--- type: Conversation title: Private channel session 402 description: "slack conversation, 25 messages, 2020-09-18." tags: - conversation - slack medium: slack message_count: 25 started_at: "2020-09-18T14:44:51" ended_at: "2020-09-18T18:11:03" duration_seconds: 12372 sources: - { id: slack_pm, resource: /sources/slack-pm.md, title: Slack / Private Message Drop, author: "process:senate-hsgac-release" } generated: { by: randpaul-corpus-pipeline/1.0, at: "2026-08-01T12:42:27Z" } status: stable --- A slack conversation of 25 messages spanning 3h 26m. # Metadata - **Started:** 2020-09-18T14:44:51 - **Ended:** 2020-09-18T18:11:03 - **Duration:** 3h 26m - **Participants:** 3 - **Source:** [slack_pm](/sources/slack-pm.md) - **Pages:** 182-185 # Participants * [Andrew Rambaut](/people/andrew-rambaut.md) * [Edward C. Holmes](/people/edward-c-holmes.md) * [Kristian G. Andersen](/people/kristian-g-andersen.md) * [Robert F. Garry](/people/robert-f-garry.md) # Transcript **[2020-09-18T14:44:51] Edward C. Holmes:** Bacteria! Insane. Yes, she's not a whistleblower - just a fantasist with an axe to grind. **[2020-09-18T14:53:30] Kristian G. Andersen:** 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. **[2020-09-18T15:02:43] Robert F. Garry:** 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. **[2020-09-18T15:04:21] Kristian G. Andersen:** 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). **[2020-09-18T15:04:50] Kristian G. Andersen:** It's just so soothing to see code run over my screen... **[2020-09-18T15:22:25] Edward C. Holmes:** Yan is the fantasist. Alina has just lost it. **[2020-09-18T15:39:56] Kristian G. Andersen:** Here's what I'm assembling - missing anything? [shared file(s): Screen Shot 2020-09-18 at 15.39.27.png] **[2020-09-18T15:40:31] Kristian G. Andersen:** MP789 is the same(ish) as the one that was initially reported on virological **[2020-09-18T15:58:43] Kristian G. Andersen:** 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 **[2020-09-18T16:02:00] Kristian G. Andersen:** I SO hoped some of these intrahost mutations near the RBD or the FCS, but sadly no. Would have been cool! **[2020-09-18T16:08:47] Edward C. Holmes:** You mean RmYN01? Yes, I've been asking Weifeng to get some analysis done on that for ages. **[2020-09-18T16:10:53] Edward C. Holmes:** I think he said he only had an incomplete genome, including the RdRp, although even though that would be really interesting. **[2020-09-18T16:11:56] Edward C. Holmes:** 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. **[2020-09-18T16:18:31] Kristian G. Andersen:** Yeah, RmYN02 - the more complete of the two genomes. Definitely another genome in there **[2020-09-18T16:20:30] Kristian G. Andersen:** 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] **[2020-09-18T16:25:42] Edward C. Holmes:** 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. **[2020-09-18T16:37:13] Kristian G. Andersen:** I'm just going to pull that minority genome out - I'll keep you posted... Yeah, this is very interesting **[2020-09-18T16:39:04] Edward C. Holmes:** Great! **[2020-09-18T17:14:52] Kristian G. Andersen:** 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] **[2020-09-18T17:40:16] Edward C. Holmes:** Great work! So annoying that these people are accusing of fabrication when they are honest scientists working hard. Makes by blood boil. **[2020-09-18T18:03:12] Kristian G. Andersen:** Here's the minor genome - probably not a complete genome, but definitely present. [shared file(s): minor_variant_genome.fa] **[2020-09-18T18:03:31] Kristian G. Andersen:** Alignment + tree [shared file(s): Alignment with minor RmYN02 RAxML Tree.nex, Alignment with minor RmYN02.nex] **[2020-09-18T18:03:54] Edward C. Holmes:** Cool! Quick tree? **[2020-09-18T18:05:24] Kristian G. Andersen:** 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] **[2020-09-18T18:11:03] Edward C. Holmes:** 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.