the Hitler Diaries (you may need to look that one up).
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Haha, good one.