Slack / Private Message Drop — page 467

@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.... [2021-01-31 14:58:58] [Kristian Andersen] Alright - it's 241-243.... [2021-01-31 14:59:42] [Robert Garry] Actually I think most are 242-244 - few are 241-243 - our chronic patient has 243 and 244. [2021-01-31 15:01:26] [Kristian Andersen] As far as I can tell - all are 241-243 ("LLA") [2021-01-31 15:02:05] [Kristian Andersen] ... but holy moly, these genomes are messy... Hmmm. [2021-01-31 15:02:08] [Robert Garry] The main reference got that wrong originally and I fell for the trap. I need to update the virological post - which I am planning on. [2021-01-31 15:02:54] [Robert Garry] Ok now I'm confused... [2021-01-31 15:04:00] [Andrew Rambaut] They (Tulio & co) are using some hokey bioinformatics that initially was very poor at indels. [2021-01-31 15:04:37] [Kristian Andersen] Yeah, they're tricky. Definitely LLA (241-243) though - just checked the Danish genomes. [2021-01-31 15:06:30] [Kristian 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] [2021-01-31 15:07:00] [Robert 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 [2021-01-31 15:08:11] [Kristian Andersen] Yeah, those DEL assignments are wrong...