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Slack / Private Message Drop, pp.85-86 [SLACK_000299] · slack_pm:msg:00871

Page text: p.85, p.86 · original PDF

Date: 2020-06-18 17:43
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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Yup - definitely well before the outbreak began (ohhhh, but what about all those parked cars, huh...?)

In context

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2020-06-18 17:37 Edward C. Holmes open

Let me see what I can do on this. I'm working with both groups.
2020-06-18 17:41 Edward C. Holmes open

Still makes no sense because the Liu et al. paper come out before the pandemic.
2020-06-18 17:41 Kristian G. Andersen open

"Liu et al. paper come out before the pandemic" > Yup.
2020-06-18 17:42 Edward C. Holmes open

Published online October 24th 2019 if I remember.
2020-06-18 17:43 Kristian G. Andersen

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 open

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.

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