Slack / Private Message Drop — page 347

I think maybe he's not very good with numbers. [2020-12-29 09:23:35] [Robert Garry] More fun with cats. [2020-12-29 09:24:17] [Robert Garry] ```Denmark cats: 69-70 deletion plus Y454F RBD mutation seen in some mink. Do not know the relationship of the cats - maybe all the same cat or cat house. Cat from Greece V1104L Lion 3 and 4 Y505H RBD mutation, not present in Lion 2. Lion 2 Q616R mutation not seen in Lions 3,4. Lions 3, 4 A626I, Lion 2 A626T``` [2020-12-29 09:31:31] [Robert Garry] SC2 mostly makes the jump to house cats with no changes. However there are some interesting RDB mutations in some lions (Y505H) and the cat or cats from Denmark (Y454F). The lions also have mutations associated with Doug, [2020-12-29 09:34:51] [Robert Garry] Alignments: [shared file(s): image.png] [2020-12-29 09:35:39] [Kristian Andersen] Very little onward transmission in cats (presumably), so I wouldn't expect much evolution to happen. Compare that to a mink farm where the virus gets a chance to spread through a whole population of thousands of animals very quickly. [2020-12-29 10:05:16] [Robert Garry] In uptown NOLA there are a lot of wild/street cats. Hundreds of cats hang out around the French quarter and the wharf. I think similar situations in some other countries as well. Certainly not the same intense situation as a mink farm, but I could see an opportunity for spread amongst the feral cats in NOLa - elsewhere dunno. That being said I agree that in the Danish cat [looking at the GSAID metadata seems that there is only one - all the same sequence] the 69/70 deletion and Y454F mutations were probably in this cat's human already - just not clear to me if as minor or major species. The alternative is selection after the species jump, but this seems less likely, but maybe that's just my bias. Lions in a zoo yes no onward transmission except to other lions. Clearly two different sequences in the three lions, which makes me think there might be some selection during the species jump or two independent transmissions. The latter seems less likely. Lions 3 and 4 sharing their virus. [2020-12-29 10:24:17] [Robert Garry] It's a *very* important distinction you're making. SC1 from eating a civet - basically one step for the adaptor mutations. The dog and the house cats mostly no changes, with the exception of the Danish cat [go figure]. The serially passaged cats had some mutations fixed. The lab mice forced passage and it took several steps to get the adaptive mutations. However, not so much with the ferret transmission in the aerosol study above - this looks basically one step for get the RBD and FCS adaption. Maybe this is a good case of selection after limited replication in the animal. The Erasmus group is pretty sound so they probably would have sequenced their virus stock to a pretty good depth I would hope. [2020-12-29 12:12:59] [Robert Garry] WELL - there's a dog with P681H hCoV-19/dog/USA/TX-TAMU-077/2020|EPI_ISL_699508|2020-07-28 and another with Q675H hCoV-19/dog/Italy/Dog399-20BA/2020|EPI_ISL_730652|2020-11-04.