Slack / Private Message Drop — page 38

SLACK_000252 So a laboratory source for a gain-of-function furin cleavage site would probably use these codons. 2. In the over 16,000 genomes in GISAID there is not one example of posterior diversity. With MERS, 93% of sequenced genomes did not pass through the index case but represented separate reservoir host to human jumps and this was apparent within 60 days of the index case. They collectively showed the most recent common ancestors among themselves was over 12 months before the index case. With SARS-CoV-2 it is acting like a 'pure culture' growth from the index case outward with no evidence of a reservoir host in the background. This would be the case for a laboratory acquired infection. 3. If you use a map of Wuhan and overlay the first four hospitals that saw cases with a map of the Metro system, you see that the hospitals straddle Line 2, which runs approximately east to west, carries 1,000,000 people a day, and is the Metro line with stops closest to both the Wuhan Institute of Virology and the original wet market that was considered an early source for the infection. There are 11 Metro lines in Wuhan, hundreds of stops on those lines, and over a dozen hospitals spread out over the city. I am working with a UCLA statistician to perform tests about the probability of this being simply an accident of statistics but the gestalt is, it does not look like a chance occurrence. But it is consistent with someone getting infected in the lab, riding Line 2 for a few days, and off you go. It might be a truism to say that the six proven cases of laboratory derived SARS escapes occurred in big cities, Beijing, Singapore, or Taipei where the labs are located. But if you follow it with the fact that MERS and SARS, both proven as true zoonotic sources, on other hand began in rural settings in China and the Middle East, respectively. I am not sure why this obvious correlation was not at least pointed out in your paper and then addressed with a cogent argument. I look forward to hearing your thoughts. Regards, Steve Steven _ MD, PhD [Andrew Rambaut] [thread - ID: 2020-05-25 10:10:53] @kristian Andersen Doesn't Bill's observation of the acquisition of the insertion from another bat coronavirus explain the exact sequence of this and what codons it uses. [Kristian Andersen] [thread - ID: 2020-05-25 10:10:53] @kristian Andersen Not quite sure if it does - CGG is part of the sequence Bill mentions, but not quite sure if CGG has to be conserved there. Need to check what those FIPs have at that site [Kristian Andersen] [thread - ID: 2020-05-25 10:10:53] @kristian Andersen Curiously, they have exactly the same polybasic site, which I previously missed - also on Virological :wink: [Kristian Andersen] [thread - ID: 2020-05-25 10:10:53] @kristian Andersen Here's what it looks like on the cat side - one CGG and one CGA. So no mystery really. [shared file(s): Screen Shot 2020-05-25 at 11.00.58 AM.png] [Robert Garry] [thread - ID: 2020-05-25 10:10:53]