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1. 2020-06-11 17:16 Edward C. Holmes open
   Have the Shi lab published all the viruses they use in these culture experiments? Do they find the same mutations that appear in SARS-CoV-2?
2. 2020-06-11 17:21 Kristian G. Andersen open
   In our paper we argue against (a) manipulation and (b) tissue culture. Our main arguments were that manipulation ishard, but the German's came out and created a reverse genetics system of SARS2 in less than two weeks, soclearly it's not that hard. Our arguments against tissue culture mostly came down to the O-linked glycans and a'mucin-like' domain. But by now it seems clear that these don't actually form a mucin-like domain, but rather those glycans modulate the function of the furin site. All our arguments about natural viruses emerging, the RBD identicalin pangolin CoVs, etc., all still stand. The main new things that bothers me the most:1. Lack of selection (a lot of the selection is for replication in a particular host species, so yes, I would assume culture would lover selection during subsequent transmission in humans - however, immune selection will still occur).2. Gain of furin cleavage of bovine CoV in tissue culture.3. Loss of furin site in tissue culture meaning it's active.4. The little details about the furin site - e.g., that it's exactly in the spot where experiments had previously inserted it,the fact that the exact sequence exist in a cat CoV, Shi herself being sketchy with details and considering lab accident, etc. But all of this can go both ways
3. 2020-06-11 17:21 Kristian G. Andersen open
   Unclear to me if they published sequences of all these viruses - it's a lot and names are changing over time (e.g.,RaTG13 had a different name previously).
4. 2020-06-11 17:23 Kristian G. Andersen open
   And yes - of the six key mutations in the RBD, one of them occur in tissue culture for SARS (*but* it's also present inthe pangolin RBD).
5. 2020-06-11 17:27 Edward C. Holmes
   Are you saying they deliberately inserted the furin cleavage site? I see no evidence of them ever doing that before. (Idon't think RaTG13 had a different name...I think there a partial sequence from another virus that is identical. Canwe do a quick zoom?
6. 2020-06-11 17:38 Edward C. Holmes open
   To me, "Loss of furin site in tissue culture meaning it's active" strongly argues AGAINST culturing as being the cause of the cleavage site insertion.
7. 2020-06-11 17:44 Kristian G. Andersen open
   Just making some dinner - let's Zoom in ~30mins?
8. 2020-06-11 17:47 Edward C. Holmes open
   Let's say 6:30 pm time. OK?
9. 2020-06-11 18:29 Edward C. Holmes open
   https://uni-sydney.zoom.us/j/98148315438

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