Chat message

Slack / Private Message Drop, p.88 [SLACK_000302] · slack_pm:msg:00891

Date: 2020-06-19 00:42
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Andrew Rambaut
speaker: Edward C. Holmes
Topics: Furin cleavage site and molecular features Natural origin / zoonotic spillover Proximal Origin paper

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

From Tommy: For the accuracy of the RBD, the GD sequences available now: 1. GD/P1L (ours), which is a 'reassembly' of the SRA dataset from Liu et al Viruses paper - this is clearly stated in the methods section of our paper. 2. GD/P2S (ours), which is the assembly from the NGS SRA data by Guangdong custom. 3. GD/1/2019 (Xiao), which is assembly from NGS SRA data of their pangolin samples, plus confirmation with PCR amplicon sequencing (Sanger/NGS unknown). 4. GD/MP789 (Liu), which is so called re-sequencing of the Viruses sample by NGS and re-assembly if I remember correctly. Their RDBs are all highly similar (almost identical), and so I think this somehow proves that this RBD sequence is real. Yes, as you said, some other papers are very nasty, they just down the pangolin sequences from GISAID and do some analysis and published, and without mentioning the source or citing the original papers. Readers are highly misled and confused where these sequences come from...

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
GD/1/2019 (Xiao), which is assembly from NGS SRA data of their pangolin samples, plus confirmation with PCR amplicon sequencing (Sanger/NGS unknown). 4.	own voice, substantive	speaker_own	asserts
Their RDBs are all highly similar (almost identical), and so I think this somehow proves that this RBD sequence is real.	needs context	uncertain explicit hedge	asserts
Yes, as you said, some other papers are very nasty, they just down the pangolin sequences from GISAID and do some analysis and published, and without mentioning the source or citing the original papers.	own voice, substantive	speaker_own	asserts

Statement

Grade

Attribution

Stance

GD/1/2019 (Xiao), which is assembly from NGS SRA data of their pangolin samples, plus confirmation with PCR amplicon sequencing (Sanger/NGS unknown). 4.

own voice, substantive

speaker_own

asserts

Their RDBs are all highly similar (almost identical), and so I think this somehow proves that this RBD sequence is real.

needs context

uncertain explicit hedge

asserts

Yes, as you said, some other papers are very nasty, they just down the pangolin sequences from GISAID and do some analysis and published, and without mentioning the source or citing the original papers.

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 23:25 Andrew Rambaut open

You should suggest they should get a preemptive post up on virological. Much better than doing a response to a published insinuation. Could be innocently presented.
2020-06-18 23:41 Edward C. Holmes open

Yes, not a bad idea. Their new paper is about clinical manifestation in pangos which they claim is the same as human COVID-19. They just sequenced the virus in passing. However, I guess they could stick the tree (above) up on Virological as that does contain new S gene data and has been Sanger sequenced. I don't think Tommy has to do anything as the provenance of the sequences is clearly stated in the paper. I do think this all a bit of a nothing issue. 100% certain that pangos had that sequence (and it ain't from a human). Here's a pango CT scan if you want one: [shared file(s): image.png]
2020-06-18 23:43 Edward C. Holmes open

P.S. Tommy also told me that some other (EgoHealth Alliance I think) pangos were CoV positive. Not quite sure what CoV though.
2020-06-19 00:42 Edward C. Holmes

From Tommy: For the accuracy of the RBD, the GD sequences available now: 1. GD/P1L (ours), which is a 'reassembly' of the SRA dataset from Liu et al Viruses paper - this is clearly stated in the methods section of our paper. 2. GD/P2S (ours), which is the assembly from the NGS SRA data by Guangdong custom. 3. GD/1/2019 (Xiao), which is assembly from NGS SRA data of their pangolin samples, plus confirmation with PCR amplicon sequencing (Sanger/NGS unknown). 4. GD/MP789 (Liu), which is so called re-sequencing of the Viruses sample by NGS and re-assembly if I remember correctly. Their RDBs are all highly similar (almost identical), and so I think this somehow proves that this RBD sequence is real. Yes, as you said, some other papers are very nasty, they just down the pangolin sequences from GISAID and do some analysis and published, and without mentioning the source or citing the original papers. Readers are highly misled and confused where these sequences come from...

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