Chat message

Slack / Private Message Drop, p.86 [SLACK_000300] · slack_pm:msg:00875

Date: 2020-06-18 18:28
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen
Topics: Furin cleavage site and molecular features Natural origin / zoonotic spillover

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

I think the main problem here is not really how that pangolin sequence ended up having that RBD, but rather whether there's anything sketchy here from a scientific standpoint. These studies are presented each as independent evidence of the pangolin virus RBD, but if all those papers are relying on a third data set - and don't actually have _any_ data from this very critical CoV RBD, then that's an issue.

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
I think the main problem here is not really how that pangolin sequence ended up having that RBD, but rather whether there's anything sketchy here from a scientific standpoint.	needs context	uncertain explicit hedge	asserts
These studies are presented each as independent evidence of the pangolin virus RBD, but if all those papers are relying on a third data set - and don't actually have _any_ data from this very critical CoV RBD, then that's an issue.	own voice, substantive	speaker_own	asserts

Statement

Grade

Attribution

Stance

I think the main problem here is not really how that pangolin sequence ended up having that RBD, but rather whether there's anything sketchy here from a scientific standpoint.

needs context

uncertain explicit hedge

asserts

These studies are presented each as independent evidence of the pangolin virus RBD, but if all those papers are relying on a third data set - and don't actually have _any_ data from this very critical CoV RBD, then that's an issue.

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.

2020-06-18 17:43 Kristian G. Andersen open

Yup - definitely well before the outbreak began (ohhhh, but what about all those parked cars, huh...?)
2020-06-18 17:51 Edward C. Holmes open

I can easily imagine that the Liu et al. data has influenced the assembly in the later papers but (i) why would this only impact nonsynonymous sites and (ii) how could it possibly have produced the human sequence when no one knew what that was? Liu et al. is clearly a 'blind' study. I've just emailed Tommy if he can assemble the same RBD without the Liu et al. data and/or if it has been Sanger sequenced. The other group have a second paper on the clinicalmanifestations that I am helping them with. They've sequenced the virus again. I've also asked if they can assemble the same RBD without the Liu et al. data and/or if it has been Sanger sequenced.
2020-06-18 17:58 Edward C. Holmes open

The similarity between the RBD and the Guangdong pangolins from the Liu et al. study alone was noted on Virological in late January. How can Liu et al. have possibly known what the human RBD would have looked like? https://virological.org/t/ncov-2019-spike-protein-receptor-binding-domain-shares-high-amino-acid-identity-with-a-coronavirus-recovered-from-a-pangolin-viral-metagenomic-dataset/362
2020-06-18 18:26 Kristian G. Andersen open

Here's the manuscript from her - please keep confidential. I haven't read it yet. [shared file(s): Matters Arising ChanZhan 2020.pdf]
2020-06-18 18:28 Kristian G. Andersen

I think the main problem here is not really how that pangolin sequence ended up having that RBD, but rather whether there's anything sketchy here from a scientific standpoint. These studies are presented each as independent evidence of the pangolin virus RBD, but if all those papers are relying on a third data set - and don't actually have _any_ data from this very critical CoV RBD, then that's an issue.
2020-06-18 18:30 Kristian G. Andersen open

I don't really see how this changes anything from the evolutionary perspective - because seeing it even once is very strong evidence. But there's no denying that if these studies have to be modified (or possibly even retracted), then that is going to send a nuke into the whole evolution conversation - whether justified or not.
2020-06-18 18:36 Edward C. Holmes open

Can we do a quick Zoom now.
2020-06-18 18:39 Edward C. Holmes open

Tommy's paper very clearly stated the provenance. Can't speak for the others.
2020-06-18 18:40 Kristian G. Andersen open

https://us02web.zoom.us/j/9673242666

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