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Slack / Private Message Drop, p.38 · slack_pm:msg:00373

Page text: p.38 · original PDF

Date
2020-05-25 10:10 (hour precision)
Type
chat message · slack
recipient
Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker
Kristian G. Andersen

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@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]

In context

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  1. 2020-05-25 10:10 Kristian G. Andersen open
    Sharing this in case there are any comments. His #1 caught my eye a little while back too, but I haven't looked into itfurther.```Dr. AndersenI read with interest your paper titled, The proximal origin of SARS-CoV-2, in which you conclude this is a natural, zoonotic-sourced infection. Three different approaches of analysis that I have done do not support this conclusion. Can you comment please:1. The furin cleavage site insert has the unusual codon usage for the RR dimer of CGG-CGG. As you probably know, the frequency of this codon usage in the SARS-CoV-2 genome is 0.09. So having two next to each other isnot likely as a random event. As support for the unlikeliness of these codons, using GISAID data, by March there isevidence of the third G being mutated out for either A or T at three-times the rate of the background mutation rate, 26/year from Nextstrain.org. 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. On the other hand, most laboratory use optimized codon primers and kits use CGG routinely; including in primers in published papers from the Wuhan Institute of Virology. SLACK_000252So 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% ofsequenced genomes did not pass through the index case but represented separate reservoir host to human jumpsand 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 'pureculture' growth from the index case outward with no evidence of a reservoir host in the background. This would bethe 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 isthe 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. Iam not sure why this obvious correlation was not at least pointed out in your paper and then addressed with acogent argument.I look forward to hearing your thoughts.Regards, Steve Steven _MD, PhD
  2. 2020-05-25 10:10 Andrew Rambaut open
    @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.
  3. 2020-05-25 10:10 Kristian G. Andersen open
    @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
  4. 2020-05-25 10:10 Kristian G. Andersen open
    @kristian Andersen Curiously, they have exactly the same polybasic site, which I previously missed - also on Virological :wink:
  5. 2020-05-25 10:10 Kristian G. Andersen
    @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]
  6. 2020-05-25 10:10 Robert F. Garry open
    @Kristian Andersen I'd just take this as more evidence for the short insertion hypothesis. A random event. The 12base 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 beenpurified out." Even with a 3X higher substitution rate don't most of the isolates still have CGGCGG after passage inhumans for at least 6 months?

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