Slack / Private Message Drop — page 261

[2020-11-17 09:15:30] [Andrew Rambaut] It appears sufficient times in mink to mean it must be selected for but possibly quite weakly. And possibly as a result of the high density. [2020-11-17 09:16:31] [Kristian Andersen] Yup - plausibly this one becomes fixed when big populations get hit. A lot of diversity in the size of the various farms - especially in Denmark (not sure about NL - but I think they have more 'mega' farms). [2020-11-17 09:17:32] [Andrew Rambaut] Here is a report I wrote for the WHO. To me the most interesting thing is the spike deletion at 69/70 that appears after Y453F and also appears after N469K in humans [shared file(s): Mink-associated_mutations_in_humans.pdf] [2020-11-17 09:18:19] [Andrew Rambaut] Note also the Utah human - also mink related, also 453F (slightly confidentially). [2020-11-17 09:19:31] [Robert Garry] One thing to be a data parasite (which implies some relationship to the host) and a data thug/thief. [2020-11-17 09:21:34] [Kristian Andersen] Thanks Andrew for sharing - very interested to get your insights into this. Will keep confidential - A LOT of disagreement in DK about how to handle that (most of those discussions driven by people that have no background in any of this...). [2020-11-17 09:26:48] [Andrew Rambaut] We (WHO working group) did talk to the SSI but they were very cagy (as you might expect). But they sharing isolates now through the WHO I believe. [2020-11-17 09:42:08] [Robert Garry] FWIW - the 69/70 S deletion comes at a region that is disordered at least in some spike structures (reddish spheres here). It's at the top of the spike but not close by to Y453 (bluish) so not obvious why the might be linked. Not like substructures that interact (for example the 6 helix bundles) where you expect compensatory/complementary mutations. [shared file(s): image.png] [2020-11-17 09:50:46] [Kristian Andersen] > We (WHO working group) did talk to the SSI but they were very cagy (as you might expect). But they sharing isolates now through the WHO I believe. Yup, no surprise there - unfortunately. And yes - I believe they have shared the isolates widely now (including with US) labs, so hopefully we'll learn more soon. I think they got a little surprised by how strongly the scientific community pushed back at them for not releasing data, so hopefully they have learned a lesson. (unfortunately way too much focus has been put on the mistakes here though - it's really important we remember that the main issue here is a parallel (raging) epidemic in mink). [2020-11-17 10:03:00] [Robert Garry] [thread - ID: 2020-11-17 10:03:00] Some wild speculation if you want to "connect" 69/70 to 453. MERS-CoV uses both [either?] a protein and a sialic acid receptor. HKU1 uses sialic acid and of course SARS CoVs use ACE2. What's not known [here's the