Chat message

Slack / Private Message Drop, p.72 [SLACK_000286] · slack_pm:msg:00730

Date: 2020-06-11 17:21
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen
Topics: Furin cleavage site and molecular features Lab-leak / accidental release hypothesis Natural origin / zoonotic spillover Proximal Origin paper

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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

Extracted statements

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Statement	Grade	Attribution	Stance
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.	own voice, substantive	speaker_own	asserts

Statement

Grade

Attribution

Stance

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.

own voice, substantive

speaker_own

asserts

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2020-06-11 17:07 Kristian G. Andersen open

Aim3: https://projectreporter.nih.gov/project_info_description.cfm?aid=9819304&icde=50404048&ddpara m=&ddvalue=&ddsub=&cr=1&csb=FY&cs=DESC&pball=
2020-06-11 17:11 Kristian G. Andersen open

> But that work isn't exclusively done at the WIV because as you say yourself the Baric lab are doing it No, that work _is_ exclusively at WIV AFAIK. Baric's lab is doing (did) gain of function research where they created reverse genetics systems to study the viruses. All of this is done in BSL-3, so much (much!) less risk of exposure. The work in Shi's lab is different - here they are taking bat CoVs and culturing them under BSL-2 in cell lines from different animals - to e.g., understand which ones can infect human cells and what type of mutations that occur inT/C may make them permissive. They probably have more than 10 papers where they describe that type of work onall kinds of SARS-like CoVs.
2020-06-11 17:14 Edward C. Holmes open

Got it, thanks. That helps.
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?
2020-06-11 17:21 Kristian G. Andersen

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
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).
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).
2020-06-11 17:27 Edward C. Holmes open

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?
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.

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