Andrew Rambaut

And you have a married blond woman in your house during lockdown.

Slack / Private Message Drop, p.16 · original PDF · in context

Need to feed the 'Eddie is a paid shrill of the Chinese Government' angle to Fox News for a presidential tweet.

Slack / Private Message Drop, p.20 · original PDF · in context

```We also demonstrate that SARS-CoV-2's entire RBM was introduced through recombination with coronaviruses from pangolins``` Nope.

Slack / Private Message Drop, p.46 · original PDF · in context

It also clarifies Sørensen's financial interest in the development ofthe_ Biovacc-19 _coronavirus vaccine_. _This context did not appear in original post_ New claims that the novel coronavirus SARS-CoV-2 was engineered have been dismissed by scientific and intelligence experts.

Slack / Private Message Drop, p.62 · original PDF · in context

I have talked to a few journalists about the origins recently but only if they seem genuinely interestedin the natural origins.

Slack / Private Message Drop, p.77 · original PDF · in context

My approach has been to keep pushing how plausible it is and ignore anything that is trying toset up lab origins without actual evidence.

Slack / Private Message Drop, p.77 · original PDF · in context

Large variety of pangolin viruses (these are illegally imported from SE Asia - so where are they getting them from).

Slack / Private Message Drop, p.77 · original PDF · in context

Shows better how the pangolin distance is exactly the same in the variable as the rest of the CTD whereas RaTG13jumps out.

Slack / Private Message Drop, p.78 · original PDF · in context

Just talked to David Quammen who is writing a piece for the New Yorker about pangolin conservation (with some CoV angles).

Slack / Private Message Drop, p.79 · original PDF · in context

Curiously all of the others in the Beijing group are from late March or early April.

Slack / Private Message Drop, p.81 · original PDF · in context

I bet they have a flashing red light on the hospital computer which goes on whenever there is a pneumonia case associated with a live animal market.

Slack / Private Message Drop, p.83 · original PDF · in context

Yes they have individual trajectories up and down but are not conditioned on a particular lockdown date.

Slack / Private Message Drop, p.92 · original PDF · in context

They all share the same transition time which is after lockdown (but allows for some lag).

Slack / Private Message Drop, p.92 · original PDF · in context

Also the pangolin RBD is only similar in amino acids - has loads of synonymous differences.

Slack / Private Message Drop, p.100 · original PDF · in context

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.

Slack / Private Message Drop, p.109 · original PDF · in context

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.

Slack / Private Message Drop, p.110 · original PDF · in context

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.

Slack / Private Message Drop, p.112 · original PDF · in context

I don't believe there was enough SC2 around in Beijing for 6 out of their 273 patients even to have multiple exposures of radically different viruses, let alone actually become infected.

Slack / Private Message Drop, p.152 · original PDF · in context

Basically Alina is going to have to make a decision as to whether she wantsto be associated with these people now.

Slack / Private Message Drop, p.169 · original PDF · in context

But then there was this bit of the speech: > But even as we strive for a vaccine, we must never cut corners, slim down the trials or sacrifice safety to speed.

Slack / Private Message Drop, p.194 · original PDF · in context

The argument that not having a close relative argues against natural origins is bonkers.

Slack / Private Message Drop, p.217 · original PDF · in context

Coronavirus have mutated in mink and that could ruin the effect of a future Covid19 vaccine.

Slack / Private Message Drop, p.249 · original PDF · in context

Actually, I have some inside information from WHO (please keep confidential): > We have tested a variant with four simultaneous changes in the spike protein (Amino acid changes: 69del, Y453F, I692V, M1229I).

Slack / Private Message Drop, p.249 · original PDF · in context

God yes - and his 2 hour podcasts are just soo excruciatingly dull -

Slack / Private Message Drop, p.254 · original PDF · in context

Some of the RBD mutations we have seen recently (eg mink) are actually reversions to the bat residues.

Slack / Private Message Drop, p.282 · original PDF · in context

@Andrew Rambaut But of course that is with a non-ACE2 RBD in bats.

Slack / Private Message Drop, p.282 · original PDF · in context

But the RNA vaccines may recombine with your viruses and integrate into your genome and all sorts of things.

Slack / Private Message Drop, p.293 · original PDF · in context

Oh - I have just seen what you just said - Malaysia is the same as the Pangolin at 6049 where it differes from WA1

Slack / Private Message Drop, p.299 · original PDF · in context

It is part of the pangolin which is more divergent than RmYN02

Slack / Private Message Drop, p.300 · original PDF · in context

Given it is synonymous and the pangolin has loads of other mutations in that area it must be coincidence.

Slack / Private Message Drop, p.300 · original PDF · in context

I am normally fairly relaxed about RBD mutations - sure they happen and they may have antigenic effects but we can be pretty sure that they are not being antigenically selected for because there isn't enough standing immunity (inmost places) or vaccination yet.

Slack / Private Message Drop, p.311 · original PDF · in context

BUT... this chronic infection scenario worries me because it may well have selected for escape from the immune response raised by the wild type virus (and thus the vaccine).

Slack / Private Message Drop, p.311 · original PDF · in context

There are actually 2 501Y lineages in the UK - the other one in South Wales (now up to about 500 genomes but associated with a hospital outbreak as well).

Slack / Private Message Drop, p.328 · original PDF · in context

Worse case would if it had selected for immune evasion, and was more transmissible, and ended up at high frequency, which could make vaccines less efficient and require a higher coverage for the higher R.

Slack / Private Message Drop, p.330 · original PDF · in context

Convelescent plasma from natural infections and vaccinees will be tested.

Slack / Private Message Drop, p.330 · original PDF · in context

Weare putting a special bit for pangolin to require 3 of the mutations and no wildtype at these sites to make sure there are no mis-classifcations.

Slack / Private Message Drop, p.332 · original PDF · in context

Off the record (although you can find them on GISAID) we now have two independent instances of E484K on top of the B.1.1.7 constellation

Slack / Private Message Drop, p.364 · original PDF · in context

This amino acid change was first described in a clinical sample in the United Kingdom in association with other novel S variants and a clade 20B backbone (ECDC, 2020; Davies et al, 2020), with the combination named as the B.1.1.7 strain and a Next Strain designation as 20I/501Y.V1 (Bedford et al, 2021).

Slack / Private Message Drop, p.397 · original PDF · in context

The same N501Ymutation was subsequently found in a clade 20C strain in South Africa, where it was associated with a different setof additional S variants (Tegally et al, 2020), with Next Strain designation as 20H/501Y.V3. ```What a fucking mess Trevor has created.

Slack / Private Message Drop, p.397 · original PDF · in context

All vaccine failures in the UK will automatically go for sequencing - I am hopeful we will be told which ones they are but who knows.

Slack / Private Message Drop, p.400 · original PDF · in context

The point is that NPI do get R<1so with vaccine as well it should be possible to avoid escape..

Slack / Private Message Drop, p.419 · original PDF · in context

Yeah, he is using the ARTIC protocol on Illumina but then some crazy semi commercial software called Genome Detective

Slack / Private Message Drop, p.444 · original PDF · in context

@Robert Garry Bates Gill is an excellent spoonerism of Bill Gates.

Slack / Private Message Drop, p.464 · original PDF · in context

The embargo is just the standard, wait until we tell you to release it but give us an accession number.

Slack / Private Message Drop, p.483 · original PDF · in context

I was quite happy with just talking about the natural origins based on the available bat and pangolin sequences but obviously that doesn't address these arguments.

Slack / Private Message Drop, p.489 · original PDF · in context

And you would introduce the perfect cleavage site and theoptimum RBD.

Slack / Private Message Drop, p.489 · original PDF · in context

Which is why people saying that a lab origin is not a conspiracy theory are completely wrong - including Bloom, Bedford etc.

Slack / Private Message Drop, p.493 · original PDF · in context

Sorry about this Bob but I am not too fond of the current structure of the piece - the intro is brief, the results technical and then the lab origins stuff is sprung in the discussion and dominates.

Slack / Private Message Drop, p.517 · original PDF · in context

So we have a common set of functional sites/effects for all the new variants: An RdRp mutation, an nsp6 modification, spike 613/614, some NTD mutations/deletions and some RBD mutations.

Slack / Private Message Drop, p.529 · original PDF · in context

I agree about the zoonosis as a route from things like bats into humans especially as these mustelids seem such good models for humans.

Slack / Private Message Drop, p.539 · original PDF · in context

We have fixed this now in the latest pangolin so P.1s will only be called based on having 5 or more of the defining mutations.

Slack / Private Message Drop, p.549 · original PDF · in context

You can see why people want it to be a lab leak - this is much more scary.

Slack / Private Message Drop, p.608 · original PDF · in context

Interestingly also there is a Malaysian case with exactly the same WA1 haplotype (Malaysia... pangolins...).

Slack / Private Message Drop, p.644 · original PDF · in context

@kristian Andersen It was someone called Mustafa Ababneh, Associate Professor of Veterinary Virology, Jordan University of Science and Technology.

Slack / Private Message Drop, p.651 · original PDF · in context

But I have just noticed that it also says that 'Pango' is kind of officially endorsing it

Slack / Private Message Drop, p.678 · original PDF · in context

Really interesting but I haven't fully got my head around it - basically it means that the bat-like NTD is sub-optimal for humans, B.1.1.7 has converged on whatever the pangolin has as an adaptation to humans (given that B.1.1.7 is the most human adapted virus yet).

Slack / Private Message Drop, p.699 · original PDF · in context

One of the PLOS Pathogens Editors-in-Chief suggested you may be able recommend possible reviewers (e.g.bioinformaticians or viral genomics researchers) who could help with this data review.

Slack / Private Message Drop, p.723 · original PDF · in context

And the WIV has recently sent a firmware update to give it 618R using 5G mobile phones

Slack / Private Message Drop, p.754 · original PDF · in context

We are adding a thing into Pangolin that as well as calling a lineage will also call a VOC/VUI based on a set ofdefinition files.

Slack / Private Message Drop, p.760 · original PDF · in context

Bill was pretty convinced but believed it could and should be tested (by testing the chimps local to the vaccine camp).

Slack / Private Message Drop, p.784 · original PDF · in context

However, I do intend to make a very few additional posts, confined entirely to scientific data that will continue tosupport the natural origin of SARS-CoV-2, and then retire permanently from the field of virology.It has been my passion since the age of 12, while in quarantine in the New York metro area in the face of the 1957Asian flu, listening to stories from my father about his recovery from poliomyelitis as a teenager.

Slack / Private Message Drop, p.843 · original PDF · in context

I.e.:> The ACE2 binding RBD in SARS-CoV-2 was not inserted or created in a lab [Confidence: high]> ....

Slack / Private Message Drop, p.849 · original PDF · in context

In one sequence of emails Inoticed you were part of an early February 2020 conference call involving several experts discussing what appearsto be, at least in part, gain-of-function research.

Slack / Private Message Drop, p.908 · original PDF · in context

I should offer to be a consultant to design a genome that would categorically disprove the lab leak.

Slack / Private Message Drop, p.916 · original PDF · in context

```But the earliest known SARS-CoV-2 sequences, whichare mostly derived from the Huanan Seafood Market, are no-tably more different from these bat coronaviruses than othersequences collected at later dates outside Wuhan.``` This is incorrect - WA1 is from Wuhan

Slack / Private Message Drop, p.946 · original PDF · in context

I wrote today's message to the group imagining it will get FOIAed.

Slack / Private Message Drop, p.955 · original PDF · in context

(edited)10:12 I've had a sparsely running DM with Kristian about origins since last summer, though I largely hadn't been paying much attention to it until things blew up recently.````I wrote today's message to the group imagining it will get FOIAed.`

Slack / Private Message Drop, p.955 · original PDF · in context

The last column is me looking outside the SARS-CoV-2 to the bats/pangolins ```S:R102T (21867:G>C) conserved S:D442N (22886:G>A) conserved S:Y449H (22907:T>C) 449F 449G S:N450T (22911:A>C) 450S (RaTG13), 450G S:P499S (23057:C>T) 499S (Cambodian bats) S:N501D (23063:A>G) 501D (RaTG13), 501T, 501V S:N501S (23064:A>G) S:Q506P (23079:A>C) conserved S:P681S (23603:C>T) missing S:V772A (23877:T>C) conserved S:Q779L (23898:A>T) conserved S:L828I (24044:C>A) conserved S:G932D (24357:G>A) conserved S:S937A (24371:T>G) conserved```

Slack / Private Message Drop, p.996 · original PDF · in context

I would just like to discuss what our strategy should be so we don't get associated with these fuckers.

Slack / Private Message Drop, p.1003 · original PDF · in context

It was estimated today that it would take 6-9 months to get an updated mRNA vaccine to deployable stocks.

Slack / Private Message Drop, p.1029 · original PDF · in context

It may have antigenic consequences in humans but that is coincidental because it is the RBD

Slack / Private Message Drop, p.1030 · original PDF · in context

All of our conclusions were written in our published and peer-reviewed papers (i.e., inNature Medicine and then updated in Cell late last year).

Slack / Private Message Drop, p.1050 · original PDF · in context

All of the emails show the establishment of the hypotheseswe later outlined in the Proximal Origins paper and then the assessment of these based on the available evidence.

Slack / Private Message Drop, p.1050 · original PDF · in context

I should have been more specific: what I mean is that both Fauci and Collins were aware that NIH funds had been subawarded to the WIV in the past for certain types of research.> But you make a good point.

Slack / Private Message Drop, p.1063 · original PDF · in context

This will be a good one to be subpoena'ed: > He's about where we were a week ago.

Slack / Private Message Drop, p.1075 · original PDF · in context

He's for escape. > > He also said that Peter Daszak, grand wizard of EgoHealth, and some others were writing a piece saying the Wuhan lab were being persecuted. > > I'll talk to Jeremy later. > > Currently, I'm more concerned that I will run out of underpants. > > Professor Edward C.

Slack / Private Message Drop, p.1075 · original PDF · in context

Yes - the 7th Feb version on google docs (basically the 'report') doesn't have pangolins in the alignment.

Slack / Private Message Drop, p.1079 · original PDF · in context

From the 8th Feb version on GoogleDocs: > Although RaTG13 remains the closest relative to 2019-nCoV across the genome as a whole, the Malayan pangolin CoVs are identical to 2019-nCoV at all six key RBD residues.

Slack / Private Message Drop, p.1079 · original PDF · in context

Analyses of these pangolin viruses are ongoing, although they do not carry the furin cleavage site insertion.

Slack / Private Message Drop, p.1079 · original PDF · in context

New EBOV case in Equateur DRC is definitely a new zoonotic jump not a survivor-associated case.

Slack / Private Message Drop, p.1110 · original PDF · in context