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Slack / Private Message Drop, p.734 [SLACK_000948] · slack_pm:msg:07685

Date: 2021-04-28 07:00
Type: chat message · slack
mentioned: Andrew Rambaut
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

Recipients on this medium are inferred from channel membership, not per-message addressing.

@Andrew Rambaut - here's the B.1 lineage. A few in the US: https://outbreak.info/situation-reports?pango=B.1&am p;muts=S%3AN501Y&muts=S%3AE484K&mut[...]AR346K&muts=S%3AP681H&loc=USA&am p;loc=USA_US-CA&selected=Worldwide

Links shared

other https://outbreak.info/situation-reports?pango=B.1&am

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-04-28 06:51 Andrew Rambaut open

Seen this one? Nelly, Pooh and Eek (plus a mutation at 144) https://github.com/cov-lineages/pango-designation/issues/57
2021-04-28 06:55 Andrew Rambaut open

'neglected' - https://twitter.com/angie_rasmussen/status/1387397186372005893
2021-04-28 06:55 Andrew Rambaut open

Perhaps Sputnik V will just spread round the world of its own accord?
2021-04-28 06:56 Kristian G. Andersen open

Wait, what????
2021-04-28 07:00 Kristian G. Andersen

@Andrew Rambaut - here's the B.1 lineage. A few in the US: https://outbreak.info/situation-reports?pango=B.1&am p;muts=S%3AN501Y&muts=S%3AE484K&mut[...]AR346K&muts=S%3AP681H&loc=USA&am p;loc=USA_US-CA&selected=Worldwide
2021-04-28 07:00 Robert F. Garry open

```1 msdngpqnqr napritfggp sdstgsnqng ersgarskqr rpqglpnnta swftaltqhg 61 kedlkfprgq gvpintnssp ddqigyyrra trrirggdgk mkdlsprwyf yylgtgpeag 121 lpygankygi iwvategaln tpkdhigtrn pannaaivlq lpqgttlpkg fyaegsrggs 181 qassrsssrs rnssrnstpg ssRGTsparm agnggdaala lllldrlnql eskisgkgqq 241 qqgqtvtkks aaeaskkprq krtatkaynv tqafgrrgpe qtqgnfgdqe lirqgtdykh 301 wpqiaqfaps asaffgmsri gmevtpsgtw ltytgaikld dkdpnfkdqv illnkhiday 361 ktfpptepkk dkkkkadetq alpqrqkkqq tvtllpaadl ddfskqlqqs mssadstqa``` Nucleocapsid sequence. Like Lassa N and several other RNA virus nucleoproteins there is a 2-domain structure. The N-term domain binds RNA. The C-term domain mediates dimerization. In btwn the two domains is a linker. In SC2 the linker is arginine serine (RS) rich. It is "intrinsically disordered" and therefore does not show up in the X-rayor cryo structures. 203-205 sequence RGT is near the end of the linker. The linker is highly phosphorylated -therefore probably regulates N function - the mutations could impact those functions which could affect assembly, virus load or virus distribution etc and yes this will impact transmissibility.
2021-04-28 07:01 Andrew Rambaut open

@Kristian Andersen I think this one is interesting because it has almost nothing else other than Phil and Doug from before and then the 4 spike mutations
2021-04-28 07:02 Andrew Rambaut open

@Kristian Andersen It is like a really pure constellation.
2021-04-28 07:02 Kristian G. Andersen open

@Kristian Andersen Agreed. We have started seeing a lot of B.1, so we'll be on the lookout.

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