Andrew Rambaut

I have not yet heard from you and would ask you to let us know as soon as possible whether or not you will be able to dothis for us.The manuscript abstract appears below.In our paper we describe some unusual characteristics of the regulatory 5' UTR sequences of SARS-CoV-2 that might imply its non-natural origin.

Slack / Private Message Drop, p.3 · original PDF · in context

We are also discussing possible therapeuticimplications of this finding - especially RNA interference and direct knock-out of the unique 5' UTR regulatory sequences of the SARS-CoV-2 virus, which, due to the high replication (and error) rate of SARS-CoV-2 might besuperior to the development of conventional immunogenic vaccines and might be an interesting idea to pursue.```5' UTR apparently has a non-natural origin.

Slack / Private Message Drop, p.3 · original PDF · in context

Should just reply to the editor - 'Did you read our paper at all'.

Slack / Private Message Drop, p.4 · original PDF · in context

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

But I wonder if you'd have time at least to cast your eye over this very brief set of notes (responding to a number of points in the Nature Medicine paper) that I have received from a molecular biologist contact of mine, who has long experience in vaccine development and gain of function research (his comments are in blue): (NATURE MEDICINE ARTICLE IN BLACK TYPE)In theory, it is possible that SARS-CoV-2 acquired RBD mutations (Fig. 1a) during adaptation to passage in cell culture, as has been observed in studies of SARS-CoV11.

Slack / Private Message Drop, p.31 · original PDF · in context

(COMMENTS FROM MOLECULAR BIOLOGIST IN BLUE TYPE) This has two problems in respect of the second half assumption 1. doesnt prove it didn't happen in a petri dish - themixing could have happened naturally in a co-infected pangolin that had two related coronavirus infections at the same time, or in a petri dish where two viruses were infecting the same human cells.

Slack / Private Message Drop, p.31 · original PDF · in context

Both equally possible, latter probably more plausible - how many co-infected pangolins are out there?

Slack / Private Message Drop, p.31 · original PDF · in context

But third scenario they don't touch onmight be the most plausible of all - rather than postulating random recombination between the two viruses - the third possibility is that a researcher deliberately inserted the pangolin spike mutation into bat virus to see what this did.

Slack / Private Message Drop, p.31 · original PDF · in context

New polybasic cleavage sites have been observed only after prolonged passage oflow-pathogenicity avian influenza virus in vitro or in vivo17.Yes if you postulated the virus found these 4 amino substitutions one by one - I agree this is highly implausible.Pluasible scenario is that it got all 4 substitutions all at the same time - ie by recombination event between twoco-cultured viruses which can happen in days OR by researcher deliberately introducing these 4 substitutions all atthe same time which is a very simple process.

Slack / Private Message Drop, p.31 · original PDF · in context

It is the acquisition en masse of these 4 key new residues and nothing in flanking sequences that raises the distinct impression that someone deliberately inserted these 4 residuesin one step - with recombination would expect some variability on either side of these 4 substitutions between bat and pangolin spike sequences - there is absolutely none - all the residues on each side are identical - this is whatis so concerning.

Slack / Private Message Drop, p.31 · original PDF · in context

Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described.

Slack / Private Message Drop, p.31 · original PDF · in context

If they did indeed find a bat virus in their stocks with99% identity apart from the polybasic cleavage site then would they be comfortable to disclose this as then the only conclusion was that COVID19 was artificially created in their lab.

Slack / Private Message Drop, p.31 · 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

So what does Trevor think about the new proof of lab origins paper?

Slack / Private Message Drop, p.55 · 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

@Robert Garry @Kristian Andersen Can you tell me anything about the RmYN02 cleavage site insertion?

Slack / Private Message Drop, p.68 · 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

Jotting down some of the new stuff: Bill's potential source of the furin site - perhaps could dig into that more.

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

I wonder which of those Beijing is going to blaim?

Slack / Private Message Drop, p.81 · 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

You probably saw it but here is the ML tree (with an outgroup root): [shared file(s): beijing_11.ml.tree.png]

Slack / Private Message Drop, p.82 · original PDF · in context

Plausible: https://www.theguardian.com/world/2020/jun/18/global-report-beijing-covid-19-cluster-may-have-begun-amonth-earlier-china-health-chief

Slack / Private Message Drop, p.82 · 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

But there was no coronavirus in Beijing so why would you need to wear masks?

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

From Jefferson's wikipedia page https://en.wikipedia.org/wiki/Tom_Jefferson_(epidemiologist) : "His views about the effectiveness of influenza vaccines and his outspokenness about them are also controversial;at a 2007 meeting on pandemic preparedness he was shunned by other vaccine researchers and ate alone."He is getting his revenge for being shunned.

Slack / Private Message Drop, p.96 · 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

I agree that it is probably unnecessary - just try the vaccine.

Slack / Private Message Drop, p.104 · 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

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.

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

This obsession with hydroxychloroquine is bonkers.

Slack / Private Message Drop, p.131 · original PDF · in context

Koonin doing mad stuff again... ```Prediction of the incubation period for COVID-19 and future virus disease outbreaks Ayal B Gussow; Noam Auslander; Yuri I Wolf; Eugene Koonin Research article Abstract: Background: A crucial factor in mitigating respiratory viral outbreaks is early determination of the durationof the incubation period and, accordingly, the required quarantine time for potentially exposed individuals.

Slack / Private Message Drop, p.143 · original PDF · in context

The predictive approach described here can directly help in establishing the appropriate quarantinedurations and thus facilitate controlling future outbreaks.

Slack / Private Message Drop, p.143 · 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

Wins a prize for the most gratuitous use of `quasispecies`: "but also describe the emergence of natural SARS-CoV-2 quasispecies with an extended ORF3b gene that may potentially affect COVID-19 pathogenesis".

Slack / Private Message Drop, p.154 · original PDF · in context

Just saw this - ```In fact, a Chinese BSL-3 lab (the Shanghai Public Health Clinical Centre), which published a Nature article reporting a conflicting close phylogenetic relationship between SARS- 35 36 CoV-2 and ZC45/ZXC21 rather than with RaTG13 , was quickly shut down for "rectification" .

Slack / Private Message Drop, p.167 · 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

Obviously RaTG13 isn't the whole story and the nutters' obsession with it ismisplaced (the existence of the pangolins and RmYN02 tell you almost as much). ```Dear Andrew,I was recently contacted by a national fact-checking body, run by Norwegian media outlets.

Slack / Private Message Drop, p.176 · 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

Because it would be an absolute tragedy if in our eagerness, we were to boost the nutjobs - the anti vaxxers,dangerous obsessives who campaign against the whole concept of vaccination and who would risk further millionsof lives.

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

Had a crazy idea of inviting Shi Zhengli from WIV.

Slack / Private Message Drop, p.205 · 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

That is the best argument against lab origin.

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

You mean they didn't fix the RBD that they messed up when they created RaTG13?

Slack / Private Message Drop, p.225 · original PDF · in context

Would be good to get out the bit about pissing off the Chinese Authorities!

Slack / Private Message Drop, p.232 · original PDF · in context

Officially it is called a 'wall of crazy': https://www.esquire.com/uk/culture/film/news/a7703/detective-show-crazy-walls/

Slack / Private Message Drop, p.233 · 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

Looks like it could be a handy outgroup for the SC2, pangolin, RaTG13 clade

Slack / Private Message Drop, p.253 · 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

To me the most interesting thing is the spike deletion at 69/70 that appears after Y453F and also appears after N469K in humans [shared file(s): Mink-associated_mutations_in_humans.pdf]

Slack / Private Message Drop, p.261 · original PDF · in context

I jotted down some scribbled notes I had been making about why SC2 is likely natural origins: https://docs.google.com/document/d/1lPzBuXW0BY0okNljUBjmOSzDvwMsiW_UGMHYcyCWD4E/edit Basically it comes down to the only lab-escape scenario that could give you SC2 is if SC2 was in the lab and then escaped.

Slack / Private Message Drop, p.268 · original PDF · in context

Next step is Harvard puts out a press release.

Slack / Private Message Drop, p.279 · 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

I think the RBD + furin site must be a top combination.

Slack / Private Message Drop, p.323 · 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

Do you know if pangolin assigned it B.1.1.7 or if it was just the presence the mutation that suggested it to them?

Slack / Private Message Drop, p.332 · 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

It is a way more likely hypothesis than the Wuhan lab in that there is provably SARS-CoV-2 in hundreds of labs doing a thousand different experiments.

Slack / Private Message Drop, p.333 · original PDF · in context

So definitely could be associated with a change in virus behaviour.

Slack / Private Message Drop, p.342 · original PDF · in context

Just sent to Bob and me (plus Christian Drosten, Trevor and Guy Hoelzer). ```Gentlemen, It appears that the mutations in the spike protein that causes PCR failure for that part of the Taqpath assay will befound to have induced a PCR selection bias, and thus contributed to the spread of the virus without increasedpathogenicity.Specifically, there will be more false negatives in tests of people with any variant with new variation in the primer target sequences, especially the 8 variants Andrew reported in the spike protein coding region.

Slack / Private Message Drop, p.356 · original PDF · in context

See second report here HKU-3-3 is a SARS-CoV-2 precusor, at least from the perspective of the spike protein.http://ipaknowledge.org/covid-19-and-sars-cov-2-research.phpAlso available herehttps://www.researchgate.net/publication/340769150_Motif_Pathogenicity_Typing_SARS-CoV-2_Coronavirus_May_Contain_a_Unique_Likely_Pathogenic_Protein_Motif_Signature_Also_Found_in_a_Natural_Isolate_from_2005```

Slack / Private Message Drop, p.356 · original PDF · in context

James thinks he is on to something that explains everything: ```Evolutionists in the know: Australia, S Korea, China all use the Beijing test - no spike protein per their protocol? https://www.health.gov.au/sites/default/files/documents/2020/06/post-market-validation-of-the-beijing-genomics-institute-bgi-sars-cov-2-real-time-pcr-platform.pdfIf so, that might explain the discrepancies... concluding that "we never could have gotten our arms around this because variants" will not fly."Not knowing enough to exclude primer sites that are evolutionarily labile" - yes, I'd buy that.IF Oz, S.

Slack / Private Message Drop, p.359 · original PDF · in context

Korea & China all used conserved primer target sites and other nations did not, it's a disgrace.CDC boasts on their website that they controlled SARS w/accurate testing and contact tracing.We still have no viable reliable testing program???```

Slack / Private Message Drop, p.359 · 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

If these constellations have no effect on vaccine elicited immunity then boy will we have dodged a bullet.

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

Perhaps say they have to pay the honorarium first into my paypal and then I have some excellent dirt about Holmes and Andersen

Slack / Private Message Drop, p.405 · 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

As you know, it is typical that GISAID receivessuch an alert when a novel strain appears, as in 2009, when GISAID was advised by the US CDC of H1N1p, and in2013, when the China CDC gave GISAID a heads up on the HPAI H7N9, and on numerous other occasions when itseemed an outbreak could occur.

Slack / Private Message Drop, p.421 · original PDF · in context

@Kristian Andersen Daszak's involvement in the WHO investigation is like "having Donald Trump run the investigation of Russian hacking of the 2016 election."

Slack / Private Message Drop, p.428 · original PDF · in context

Mind you, the retracted Hydroxychloroquine paper is #5

Slack / Private Message Drop, p.428 · original PDF · in context

```Dear Permanent Missions to the United Nations in New York: Phase III vaccine trial participants are in the process of losing their immunity and will become individual superspreaders once they become infected.

Slack / Private Message Drop, p.434 · original PDF · in context

I warned you about the vaccines causing mass amounts ofdeaths, but you did not listen, so now your leaders must face the consequences of those deaths.I will fix this mess for you, but you must give me absolute power.

Slack / Private Message Drop, p.434 · original PDF · in context

This version includes my first fifteen official acts and my first most wanted list, with China President Xi Jinping listed at #2.Every day you do not appoint me is another day that your leaders will be morally responsible for the deaths that will occur.Sincerely,Brady L.

Slack / Private Message Drop, p.434 · 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

So the Cambobat has the RBD that RaTG13 lost through recombination and is slightly closer than the GD pango by the looks?

Slack / Private Message Drop, p.450 · 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

If it was in fact a lab origin then there was SC2 progenitor in WIV or where-ever and there has been aconspiracy to hide that fact.

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

When testing vaccines against B.1.351, are they using one with Leif and Karen?

Slack / Private Message Drop, p.496 · 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

Or it could be adescription of the new genomes and what they mean for natural origins.

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

Would the glycan's affect the accessibility of the cleavage site to furin and thus these 677 mutations be moderating/enhancing cleavage?

Slack / Private Message Drop, p.518 · original PDF · in context

@Robert Garry Some discussion in another place on where the RBD ends in SC2: is it 331N - 526G (what we had in Prox) or 527?

Slack / Private Message Drop, p.524 · 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

In particular I am wondering if partially-effective measures may have driven evolution for transmissibility in the same way that ineffective vaccines can.

Slack / Private Message Drop, p.530 · original PDF · in context

This would be an explosively political hypothesis given all the anti-lockdown stuff going on.

Slack / Private Message Drop, p.530 · 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

I don't believe that 'variant' is doing anything special.

Slack / Private Message Drop, p.541 · 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

And shows that hotel quarantine is going well.

Slack / Private Message Drop, p.553 · original PDF · in context

Here is the list of places from which travel is banned (i.e., you do hotel quarantine): ```Angola Argentina Bolivia Botswana Brazil Burundi Cape Verde Chile Colombia Democratic Republic of the Congo Ecuador Eswatini French Guiana Guyana Lesotho Malawi Mauritius Mozambique Namibia Panama Paraguay Peru Portugal (including Madeira and the Azores) Rwanda Seychelles South Africa Suriname Tanzania United Arab Emirates (UAE) Uruguay Venezuela Zambia Zimbabwe``` Notice any commonalities?

Slack / Private Message Drop, p.554 · original PDF · in context

From what I am hearing it is difficult toculture SARS-CoV-2 from many samples so I would imagine sampling bats (say) you would be just hoping for RNA rather than infectious virus.

Slack / Private Message Drop, p.575 · original PDF · in context

But that means these ideas about WIV sampling viruses from the wild and one of the accidentally escapes might bewrong?

Slack / Private Message Drop, p.576 · original PDF · in context

The reality is of course that ifwe found evidence of lab origins or whatever we would be straight down to Nature/Science with it.

Slack / Private Message Drop, p.579 · 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

So annoying it has been taken up by the GOF debate (which I have some sympathy with) - no one (except the real crazies) are suggesting this is GOF research surely?

Slack / Private Message Drop, p.614 · original PDF · in context