Private channel session 402
25 messages over 3h 26m, 2020-09-18 – 2020-09-18.
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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Bacteria! Insane. Yes, she's not a whistleblower - just a fantasist with an axe to grind.
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Yup. For what it's worth, I decided to reassemble all these bloody genomes to take a look myself. I'll post it all onvirological once I'm done.
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It can't hurt - Unfortunately, it won't stop the Captain or the Inspector. It may be a counterweight. Reading through Alina's latest tweet emesis, she is as Eddie says definitely a fantasist. I'm also starting to think that Gao may bepaying her by the word.
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Agreed - this won't change anything but I want to at least have something I can point to. It's just so so dumb. Really.(luckily, I'm enjoying this since it's been a long time I last did some *actual* work, so I'm happy to be assembling shit again).
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It's just so soothing to see code run over my screen...
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Yan is the fantasist. Alina has just lost it.
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Here's what I'm assembling - missing anything? [shared file(s): Screen Shot 2020-09-18 at 15.39.27.png]
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MP789 is the same(ish) as the one that was initially reported on virological
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Pretty interesting. Looking at RmYN02 the consensus is totally solid, however, I actually think there's another closely related bat CoV in there at a ~15% frequency. I'll dig a little deeper, but Tommy might be interested in looking at that
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I SO hoped some of these intrahost mutations near the RBD or the FCS, but sadly no. Would have been cool!
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You mean RmYN01? Yes, I've been asking Weifeng to get some analysis done on that for ages.
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I think he said he only had an incomplete genome, including the RdRp, although even though that would be really interesting.
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Sorry, you mean in the RmYN02 reads? I seem to remember Weifeng discussing that before. Might even be noted in the paper. Can't remember. RmYN02 is pooled from a number of bats - 11 or 13, I can't quite recall.
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Yeah, RmYN02 - the more complete of the two genomes. Definitely another genome in there
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It's another bat CoV closely related (but not identical) to others previously sequenced. Every yellow bar is an intrahost variant >10% (SNPs are all linked as far as I can tell, so I think it's just one additional genome) [shared file(s): Screen Shot 2020-09-18 at 16.19.28.png]
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Yes, I agree. I'll check back what we did - if anything - about this. It would be really interesting to see a phylogeny with that, RmYN02 and RmYN01 included.
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I'm just going to pull that minority genome out - I'll keep you posted... Yeah, this is very interesting
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Great!
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Here's what I have assembled so far - all look great. Only need to assemble one of the remaining pangolin CoVs, which has a huge dataset. RBD in green. Conclusion? Nothing to see here.... as expected. [shared file(s): MP789.jpg, P1E.jpg, P2S.jpg, P2V.jpg, P3B.jpg,P4L.jpg, P5E.jpg, P5L.jpg, RaTG13.jpg, RmYN02.jpg]
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Great work! So annoying that these people are accusing of fabrication when they are honest scientists working hard. Makes by blood boil.
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Here's the minor genome - probably not a complete genome, but definitely present. [shared file(s): minor_variant_genome.fa]
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Alignment + tree [shared file(s): Alignment with minor RmYN02 RAxML Tree.nex, Alignment with minor RmYN02.nex]
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Cool! Quick tree?
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And some stats. This is all some fast hacked together stuff, so the boys should take a closer look. Tree above - quick ML tree. You'll see close clustering with the consensus genome, but this might be an artifactbecause non-coverage in the minor genome would just display the consensus genome. Definitely worth looking alittle closer. [shared file(s): variants.tsv, variants_pos.pdf]
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Got it! Sorry, our posts crossed. I'll have a chat to Weifeng. Nice one. Is RmYN01 closer than ZC45? I'm trying to get more bat ronas as we speak (through a very unusual source). More later.