Chat message

Slack / Private Message Drop, p.179 [SLACK_000393] · slack_pm:msg:01842

Date: 2020-09-17 14:16
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Andrew Rambaut
speaker: Edward C. Holmes
Topics: Natural origin / zoonotic spillover

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The pangolin viruses from the Viruses paper were first assembled in that Virological post.

Extracted statements

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Statement	Grade	Attribution	Stance
The pangolin viruses from the Viruses paper were first assembled in that Virological post.	own voice, substantive	speaker_own	asserts

Statement

Grade

Attribution

Stance

The pangolin viruses from the Viruses paper were first assembled in that Virological post.

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.

2020-09-17 14:05 Edward C. Holmes open

No, the pango data is elsewhere. Just look in Tommy's paper. It was RmYN02 that went to the Chinese databases. Let me make this very clear: the Guangdong pangolin viruses have been sequenced multiple times by multiple groups. They have also been Sanger sequenced. Plus there are Pangolins from Guangxi that have been sequenced. There is nothing wrong with the pangolin sequences. Inspector Clouseau's argument is that Guangdong pangolins are a single outbreak - and she's right about that - and then she seems to think that Guangdong pangolins may have gotten their viruses from humans which is just crazy. She also persistently claims that all the pangolin sequences were all derived from the one in the Viruses paper (pre-pandemic of course) which is untrue: there's aseparate assembly in Tommy's paper.
2020-09-17 14:07 Edward C. Holmes open

The pangolin viruses were Sanger sequenced here and this paper clearly shows that these animals are sick: https://www.biorxiv.org/content/10.1101/2020.06.22.164442v1
2020-09-17 14:08 Edward C. Holmes open

Do not fall into the stupid narrative set by Alina Chan. The idea that these viruses are fake is insulting.
2020-09-17 14:10 Kristian G. Andersen open

"the Guangdong pangolin viruses have been sequenced multiple times by multiple groups. They have also been Sanger sequenced. Plus there are Pangolins from Guangxi that have been sequenced" Yup, I know this - hence I have no concerns about the data. Would still be nice to be able to say "yes, I looked at itdummy, and the data is perfectly fine" (as I just did with RaTG13). I'll grab the data and play around with it a bit.
2020-09-17 14:16 Edward C. Holmes

The pangolin viruses from the Viruses paper were first assembled in that Virological post.
2020-09-17 14:21 Edward C. Holmes open

All reads from Tommy's paper are on the SRA. The Guangdong ones are P1L and P2S. P2S is from the scales and at a bit patchy. All explained in the paper.
2020-09-17 14:36 Edward C. Holmes open

What *really* pisses me off is that everything is explained very carefully in Tommy's paper - the provenance of the sequences, how they were sequenced and analysed - and ALL the data is publicly available on GISAID/SRA. Asclean as it gets - take a look. But fucking Alina has managed to sow doubt by linking it to those dodgy pangolin papers.
2020-09-17 14:38 Kristian G. Andersen open

Yeah, I totally agree Tommy's paper is very clear on this - the issue is that the other paper definitely isn't. But that doesn't take away the fact that Tommy's study is clean. Typical conspiracy way of dealing with inconvenient data.
2020-09-17 14:39 Edward C. Holmes open

Agreed. So fucking annoying.

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