Chat message

Slack / Private Message Drop, p.178 [SLACK_000392] · slack_pm:msg:01830

Date: 2020-09-17 08:07
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry
Topics: Natural origin / zoonotic spillover Proximal Origin paper

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I agree with Andrew that the main point is that our analysis would not have changed much at all without RaTG13. The pangolin CoVs (that Alina seems focused on) and other BtCoVs were sufficient for the Proximal Origins analysis. I do recall a PR that talked of a 99% CoV that unfortunately never came.

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
The pangolin CoVs (that Alina seems focused on) and other BtCoVs were sufficient for the Proximal Origins analysis.	needs context	uncertain explicit hedge	asserts

Statement

Grade

Attribution

Stance

The pangolin CoVs (that Alina seems focused on) and other BtCoVs were sufficient for the Proximal Origins analysis.

needs context

uncertain explicit hedge

asserts

In context

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

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.
2020-09-17 07:10 Kristian G. Andersen open

I suspect the data is scattered across repos
2020-09-17 08:07 Robert F. Garry

I agree with Andrew that the main point is that our analysis would not have changed much at all without RaTG13. The pangolin CoVs (that Alina seems focused on) and other BtCoVs were sufficient for the Proximal Origins analysis. I do recall a PR that talked of a 99% CoV that unfortunately never came.
2020-09-17 08:13 Andrew Rambaut open

> Update from Vegard: ```Quick update: We were in the end able to obtain a decent assembly of RaTG13. The description of their approachis lacking to say the least, but the genome seems legit enough, and seems extremely unlikely to involve any sort offraud.We'll post a little commenn on virological, as there might be others looking into the same question.```
2020-09-17 08:14 Kristian G. Andersen open

Hah - I'm glad they're so thorough before bugging other scientists... I'm downloading the raw data now - lemme have a quick look
2020-09-17 09:05 Kristian G. Andersen open

Yeah, no concerns really @Andrew Rambaut [shared file(s): RaTG13.jpg]
2020-09-17 09:06 Kristian G. Andersen open

Very few unresolved bases (a handful)

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