Alina Chan Profile picture
Sep 17, 2020 33 tweets 8 min read Read on X
My thoughts about the Yan whistleblower report on SARS2 origins have been percolating over the past few very busy days. I'm ready to share them in this thread:
(1) why+how whistleblowers must be protected
(2) what the report gets right and what it gets wrong
How did this all start? Dr. Limeng Yan arrived in the US at the end of April, escaping China in fears of being disappeared. She is a whistleblower, who has worked for years on vaccines and is co-first author on a Nature paper (July 2020) about SARS2. pubmed.ncbi.nlm.nih.gov/?term=limeng+y…
In fact, Yan blew the whistle on 2 of the senior authors of that Nature paper - claiming that these experts knew about the human-to-human transmissibility of SARS2 but failed to relay this crucial information to the WHO in a timely manner. nature.com/articles/s4158…
It's currently difficult to ascertain what evidence Yan has to support the above claim. She has shown journalists some exchanges. And it seems to be common knowledge now that there were weeks of delay in informing the WHO that SARS2 was a human-transmissible virus.
The lab origins controversy started when Yan claimed that RaTG13, the closest related virus genome to SARS2, published by the WIV was fabricated, and that SARS2 was derived from SARS viruses from Zhoushan - one was successfully isolated in suckling rats. ncbi.nlm.nih.gov/pmc/articles/P…
Before I get into a scientific review of Yan's report, I think it is essential to 1st address a glaring problem in science (and probably other fields): whistleblowers. Why they are rare. Why they can sometimes be incoherent or make unsubstantiated claims. How to get the truth.
Whistleblowers are extremely important people - for the health and sustainability of any organization or field. They're a rare type of people who will risk their lives and careers to make sure no more harm comes to other people... statnews.com/2019/05/01/fro…
Whistleblowers often live in fear and have been abused, gaslit, and traumatized for extended periods by not only their employer (and lawyers), but more importantly by their colleagues (friends) and even spouse/family (such as in the case of Yan). They're often naive/idealistic...
They never envisioned being in a workplace that would turn a blind eye to misconduct, knowingly endanger people's lives or well-being. Suddenly, they have to decide whether to say something and risk everything they've worked for, everything that's safe OR keep quiet and move on.
You can't pick your whistleblower. They're not going to be in the clearest state of mind after abuse. If it's the first time they're blowing the whistle, they're not going to have documented every email and message.

More importantly, the whistleblower cannot pick their savior.
If there is one thing that this entire saga has made clear - it is that whistleblowers (as it pertains to SARS2) have no obvious safe route of sharing their information.

Seriously, who should a SARS2 origins whistleblower go to? Besides this anti-CCP billionaire + Bannon et al.?
I'm just a postdoc in a foreign country. But shouldn't someone in charge be publicizing a safe way for whistleblowers to relay SARS2 origins information? A whistleblower protection program?

This would safeguard against the political manipulation of any forthcoming whistleblower.
The best approach to obtaining the truth from a whistleblower is to remove their dependency on their host/savior. Someone who they now have to rely on for security the rest of their life. Do people seriously think that this is not a consideration for whistleblowers?
So before we get into the scientific discussion of Yan's report, I want this consideration - what it's like to be a whistleblower in a foreign country, you know no one, in a hostage-like situation under powerful political figures - to be at the top of everyone's minds.
Yan's report makes 3 claims:
(1) SARS2 is similar to the Zhoushan viruses isolated and studied by Chinese military labs.
(2) The receptor binding motif of the spike was genetically manipulated.
(3) The infamous S1/S2 furin cleavage site (FCS) was artificially inserted.
The underlying premise of claim (1) is that other more closely related SARS2-like viruses suffer from debilitating integrity issues. RaTG13 - obfuscation of source and links to SARS-like cases, sample processing+sequencing, downstream experiments (?).
GD pangolin CoV - the one virus with a SARS2-like receptor binding domain (RBD) - please see our preprint, which has been under editorial review for 16 weeks, but we think we can see the light at the end of the tunnel now... biorxiv.org/content/10.110…
Due to these issues, Yan et al. refuse to incorporate any of the newly published SARS2-like viruses in her analysis. This is a major weakness of the report that has been pointed out by numerous experts.

I would argue that at least the 4991 RdRp fragment should be considered.
Thus, I would describe the claim that RaTG13 is fabricated and the claim that SARS2 is derived from the Zhoushan viruses (published in 2018) are gut speculations by Yan, who clearly believes that SARS2 is a product of gain of function research by the Chinese government.
My position on this: I don't know. Someone should be looking into the origins of RaTG13 and GD pangolin CoV. What was the sampling+sequencing process? Are there still ways to verify these samples (the former has disintegrated)? Were similar viruses discovered but not reported?
What I do know: claiming SARS2 was derived from the Zhoushan viruses that are >3000 mutations different -- this has destroyed the report's credibility, and, more importantly, diverted attention away from RaTG13, miners, and the missing WIV virus database (the 2nd Zenodo article).
Ok, on to (2). This 2nd claim relies on the 1st claim being true, which is, again, its greatest weakness. Instead of just going with "RBD was copied from another virus", Yan et al. perform enzymatic gymnastics to figure out how it could have gotten into the Zhoushan virus.
What claim (2) kind of gets correct - and I'm paraphrasing here - is that labs (including the WIV) have been codon optimizing spikes and swapping in RBMs to study receptor binding for over a decade. (Actually, this study did introduce an EcoRI site...) jvi.asm.org/content/82/4/1…
But this fixation on cloning sites is irrelevant to determining whether SARS2 was ever manipulated in a lab. Ralph Baric, UNC, long time collaborator of Shi, WIV says as much in his recent interview.

*PLEASE RELEASE THE UNDUBBED VERSION*

huffingtonpost.it/entry/e-possib…
Scientists have been able to clone coronavirus genomes seamlessly for years. They introduce cloning sites to show you that a genome has been manipulated. Another reason to retain a cloning site could be to monitor a feature, e.g. FCS, that tends to be lost during cell passage.
Which leads us to (3) the FCS - the most highly debated feature of SARS2. Why?

SARS2 is the only SARS family virus (out of dozens, maybe 100s, sampled) with an S1/S2 FCS.

The FCS has been actively researched, even in SARS1 & MERS, found to enhance virus tropism and infectivity.
Again, the fixation on whether there is a cloning site surrounding the FCS is unhelpful.

The underlying thought here is that a lab could have been interested enough to follow up on earlier studies of introducing an FCS into SARS virus to see how it enhances pathogenicity.
For more details, please see this earlier thread - it is long and technical:
The rest of the Yan report delineates a cloning plan for creating the SARS2 genome, which, unfortunately, obscures critical observations with the terrible, terrible restriction cloning strategy and the desperation of somehow deriving SARS2 from the Zhoushan viruses.
The top points:
1. There are likely unpublished virus genomes closely related to SARS2.
2. The spike is generally modified alone before cloning into the larger genomic backbone.
3. Cloning can occur seamlessly. No need for RE site insertions!
4. It can be done in weeks-months.
5. There is a possibility of serial passaging in humanized mice or small animals. The WIV Science Magazine interview says these small animal experiments were conducted at BSL3 using SARS-like viruses. sciencemag.org/news/2020/07/t…
The Yan report ends by emphasizing the dangers of SARS2 and the importance of an independent audit of the WIV - which Peter Daszak, long time friend, collaborator, and funder of the Shi lab has now taken upon himself to lead the charge on.telegraph.co.uk/global-health/…

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More from @Ayjchan

May 14
The soft corruption behind the Proximal Origin letter must be investigated and the authors and their handlers held accountable.

How else will you deter scientists from hiding the involvement of powerful funders in their papers and their "scientific" conclusions?
Jeremy Farrar, the scientist who orchestrated the Proximal Origin letter was not named as an author or acknowledged. He was the director of the Wellcome Trust and had funded one of the authors.

Farrar is now @WHO chief scientist.
@WHO None of these major funders who funded the Proximal Origin authors were acknowledged in the paper although Kristian Andersen privately thanked them for their advice and leadership as they worked on the letter.
Read 7 tweets
May 7
The executive order signed on Monday was not a ban or moratorium on risky pathogen research with the potential to cause pandemics.

It was a charge for OSTP and other agency heads to come up with a new policy & strategy for governing and tracking such research in under 180 days.
I do not see any wording in the executive order asking scientists to pause their research if it falls under the definition of dangerous gain-of-function.
whitehouse.gov/presidential-a…
The executive order is a step in the right direction and I hope that @WHOSTP47 will come up with an improved policy and strategy for pathogen research with catastrophic risks.

But right now, the executive order is not a ban or even a moratorium.
Read 8 tweets
Apr 10
Regarding the possibility that Covid may have spread at the Oct 2019 Wuhan military games, my main question is why noone across multiple countries had the presence of mind to collect & store samples from patients till tests were available.

There should be changes going forward.
According to Under Secretary of Defense for Personnel and Readiness: "Service members were not tested... as testing was not available at this early stage of the pandemic."
freebeacon.com/wp-content/upl…
"athletes noticed that something was amiss in the city of Wuhan.. described it as a “ghost town.”"

"athletes from several countries.. claimed publicly they had contracted what they believed to be covid.. based on their symptoms and how their illnesses spread to their loved ones"
washingtonpost.com/opinions/2021/…
Read 13 tweets
Mar 13
I encourage experts who have insisted on a natural origin of Covid-19 to gracefully change their public stance instead of doubling down on the threadbare evidence for the wet market hypothesis.

You could acknowledge that you initially trusted your colleagues in China/US to tell the truth. But time and time again over the past 5 years, it has been shown that they withheld critical evidence from you and the public:
1⃣The 2018 Defuse proposal
2⃣Low biosafety standards for experiments where live viruses are produced and used in human cell infection studies
3⃣Risky pathogen experiments and surprising gain of function
4⃣Missing pathogen sample database, viruses discovered after 2015 largely not shared with US collaborators
5⃣Closest virus relative that we know of was collected from a mine where people died from suspected SARS-like virus infection

The studies published last month where Wuhan scientists experimented with potentially dangerous pathogens at low biosafety opened your eyes to the level of reckless ambition in their research.

Given these betrayals, it is fully within reason to retract your trust and re-evaluate all the available evidence. Those of you who have access to intelligence could say that the non-public evidence has cast a new light on the public evidence and strengthens the case for a lab origin of Covid-19.

This is better than continuing to argue that you somehow know all the viruses in the Wuhan lab's collection and somehow know they didn't follow through on their 2018 plans to put furin cleavage sites into SARS-like viruses and study these at low biosafety exactly like they said they would.
For those experts who haven't even looked at the Defuse proposal and its drafts, the Wuhan-US scientists clearly said they were interested in furin cleavage sites at the spike S1/S2 junction, and would insert these into novel SARS-like viruses in the lab (not closely related to the 2003 SARS virus as that would be dangerous). They would test the ability of these SARS-like viruses with inserted cleavage sites to infect human cells and cause pathogenesis in vivo.

The Wuhan lab was regularly synthesizing novel coronavirus genomes without leaving any sign of lab manipulation. They used a protocol with trypsin-supplemented media to retain cleavage sites in the viruses. They did much of the work, including infection experiments in human cells, at BSL-2. Their US collaborator Ralph Baric has repeatedly criticized them for doing the work at low biosafety.

h/t @emilyakopp for FOIA'ing the Defuse proposal drafts.Image
Image
Some virologists may argue that the furin cleavage site in SARS-CoV-2 doesn't look canonical. You should read the citation in the Defuse draft for the computational model used to predict furin cleavage sites. The paper says it doesn't rely on the canonical motif and instead looks at a 20-residue sequence to make its predictions. The PRRAR motif exists in a feline coronavirus, MERS has a PRXXR S1/S2 furin cleavage site, and the RRXR motif is a functional furin cleavage site in numerous other proteins.
Read 13 tweets
Mar 12
According to Zeit Online, German Chancellery consulted with US Director of National Intelligence in 2023, who said there was nothing to the lab leak hypothesis.

They doubted "Eierköpfe" (egghead) scientists in intelligence knew better than leading virologists around the world.
In the US, something similar was happening where scientists in intelligence agencies also assessed a likely lab origin of Covid but were sidelined.

"The dominant view within the intelligence community was clear when... the director of national intelligence, and a couple of her senior analysts, briefed Biden... concluded with “low confidence” that Covid-19 had emerged when the virus leapt from an animal to a human."
wsj.com/politics/natio…
In both cases, government leaders favored the opinions of leading virologists over the scientists working in intelligence. Even though some of the leading virologists were public advocates and funders of "gain-of-function" research of concern with pathogens.
Read 4 tweets
Mar 12
German intelligence now assesses a 80-95% likelihood of a lab origin of Covid-19. Image
Image
Read 4 tweets

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