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Slack / Private Message Drop, p.962 [SLACK_001176] · slack_pm:msg:10017

Date: 2021-06-23 04:07
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Andrew Rambaut
speaker: Edward C. Holmes

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Might possibly add that the tree is hard to root because of distant outgroup and reversions and the intermediates might be miscalls. I'll email him tomorrow.

In context

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2021-06-23 02:38 Andrew Rambaut open

```@Kristian I have dug out some analysis of the early haplotypes I did way back and updating it. I realise it overlapswith what Joel's student is doing so I will make sure it doesn't impact on that - it is for internal use of this group. I also have in mind a rebuttal of the Italian Job.``` Meant to put this on this Channel.
2021-06-23 02:42 Edward C. Holmes open

I suspect the Italian Job paper will have great trouble getting published. It was only in review at NEJM. I can't believe for a sec they will take it.
2021-06-23 03:28 Andrew Rambaut open

No but they will push it out somewhere. I assume they are not preprinting it so it doesn't get demolished whilst tryingto slip it in a high-impact
2021-06-23 03:50 Andrew Rambaut open

Jeremy just emailed Eddie and me (he just wants to know if he should worry, I think). Eddie you may have gone tobed now. I was planning to reply with -```A total red herring delivered with unsupported insinuation of malfeasance. All of the actual data is in Table 1 of the cited paper, and is exactly the same as reconstructed by Jesse from the 'deleted' reads. The paper was published after the data was deleted so if they wanted to hide something they could have simply not published it. The data just shows there were other haplotypes in Wuhan in January which we knew already - we also now that some aren't associated with the Huanan market. But that was discussed in the WHO report already. It fits very well with the idea there were multiple markets with captive wild animals acting as a more distributed source of human infections until ittook hold in a few transmission chains. ```Should I add anything else?
2021-06-23 04:07 Edward C. Holmes

Might possibly add that the tree is hard to root because of distant outgroup and reversions and the intermediates might be miscalls. I'll email him tomorrow.

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