Private channel session 878

17 messages over 1h 53m, 2021-01-26 – 2021-01-26.

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.

1. 2021-01-26 16:26 Robert F. Garry open PDF p.455
   Alignment including Thai Bat CoV and Cambodian Bat CoV. Take homes: Thai Bat spike and RmYN02 spike are nearly identical, including at the S1/S2 cleavage site. Cambobatcov RBD is very similar to PangoGD RBD and SARS-CoV-2 RBD. 5/6 pf the PO1 key residues. Cambobatcov also has the Furin landing site QTQTN, like RaTG13, GD Pango and SARS-CoV-2, that is often deleted on extended cell passage. [shared file(s): image.png]
2. 2021-01-26 16:38 Kristian G. Andersen open PDF p.455
   Nice! Bob, can you please share the actual alignment? Would like to try and merge it with what I have.
3. 2021-01-26 16:41 Edward C. Holmes open PDF p.455
   Great work Bob! Hoping to get the Yunnan bat virus sequences soon.
4. 2021-01-26 17:20 Kristian G. Andersen open PDF p.455
   Here's the paper from David Ho - B.1.351 not looking good: https://www.biorxiv.org/content/10.1101/2021.01.25.428137v2.full.pdf
5. 2021-01-26 17:22 Kristian G. Andersen open PDF p.456
   How people can look at this data and conclude that "it'll be totally fine for vaccines - all good news", I simply don't understand. Either it's delusional or it's because we have now (yet again) turned to wishful thinking. There is little doubt in my mind we'll have to update the vaccine. Will B.1.351 kill them completely? Very likely not -however, there's going to be a hard hit to the efficacy because of this.
6. 2021-01-26 17:22 Edward C. Holmes open PDF p.456
   I thought not...
7. 2021-01-26 17:23 Edward C. Holmes open PDF p.456
   Fucker as you say...
8. 2021-01-26 17:24 Kristian G. Andersen open PDF p.456
   The Moderna paper yesterday (which looks more promising) they literally took the serum at the very peak (a week after the booster) so the data would look better. In this paper they wait a few weeks and see a more worrisome effect - similar to the observations from RSA. In any case - it sounds like Moderna is already working on an updated design, so that's the right thing to do - I just hope that work gets fast-tracked.
9. 2021-01-26 17:27 Robert F. Garry open PDF p.456
   @Kristian Andersen Of course, I'll send when I get back to the office computer.
10. 2021-01-26 17:36 Edward C. Holmes open PDF p.456
    Indeed! Sounds like an update is needed ASAP.
11. 2021-01-26 17:44 Kristian G. Andersen open PDF p.456
    I don't necessarily think it needs to get into people ASAP, but the whole process absolutely needs to be started ASAP - it's not a simple "six week and we're done" process. Better have this ready to go over the summer.
12. 2021-01-26 17:46 Edward C. Holmes open PDF p.456
    Totally agree.
13. 2021-01-26 18:04 Kristian G. Andersen open PDF p.456
    Just looking at that CamboBat paper - very interesting. One thing they miss - that mismatch in the key RBD residue where CamboBat has "P" and the PangoCoV and SC2 have "F" (and SC1 / RmYN02 have "L") the "pre"-SARS CoVs from e.g., civets ALSO have "P". Pretty interesting. [shared file(s): Screen Shot 2021-01-26 at 5.59.43PM.png, Screen Shot 2021-01-26 at 6.03.31 PM.png]
14. 2021-01-26 18:09 Edward C. Holmes open PDF p.456
    Oh cool! It's really not much of a paper.
15. 2021-01-26 18:14 Kristian G. Andersen open PDF p.457
    No, it really isn't - more of a genome announcement (although, quite a genome!)
16. 2021-01-26 18:16 Edward C. Holmes open PDF p.457
    Yes, it's a beaut.
17. 2021-01-26 18:19 Robert F. Garry open PDF p.457
    They had lots of opportunities to really get into sarbecovirus evolution -they didn't.