Chat message

Slack / Private Message Drop, pp.176-177 [SLACK_000390] · slack_pm:msg:01824

Date: 2020-09-17 06:43
Type: chat message · slack
mentioned: Kristian G. Andersen
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut
Topics: Furin cleavage site and molecular features Natural origin / zoonotic spillover

Recipients on this medium are inferred from channel membership, not per-message addressing.

Just had the following email. It seems reasonable to get to the bottom of what is up with RaTG13 (I imagine it was sloppy work under extreme pressure). Obviously RaTG13 isn't the whole story and the nutters' obsession with it ismisplaced (the existence of the pangolins and RmYN02 tell you almost as much). ```Dear Andrew,I was recently contacted by a national fact-checking body, run by Norwegian media outlets. The topic was the conspiracy surrounding an alleged release of sars-cov-2 from a Chinese lab. They pointed me to this so-called Yan-report, detailing how sars-cov-2 could possibly have been generated by functional genetics. The "Yan-report" seems obsessed with RaTG13, and cite a number of preprints (most crap, but some less so)questioning the veracity of the sequence. As RaTG13 is kind of central in arguments re the origin of sars-cov-2, Iwanted to have a quick look at the sequence data.I am looking at this now together with my colleague Ola Brynildsrud, and so far, we have not been able to re-create the RaTG13 genome in GenBank from the published metagenome fastqs and sanger amplicons published with the RaTG13 genome: paper:https://www.nature.com/articles/s41586-020-2012-7sequence data:https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP249482&o=acc_s%3AaI wanted to check whether any of you proper Covid people have looked into this dataset, or simply used the published GenBank sequence. The best would probably be to post the question on virological, but I dont have a userthere.It might well be that the authors have been sloppy in uploading all their raw sequence data, but as said, the published raw data does not seem to be enough to generate the RaTG13 assembly, not even when we have said assembly to align reads against. But we're still working on this. Kind regards,Vegard EldholmNorwegian Institute of Public Health```I don't know how much further you want to get into this @Kristian Andersen but I think he is going to email you.

Links shared

journal https://www.nature.com/articles/s41586-020-2012-7sequence
gov https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP249482&o=acc_s%3AaI

Extracted statements

Rule-extracted, not adjudicated. The grade says what may be done with each one; read the document above before relying on any of them.

Statement	Grade	Attribution	Stance
Obviously RaTG13 isn't the whole story and the nutters' obsession with it ismisplaced (the existence of the pangolins and RmYN02 tell you almost as much). ```Dear Andrew,I was recently contacted by a national fact-checking body, run by Norwegian media outlets.	quoted / not their view	quoted_external message body appears to be pasted content	asserts

Statement

Grade

Attribution

Stance

Obviously RaTG13 isn't the whole story and the nutters' obsession with it ismisplaced (the existence of the pangolins and RmYN02 tell you almost as much). ```Dear Andrew,I was recently contacted by a national fact-checking body, run by Norwegian media outlets.

quoted / not their view

quoted_external message body appears to be pasted content

asserts

In context

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

2020-09-17 05:34 Robert F. Garry open

The Lancet investigation appears to have been born in the greenroom of MSNBC where Daszak and Sachs have been guests (both in NYC so convenient). It would not surprise me if the Deep Throat team hasn't been lobbying Richard Horton for this as well since the ignorant noncoronavirologists probably left stones unturned and lack credibility.
2020-09-17 05:44 Robert F. Garry open

As for GVP - I noticed that the price tag has drifted to $4B. :exploding_head: K -Good job at CREID with the slide -not lost on the Grand Wizard - The GVP congame and scam is not going to go away easily and all it will do is draw money from long-term processes, like CREID, that will work or at least help.
2020-09-17 06:08 Robert F. Garry open

As for the Fucking weather analogy it's false. In fact the weather analogy fits much more to your Nature response toGVP. What really happens is that you detect "outbreaks" of weather systems first [you can see some of these on the attached map] then you can track and predict where they go and when they go. I just wasted 2 days prepping forSally that for days was said to be heading straight to NOLa and ended up 200 miles to the east - Katrina was goingto Pennsicola, FL as a Tropical Storm - wrong- the predictions are not perfect. [shared file(s): image.png]
2020-09-17 06:43 Andrew Rambaut

Just had the following email. It seems reasonable to get to the bottom of what is up with RaTG13 (I imagine it was sloppy work under extreme pressure). Obviously RaTG13 isn't the whole story and the nutters' obsession with it ismisplaced (the existence of the pangolins and RmYN02 tell you almost as much). ```Dear Andrew,I was recently contacted by a national fact-checking body, run by Norwegian media outlets. The topic was the conspiracy surrounding an alleged release of sars-cov-2 from a Chinese lab. They pointed me to this so-called Yan-report, detailing how sars-cov-2 could possibly have been generated by functional genetics. The "Yan-report" seems obsessed with RaTG13, and cite a number of preprints (most crap, but some less so)questioning the veracity of the sequence. As RaTG13 is kind of central in arguments re the origin of sars-cov-2, Iwanted to have a quick look at the sequence data.I am looking at this now together with my colleague Ola Brynildsrud, and so far, we have not been able to re-create the RaTG13 genome in GenBank from the published metagenome fastqs and sanger amplicons published with the RaTG13 genome: paper:https://www.nature.com/articles/s41586-020-2012-7sequence data:https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP249482&o=acc_s%3AaI wanted to check whether any of you proper Covid people have looked into this dataset, or simply used the published GenBank sequence. The best would probably be to post the question on virological, but I dont have a userthere.It might well be that the authors have been sloppy in uploading all their raw sequence data, but as said, the published raw data does not seem to be enough to generate the RaTG13 assembly, not even when we have said assembly to align reads against. But we're still working on this. Kind regards,Vegard EldholmNorwegian Institute of Public Health```I don't know how much further you want to get into this @Kristian Andersen but I think he is going to email you.
2020-09-17 06:44 Andrew Rambaut open

(I just don't know enough about sequencing bioinformatics and genome assembly to look at this).
2020-09-17 06:57 Kristian G. Andersen open

I might take a look at the sequence data - overall, I have no concerns though given that this is how sequencing oflow-coverage genomes often occurs. Patchwork....
2020-09-17 07:01 Andrew Rambaut open

I guess the question is has there been any 'imputation'? From the above it would seem they can't even get the consensus when they map to the actual consensus?
2020-09-17 07:03 Andrew Rambaut open

It would also matter which bits are low coverage. I would prefer to move on but it would be good to be armed with the knowledge - who knows where this will go next.

Full conversation →