Slack / Private Message Drop — page 301

Okay, cool - I'll have a chat with Karthik too - we haven't been able to get good estimates of the root TMRCA recently, but that may very well be on us. [2020-12-06 11:18:28] [Kristian Andersen] I'm heading out for an hour, but once I'm back lemme just clean up these alignments a little and share - just so we have them archived here. :beer: [2020-12-06 11:38:12] [Andrew Rambaut] > On January 21, the Centers for Disease Control and Prevention (CDC) confirmed the first U.S. case in a 35-year-old man living in Snohomish County. He had returned from Wuhan, China after visiting his family there, to the U.S., landing at Seattle-Tacoma International Airport on January 15, without any symptoms. [2020-12-06 11:41:45] [Andrew Rambaut] And of course at that time Imperial College estimated Wuhan had 190-4000 cases by 12th Jan based on 3 exported cases. [2020-12-06 12:00:43] [Eddie Holmes] [thread - ID: 2020-12-06 09:33:59] @Kristian Andersen They also used my quote out of context...I was just referring to some of those shonky studies, particularly the Indian-origin one. [2020-12-06 12:02:25] [Kristian Andersen] Yeah, clearly a lot more cases going around at that time than was appreciated - and obviously not (directly) linked to the seafood market. We don't really see any evidence of other "WA1" lineages in Wuhan, do we? All those early ones were "Hu-1"? [2020-12-06 12:06:22] [Kristian Andersen] Probable scenario - ongoing undetected transmission in Wuhan building up, then a big super spreading event at the seafood market where it gets detected. Cases following are then connected to that event and most genomes are sequenced from the super spreading event, but not the emergence. Makes sense I think [2020-12-06 12:07:33] [Kristian Andersen] The emergence itself could have been anywhere, but transmission probably got going in Wuhan (but not at the seafood market - that's a SSE) [2020-12-06 12:07:57] [Kristian Andersen] "Anywhere [in China]" [2020-12-06 12:08:43] [Eddie Holmes] Total sense and I fully agree. I suspect the emergence event took place elsewhere and was imported into Wuhan. [2020-12-06 12:09:16] [Eddie Holmes] Can you just summarise where the root should fall? I didn't follow all that chain. [2020-12-06 12:11:07] [Kristian Andersen]