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Slack / Private Message Drop, p.344 [SLACK_000558] · slack_pm:msg:03624

Date: 2020-12-28 14:05
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry

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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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journal https://academic.oup.com/cid/article/71/9/2428/5811871

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

2020-12-28 12:30 Robert F. Garry open

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.
2020-12-28 13:25 Robert F. Garry open

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...
2020-12-28 14:05 Robert F. Garry

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.
2020-12-28 14:41 Robert F. Garry open

Tiger: https://mra.asm.org/content/9/22/e00468-20 Identical in S to Wu-1 except D614G.
2020-12-28 14:41 Edward C. Holmes open

Tigers keep getting infected. Very interesting.
2020-12-28 14:44 Edward C. Holmes open

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]
2020-12-28 14:46 Edward C. Holmes open

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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