Private channel session 728
21 messages over 5h 17m, 2020-12-28 – 2020-12-28.
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.
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FWIW - the same story in dogs https://www.nature.com/articles/s41586-020-2334-5 [not sure how I missed this one]. Both the cat and dog S sequences are 99% similar to Wu-1 S. The dog seq is identical except for D614G.
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https://www.biorxiv.org/content/10.1101/2020.11.16.384917v1.full.pdf A little more about cats. Serial passage does select for a few variants: The ones that get fixed are S H655Y andE S67S. According to the authors: "S H655Y isnear the polybasic cleavage site, residin between the receptor binding domain and the fusion peptide, and is thoughtto modulate Spike glycoprotein fusion efficiency 55,56,59 262 . E S67S has not been documented elsewhere." It's not that near the FCS, but I take the point...
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Continuing my learning exercise for today. https://academic.oup.com/cid/article/71/9/2428/5811871 Infection of hamsters occurs effectively, and there are moderate symptoms. I haven't found much sequence data except Spike in this paper. There was only one mutation in one "serial" [contact] animal. S H655Y just like in the serial cats in the previous example, which is probably not a coincidence. Hamsters have Q34 instead of H34, but have Y41/K353 like humans.
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Tiger: https://mra.asm.org/content/9/22/e00468-20 Identical in S to Wu-1 except D614G.
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Tigers keep getting infected. Very interesting.
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And here is a new data point for your consumption only - that Cambodian bat virus that mentioned in that Nature news piece without any info...closer than I expected: [shared file(s): data_fullgenome_aligned.fas.tree.pdf]
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Bob - I was also involved in a cat study: [shared file(s): A household case evidences shorter shedding of SARS CoV2 in naturally infected cats compared to their human owners.pdf]
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Indeed - several zoos and various cats including leopards and lions.
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I don't have the sequence for that Cambodian virus and I'll see I can get hold of the key bits of the spike protein. Iwas told it was 'quite divergent'.
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@Eddie Holmes Oh that's very interesting! Will be interested to see Spike.
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@Eddie Holmes I'll see what I can do...complex politics.
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Thanks Eddie - @Kristian Andersen It suddenly occurs to me that the monkey passaged virus data might be interesting - weren't there changes in the spike?
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The cats are very interesting as previously discussed here. Surely seems like they are getting infected pretty easily.In the zoos the cats are probably getting infected by the airborne route. People coughing and breathing into open cages? I suppose that the zookeepers could infecting them somehow, but there are not too many instances ofpeople and these big cats together in very close quarters except under very controlled conditions [like a vet doing anexam]. As for origins, it does put a heavy spotlight back on the Feliforms.
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If it is moving around zoos in an airborne manner then the infections in felids are even more striking as you would expect supposedly high risk animals like great apes also to be infected. Yet, it is consistently not apes and consistently is tigers.
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@Eddie Holmes That _*is*_ close - interesting....
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@Robert Garry - not sure if there were changes in the passaged viruses - something to ask Mark when he's back (1/4 - same for the rest of the lab).
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@Eddie Holmes And here's a simplot. There's clearly a region from ~8-18 Kb where it is about as close to SARS-CoV-2 as RaTG13... [shared file(s): SimPlot.bmp]
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@Eddie Holmes Interesting stuff going on in ORF1 too
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@Eddie Holmes Indeed.
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@Eddie Holmes I hate coronaviruses - so many trees across different parts of the genome - clearly they're just shuffling shit around like they were bacteria. Pretty concerning.
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@Eddie Holmes Yes, and trying to work out the exact history of recombination events is bloody difficult.