--- type: Conversation title: Private channel session 899 description: "slack conversation, 49 messages, 2021-01-31." tags: - conversation - slack medium: slack message_count: 49 started_at: "2021-01-31T14:01:54" ended_at: "2021-01-31T16:43:38" duration_seconds: 9704 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 49 messages spanning 2h 41m. # Metadata - **Started:** 2021-01-31T14:01:54 - **Ended:** 2021-01-31T16:43:38 - **Duration:** 2h 41m - **Participants:** 4 - **Source:** [slack_pm](/sources/slack-pm.md) - **Pages:** 466-471 # 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 **[2021-01-31T14:01:54] Robert F. Garry:** Just sent a google drive invite - https://docs.google.com/document/d/17-2hi7-fNsjE44himeCkm1PoZ7_-ncvpxUlhShZzDCU/edit Please send feedback - would be great if all could join but understand any declines or hesitancy. Nothing in stone, including the "tone." There's some decent science hidden there. **[2021-01-31T14:17:00] Edward C. Holmes:** Brill, thanks Bob!! I'll get onto it. **[2021-01-31T14:48:35] Kristian G. Andersen:** @Andrew Rambaut - do you have a good read on what deletions in the S the B.1.351 lineage has? The original genomes didn't have any, CoVariants lists 242-245, Florian mentioned 242-244, but I see 241-243.... **[2021-01-31T14:58:58] Kristian G. Andersen:** Alright - it's 241-243.... **[2021-01-31T14:59:42] Robert F. Garry:** Actually I think most are 242-244 - few are 241-243 - our chronic patient has 243 and 244. **[2021-01-31T15:01:26] Kristian G. Andersen:** As far as I can tell - all are 241-243 ("LLA") **[2021-01-31T15:02:05] Kristian G. Andersen:** ... but holy moly, these genomes are messy... Hmmm. **[2021-01-31T15:02:08] Robert F. Garry:** The main reference got that wrong originally and I fell for the trap. I need to update the virological post - which I amplanning on. **[2021-01-31T15:02:54] Robert F. Garry:** Ok now I'm confused... **[2021-01-31T15:04:00] Andrew Rambaut:** They (Tulio & co) are using some hokey bioinformatics that initially was very poor at indels. **[2021-01-31T15:04:37] Kristian G. Andersen:** Yeah, they're tricky. Definitely LLA (241-243) though - just checked the Danish genomes. **[2021-01-31T15:06:30] Kristian G. Andersen:** Here's what I have - I think somewhat accurate, although I'm not convinced some of the other mutations are really there... [shared file(s): Screen Shot 2021-01-31 at 3.05.48 PM.png] **[2021-01-31T15:07:00] Robert F. Garry:** Somthings off Virus name: hCoV-19/Denmark/DCGC-32298/2021 Accession ID: EPI_ISL_869302 Type: betacoronavirus GISAID Clade GH PANGO Lineage B.1.351 (version: 2021-01-22) AA Substitutions Spike A243del, Spike A701V, Spike D80A, Spike D215G, Spike D614G, Spike E484K, Spike K417N, Spike L18F, Spike L242del, Spike L244del, Spike N501Y, E P71L, N P13S, N T205I, NS3 Q57H, NS3 S171L, NSP2 T85I, NSP3 K837N, NSP5 K90R, NSP6 F108del, NSP6 G107del, NSP6 S106del, NSP12 P323L, NSP14 F240V, NSP14 V14L **[2021-01-31T15:08:11] Kristian G. Andersen:** Yeah, those DEL assignments are wrong... **[2021-01-31T15:08:39] Robert F. Garry:** irus name: hCoV-19/South Africa/KRISP-EC-K006856/2020 Accession ID: EPI_ISL_736936 Type: betacoronavirus GISAID Clade GH PANGO Lineage B.1.351 (version: 2021-01-22) AA Substitutions Spike A243T, Spike A701V, Spike D80A, Spike D215G, Spike D614G, Spike E484K, Spike K417N, Spike L18F, Spike L241del, Spike N501Y, Spike Q239del, Spike T240del, E P71L, N T205I, NS3 Q57H, NS3 S171L, NSP2 T85I, NSP3 K837N, NSP5 K90R, NSP6 F108del, NSP6 G107del, NSP6 S106del, NSP12 M124I, NSP12 P323L Passage details/history: Original **[2021-01-31T15:09:40] Robert F. Garry:** Here's one with LLA, but only three include LLA on GSAID. **[2021-01-31T15:10:49] Kristian G. Andersen:** Here's the full alignment from RSA - the deletion is out of frame, so that's probably why there's some confusion. LLAis definitely what's deleted, so that's 241-243. This fucking virus... [shared file(s): Nucleotide alignment.geneious] **[2021-01-31T15:11:28] Robert F. Garry:** Actually happy to hear all this ! **[2021-01-31T15:12:45] Robert F. Garry:** Needs to be fixed on GSAID **[2021-01-31T15:15:24] Kristian G. Andersen:** And NextStrain... And Covariats... I'll make sure we get it right on Outbreak.info :wink: **[2021-01-31T15:16:02] Robert F. Garry:** But now I need to unfix the Christmas Card.:rage4: **[2021-01-31T15:16:18] Kristian G. Andersen:** Sorry Bob... **[2021-01-31T15:17:42] Robert F. Garry:** It what I got when I did the alignment myself which is why it shows up in our virological post that way. Somehow Ithought I got it wrong. **[2021-01-31T15:18:41] Kristian G. Andersen:** Trust yourself man! :wink: **[2021-01-31T15:27:33] Andrew Rambaut:** The problem is it is ambiguous where the deletion is: **[2021-01-31T15:27:37] Andrew Rambaut:** shared file(s): image.png **[2021-01-31T15:29:39] Andrew Rambaut:** Actually in nucleotides it could be one base further towards 3' **[2021-01-31T15:30:50] Andrew Rambaut:** Definitely deletes 2 Ls and an A but could be LLA or LAL. **[2021-01-31T15:32:48] Robert F. Garry:** Oh my...can we look at the del in the Tulane patient as a tie-breaker? **[2021-01-31T15:34:11] Kristian G. Andersen:** I extracted the ORF and aligned in AA space - all come out with LLA deleted. **[2021-01-31T15:36:10] Andrew Rambaut:** But you could delete LAL and get the same amino acid sequence **[2021-01-31T15:36:38] Robert F. Garry:** The whole region is subject to various deletions in some other immune compromised patients. **[2021-01-31T15:37:27] Kristian G. Andersen:** I'll just accept I don't understand sequences... :wink: **[2021-01-31T15:37:53] Andrew Rambaut:** Always look at the nucleotide sequences, man. **[2021-01-31T15:38:49] Andrew Rambaut:** An interesting repeat here CTTTA CTTG CTTTA - don't know if it means anything **[2021-01-31T15:38:51] Kristian G. Andersen:** NEVER **[2021-01-31T15:39:05] Andrew Rambaut:** Just looks nice **[2021-01-31T15:39:08] Kristian G. Andersen:** Recombination. I'm telling you **[2021-01-31T15:39:48] Kristian G. Andersen:** We should volley it over to Billy - I'm sure he'd figure this one out for us. **[2021-01-31T15:40:44] Robert F. Garry:** Put Yuri on it - I'm sure that some blasterbating will solve the riddle. **[2021-01-31T15:40:48] Andrew Rambaut:** We should have a convention - when ambiguous, always call the most 5' position or something. **[2021-01-31T15:56:16] Andrew Rambaut:** Virus taxonomists really don't seem to understand virus evolution: ```I have a very stupid question before delving into the madness of a WHO-supported global and uniform SARS-CoV-2 nomenclature this week: As a taxonomist the name SARS-CoV-2 has always bothered me. In all organismal taxonomies, any taxon has only a single member, i.e., there is only one animal per species (except if there are subspecies, but then there is only animal per subspecies). The logic behind this is obvious: either something is a representative of "same" (for instanceyou and me are genetically so much alike that we are both [isolates of] "human") or something is distinct from something else and hence needs to be… **[2021-01-31T15:58:55] Andrew Rambaut:** I just sent Jens a link to Boni et al which presumably will blow his mind trying to fit all that recombination into nestedtaxonomic boxes. **[2021-01-31T16:08:11] Edward C. Holmes:** The problem lies in 'In all organismal taxonomies...'. What are these people on? **[2021-01-31T16:11:26] Andrew Rambaut:** My reply: ```The problem is that taxonomy doesn't really work for virus as far as I am concerned as there is essentially astructured continuum of diversity - i.e. completely artifactual notions of species. And with recombination that just makes thing completely arbitrary. I don't mind labelling bits of the phylogenetic tree for convenient discussion but Ithink we get too focused on trying to replicate a metazoan taxonomy on viruses. That said - to answer you final question - yes, SARS1 and SARS2 are completely distinct (not even sibling clades)with the diversity within each minuscule compared to the divergence between them. This paper gives an overview oftheir relative positions (and some… **[2021-01-31T16:12:15] Andrew Rambaut:** Glad I can't make the WHO nomenclature meeting this week - will be carnage. **[2021-01-31T16:26:06] Kristian G. Andersen:** Lol. Jens was right about one thing though - that was indeed a dumb question. "What do you mean, we can't fit these little things into neat little boxes?! Nein!!" **[2021-01-31T16:37:16] Edward C. Holmes:** The WHO nomenclature thing will be horrendous. Tulio and Jens is an interesting combination. **[2021-01-31T16:43:38] Robert F. Garry:** Germans and their neat little boxes - yes I believe it's a thing...