Andrew Rambaut

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

Slack / Private Message Drop, p.4 · 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

@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

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

I wonder which of those Beijing is going to blaim?

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

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

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

Slack / Private Message Drop, p.104 · 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

Had a crazy idea of inviting Shi Zhengli from WIV.

Slack / Private Message Drop, p.205 · 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

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

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

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

Slack / Private Message Drop, p.323 · 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

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

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

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

Mind you, the retracted Hydroxychloroquine paper is #5

Slack / Private Message Drop, p.428 · 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

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

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

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

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

Slack / Private Message Drop, p.541 · 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

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

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

https://www.bloomberg.com/news/articles/2021-03-26/former-cdc-chief-says-he-thinks-co[...]=social&utm_sour ce=twitter&cmpid=socialflow-twitter-business

Slack / Private Message Drop, p.635 · original PDF · in context

I think you could argue that the pangolin is actually less likely to be the intermediate for SC2.

Slack / Private Message Drop, p.700 · original PDF · in context

I think clearly WIV were really shit at creating SC2

Slack / Private Message Drop, p.700 · original PDF · in context

Vaccination may still reduce probability of onwards transmission.

Slack / Private Message Drop, p.708 · original PDF · in context

So much convergence and parallel mutations and spike mutational 'bursts' now I think we have to move beyond trying to find a special explanation for B.1.1.7

Slack / Private Message Drop, p.722 · original PDF · in context

Yeah - it is obviously one way of manufacturing vaccine.

Slack / Private Message Drop, p.735 · original PDF · in context

Do you think Russia are just going for the win on number of vaccinations?

Slack / Private Message Drop, p.735 · original PDF · in context

I forgot to add in p(f) = probability that WIV is fibbing

Slack / Private Message Drop, p.768 · original PDF · in context

We have been in a pretty strong lockdown over the entire vaccination period so decline in cases probably not downto vaccine (much improved death rate of course).

Slack / Private Message Drop, p.823 · original PDF · in context

I suggested on Twitter it was as likely that some one from USAMRIID infected themself and then flew to Wuhanas it was for someone from WIV to have leaked it.

Slack / Private Message Drop, p.888 · original PDF · in context

I think we should not mention manipulation - no furin site, no passaging, nothing - that is all dumb and has been dealt with.

Slack / Private Message Drop, p.906 · original PDF · in context

Judging from Bob's map, Huanan market is in Jianghan?

Slack / Private Message Drop, p.972 · original PDF · in context

The loss of furin cleavage and some RBD mutations seems like it might be non-human

Slack / Private Message Drop, p.997 · original PDF · in context

Just saying... ifyou wanted to insert an RBD, perhaps you would just insert the variable loop.

Slack / Private Message Drop, p.1007 · original PDF · in context

Do we know when the financial year spans in China?

Slack / Private Message Drop, p.1008 · original PDF · in context

I think Sanjay or whoever misunderstands that a 'PCR test' isbasically reagents.

Slack / Private Message Drop, p.1009 · original PDF · in context

Although with all the sub-genomic mRNAs being created in the second round perhaps it is worth distinguishing the actual production of the gRNA from mRNAs

Slack / Private Message Drop, p.1013 · original PDF · in context

Yes - Tom has identified that insertion in a human mRNA

Slack / Private Message Drop, p.1028 · original PDF · in context

This evening I think we may be back to square one with respect to vaccination and prior immunity.

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

A non-human host would also explain adaptation in the RBD to a different ACE-2?

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

I know that Civets are not a favoured host but again, perhaps that would explain the RBD - i.e. mustelids are closerto humans, civets require more adaptation.

Slack / Private Message Drop, p.1031 · original PDF · in context

Should I address this - `- Were you aware, while you were on that call, that Anthony Fauci had historically funded research at the Wuhan Institute of Virology?` I mean I was aware that EHA had been doing work with them althoughI am not sure I knew specifically that NIH funded it.

Slack / Private Message Drop, p.1059 · original PDF · in context

Or was there some special mechanism through NIAID's director?Or just ignore that one?

Slack / Private Message Drop, p.1059 · original PDF · in context