Slack / Private Message Drop — page 39

@Kristian Andersen I'd just take this as more evidence for the short insertion hypothesis. A random event. The 12 base pair insertion is - as ProfBill pointed out - out of frame. So if the insertion of the RR was purposeful why also create a proline insertion and put the 12 bases in out-of-frame? Not sure I buy that the "terminal G would have been purified out." Even with a 3X higher substitution rate don't most of the isolates still have CGGCGG after passage in humans for at least 6 months? [2020-05-25 11:39:50] [Kristian Andersen] [thread - ID: 2020-05-25 10:10:53] @Kristian Andersen Yeah, agreed - and yes, that last part of this would have been 'purified out' is pure bs. [2020-05-25 11:49:14] [Robert Garry] [thread - ID: 2020-05-25 10:10:53] @Kristian Andersen https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713968/ The FIP story would be interesting - even if it turns out wasn't what did in my daughter's cat. [2020-05-25 12:09:42] [Robert Garry] [thread - ID: 2020-05-25 10:10:53] @Kristian Andersen For what it's worth those cat CoV spikes with the PRRAR also have predicted O-glycans. [2020-05-25 12:27:33] [Kristian Andersen] [thread - ID: 2020-05-25 10:10:53] @Kristian Andersen Yeah, I noticed that - very interesting. Might come back to that BMP paper with these glycans actually regulating the site - so cool biology in there to be found I think... [2020-05-25 14:00:02] [Robert Garry] Well - I guess this was good while it lasted at least according to Mr Arumugham and Ms Markson. [2020-05-25 15:22:17] [Eddie Holmes] "Since codon usage in coronaviruses are not greatly influenced by the host it resides in, this means a jump to humans must have been in a host which did not have even a few months history with the virus, otherwise the terminal G would have been purified out". There are a number leaps in logic and evidence at this point. [2020-05-25 15:37:44] [Eddie Holmes] HKU9 has CGG CGG - send him Bill Gallaher's link. [2020-05-25 16:08:39] [Kristian Andersen] https://www.abc.net.au/news/2020-05-26/china-coronavirus-dossier-came-out-of-us-state-department/12282994 [2020-05-25 17:05:41] [Kristian Andersen] It's now two for two - phylogenetics can be hard... @Andrew Rambaut, I assume your preprint must have prompted this...? (separately, I blame you for convincing me that the hypothesis was right!! :wink: ). https://twitter.com/trvrb/status/1265063921880150016?s=20 [2020-05-25 18:12:22] [Eddie Holmes]