Private channel session 247

53 messages over 6h 32m, 2020-07-27 – 2020-07-27.

A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.

2020-07-27 13:37 Robert F. Garry open PDF p.108

Nice paper coming Andrew! I hope I did not botch the discussion of the phylogenetic trees, etc. to the reporter toobadly.
2020-07-27 14:05 Andrew Rambaut open PDF p.108

Thanks! More stuff to wind up Ebright and the others.
2020-07-27 14:19 Kristian G. Andersen open PDF p.108

Is this the "Nature Microbiology" paper I have been dodging reporters on today?
2020-07-27 14:25 Andrew Rambaut open PDF p.108

Yeah. Just some phylogenies, recombination and date estimates of SARS related coronaviruses. Nothing you haven't heard already.
2020-07-27 14:39 Kristian G. Andersen open PDF p.109

Cool! One interesting thing I got from Trevor though - if he tries to date SARS2 via the related viruses (of which we now have a few), he gets a relatively nice signal for 2014/2015. Doesn't mean anything in isolation, but I still keepcontemplating that 'pre' circulation scenario for emergence. They need to go hunt some more viruses in those Yunnan caves!
2020-07-27 14:40 Andrew Rambaut open PDF p.109

It is meaningless to date SARS2 with related viruses - makes no sense.
2020-07-27 14:41 Kristian G. Andersen open PDF p.109

I thought so too, but honing in on specific parts of the genomes that were homologous it seemed like it could bedone - no idea about the details though.
2020-07-27 14:43 Andrew Rambaut open PDF p.109

It also makes no sense that the SARS2 diversity circulating now was part of the pre-circulating scenario. The Wuhanhaplotype may have been around for a month or two prior to Dec 2019 but not much longer given the transmissibilityof the virus. This virus doesn't lurk unobserved.
2020-07-27 14:45 Andrew Rambaut open PDF p.109

Has Trevor found his next thing to go off on Twitter about?
2020-07-27 14:46 Kristian G. Andersen open PDF p.109

"This virus doesn't lurk unobserved" - as is, definitely true - but I _do_ wonder if a pre-furin site virus could. But Iagree with you - I'm not sure such an analysis makes sense given our limited sampling. Assuming SARS2 came outof Yunnan diversity (which seems likely), it would be cool to go do some in-depth sampling from there. And yes, maybe we'll get the big reveal on Twitter :wink:
2020-07-27 14:48 Andrew Rambaut open PDF p.109

But if the acquisition of the furin site is the point at which it becomes epidemic then once again we are back to the common ancestor of the current diversity being in late 2019. We don't have any other nodes to date.
2020-07-27 14:50 Kristian G. Andersen open PDF p.109

.... ehm, yes. That is, of course, true... Unless it's been in a freezer since that outbreak in the Mojiang mine...:parrot:
2020-07-27 14:55 Kristian G. Andersen open PDF p.109

And @Robert Garry - I have come around on challenge testing... What I really want to see is early challenge trials invery small (~10-20) groups of people to establish efficacy. If it doesn't work in those, no need to move forward... I'm SUPER uncomfortable with 30,000 people now getting the Moderna vaccine - can you imagine how detrimental thisis going to be for (COVID and otherwise) vaccine research if this vaccine actually isn't safe? Or may even lead toADE?Let's hope it works...
2020-07-27 15:03 Robert F. Garry open PDF p.110

Yeah - that's a good idea - you could get down to the best set of candidates with 10-20 person trials in a few months. Same with the monoclonals, though showing protection in animals before the in-ppl screening would be good.
2020-07-27 15:09 Kristian G. Andersen open PDF p.110

Yup.
2020-07-27 15:09 Kristian G. Andersen open PDF p.110

Okay, so back to topic - Eddie and I just received this from Jon. This is serious !channel, so we need to consider this carefully. [shared file(s): Screen Shot 2020-07-27 at 3.08.41 PM.png]
2020-07-27 15:10 Robert F. Garry open PDF p.110

Moderna trial started today in Louisiana BTW
2020-07-27 15:13 Kristian G. Andersen open PDF p.110

Who the hell could this person be? Obviously the person gets some of the details (and intentions) wrong, but everything is otherwise pretty much correct - that is so extremely deep knowledge about how this played out.
2020-07-27 15:14 Andrew Rambaut open PDF p.110

Ron talked to someone? He seemed like the one that really wasn't getting the point.
2020-07-27 15:14 Kristian G. Andersen open PDF p.110

I can't imagine this being Christian
2020-07-27 15:15 Kristian G. Andersen open PDF p.110

It's Ron or Marion I assume
2020-07-27 15:15 Andrew Rambaut open PDF p.110

No. I talked to Christian at the WHO meeting and we had an interesting chat - he thought it had been circulating inhumans for a while before the furin site appeared.
2020-07-27 15:16 Kristian G. Andersen open PDF p.110

Seems like it must be Ron.
2020-07-27 15:16 Andrew Rambaut open PDF p.110

I can't see it being Marion either.
2020-07-27 15:17 Kristian G. Andersen open PDF p.110

I would be surprised if Marion was behind this, but I can't rule it out. I'm almost certain it's not Christian. I'm wondering if somebody could have mentioned this to e.g., Baric and then this is actually Baric - he always seemed pissed about the whole situation.
2020-07-27 15:18 Edward C. Holmes open PDF p.111

But we sent them all a draft, inc. Ron. Email of Feb 10.
2020-07-27 15:19 Kristian G. Andersen open PDF p.111

The subject of the email is interesting - "The authors who wrote the paper saying that SARS-CoV-2 is not human engineered first tried convincing Anthony Fauci of the opposite". Probably somebody in America?
2020-07-27 15:19 Edward C. Holmes open PDF p.111

Here's the summary of Feb 7 sent to all people. [shared file(s): Summary.Feb7_MF.pdf]
2020-07-27 15:20 Kristian G. Andersen open PDF p.111

This part has me stumped "after quietly raising the alarm (*or "spreading the rumor", as Jeremy Farrar apparently put it*) "
2020-07-27 15:21 Kristian G. Andersen open PDF p.111

Who would be privy to that information if Jeremy really said that?
2020-07-27 15:21 Andrew Rambaut open PDF p.111

This channel starts on the 1st of Feb just prior to the phone call.
2020-07-27 15:21 Edward C. Holmes open PDF p.111

Feb 9 from Jeremy, sent to all "We now have (and we will get more) the pangolin data (Eddie has) we think we cantie this up even tighter with the next iteration and make a conclusive statement which will then be the go to scientific statement to refer to.Eddie and I have just come off a call with the National Academy of Medicine in the US - who the White House has asked to produce a report on this...."
2020-07-27 15:21 Kristian G. Andersen open PDF p.111

Quick Zoom?
2020-07-27 15:22 Edward C. Holmes open PDF p.111

ok.
2020-07-27 15:22 Edward C. Holmes open PDF p.111

It's just sour grapes if you ask me.
2020-07-27 15:23 Kristian G. Andersen open PDF p.111

https://us02web.zoom.us/j/9673242666
2020-07-27 15:26 Andrew Rambaut open PDF p.111

The document from the 2nd Feb: https://docs.google.com/document/d/1-bJCwpJCGAGDtUr_uVh9-E9i4PeevGb_rgdWXVDA1m4/edit
2020-07-27 15:41 Andrew Rambaut open PDF p.112

https://docs.google.com/document/d/1HOVHVaahY2wMwAij_Mb-rLTV3QomBai-DwRDcn506OE/edit#
2020-07-27 16:23 Andrew Rambaut open PDF p.112

In the document history is a named version from the 4th Feb called 'First Distributed Version'. Looking at my emails Eddie passed this version on the 4th to Jeremy who then distributed it to Fauci and others.
2020-07-27 16:27 Andrew Rambaut open PDF p.112

We then reworked it and Jeremy sent it round the full group on the 8th. Ron replied about a point so definitely saw it.
2020-07-27 16:28 Andrew Rambaut open PDF p.112

Jeremy's email - ```Kristen, Andrew, Bob, Eddie have reworked the summary and it is attached here. We are pushing to get the sequence data from the reports on the pangolins, but do not have currently, clearly that isvery important to incorporate. Interested in your viewsIs this reasonably balanced given the data?Is there anything anyone disagrees with?Is there anything more in relation to what would seem to be the two possibilities Nature, Intermediate host, evolution and passage Future data you may have Advice on whether KA, AR, RG and EH should publish this. These and other thoughts welcome in confidence.```
2020-07-27 16:36 Kristian G. Andersen open PDF p.112

Very good - and I remember the followup to that where I'm actually saying that we need to get more conclusive data before we can say one thing or the other. I think our paper trail is good
2020-07-27 16:37 Kristian G. Andersen open PDF p.112

One thing though - and @Eddie Holmes this is important - we _*need*_ to talk to Jeremy or Tony first before saying _*anything*_ about a meeting. If we confirm that the meeting did happen, then we automatically confirm that Tony and Jeremy were present - we can't do that, without getting their consent. I'll reach out to Tony (and Francis) to seeif I can get a moment with them - Eddie, will you please do the same with Jeremy? Or should we do all three at the same time?
2020-07-27 17:29 Edward C. Holmes open PDF p.112

Agreed. I've now emailed Jeremy.
2020-07-27 18:12 Edward C. Holmes open PDF p.112

On the plus side, this may be the Altmetric boost we need...
2020-07-27 18:12 Kristian G. Andersen open PDF p.112

Exactly!
2020-07-27 19:02 Kristian G. Andersen open PDF p.113

Obviously the person writing the email... [shared file(s): Screen Shot 2020-07-27 at 7.02.03 PM.png]
2020-07-27 19:50 Edward C. Holmes open PDF p.113

I'm not sure what I would conclude except that it is completely inappropriate to discuss the thoughts of the editors atNature. In addition, they completely fail to note that it was Clare that suggested Nature Medicine!! Clare seems tohave rejected the paper largely on the grounds that she thought it would go out of date quickly.
2020-07-27 19:55 Kristian G. Andersen open PDF p.113

Yeah, but only a reviewer would be privy to this information - nobody on the call (unless they reviewed the paper) would know this.
2020-07-27 20:03 Edward C. Holmes open PDF p.113

May be. I dunno.
2020-07-27 20:07 Kristian G. Andersen open PDF p.113

It's possible Ron was that reviewer too - and then just relayed the whole story to Ralph. More likely, Ralph was the reviewer and talked to Ron about it and Ron probably said "that's funny, let me tell you something...". Ralph then got pissed when he saw Jon's article - once again not citing him - with our quotes once again stating that this is a natural virus. In the Baric universe, I could see how that would blow a fuse.
2020-07-27 20:08 Edward C. Holmes open PDF p.113

Yes, that makes sense to me.
2020-07-27 20:09 Kristian G. Andersen open PDF p.113

Or, alternatively, @Robert Garry did it to boost our Altmetric score. That's a legit move.