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We now finally have the story of the behind-the-scenes crisis management by Peter Daszak and Shi Zhengli regarding RaTG13 (and other unpublished viruses).🧵👇

The story begins in May 2021, when yours truly posted Yu Ping's 2019 WIV thesis on Twitter. It listed, among other things, "Ra4991" with lower spike identity to SARS (75.4%) than the published RaTG13 (76.6%).

About a month later, on 23 June 2021, Clare Thomas (Nature Senior Editor) emails Shi Zhengli, saying she had been "contacted by someone" but had "not looked at the thesis itself," and requests clarification regarding the discrepancy.

2 days later, Clare reminds Shi again that they have an obligation to look into the apparent discrepancy.

(There were, and still are, many other anomalies surrounding RaTG13.)

2 more days later, Shi Zhengli clarifies to the Nature editor that the discrepancy was an artifact of using different bioinformatics software: the 2020 Nature paper used NCBI's BLASTp, while the 2019 thesis used Mafft and Bioedit.

She also notes that the thesis was under "embargo", and she "doesn't know why this thesis was uploaded" and "misused by the conspiracy people."

"Conspiracy people" meant us. But how that supposedly embargoed thesis found its way to Twitter is another story. I can't tell it yet because sharing it could put people in China at risk.

In any case, we had also independently reached the same conclusion that the RaTG13-Ra4991 discrepancy was explained by differences in bioinformatics, thanks to @EtaitLife, who had reverse-engineered, reconciled the differences and replicated the results by December 2021.

So far so good.
web.archive.org/web/2021121619…

Then in Sept 2021, @theintercept published over 900 pages of documents obtained via a FOIA lawsuit against the NIH. These documents revealed the full, unredacted details of EHA's grant R01 AI110964 ("Understanding the Risk of Bat Coronavirus Emergence") to WIV.

The public finally saw that EHA and WIV were manipulating bat coronaviruses to test their ability to infect humanised ACE2 mice.
theintercept.com/2021/09/09/cov…

Jesse Bloom then politely asked Daszak / EcoHealth about the ACE2-utilizing bat coronaviruses mentioned in the grant proposal, citing the "resource sharing section" of the grant, which requires raw viral genetic data to be released "no later than 6 months after it was acquired".

EHA/WIV did these experiments in 2019 (or earlier), the 6-month window had long passed.

The next day, Daszak does something stunning.

He alerts WIV scientists (Shi Zhengli and Peng Zhou) that Jesse Bloom is requesting genomic data regarding bat coronaviruses studied under EHA’s NIH grant, and explicitly instructs the WIV not to share the data with Bloom.

He then openly admits that EHA was "fighting" the disclosure to keep US taxpayer-funded research on bat coronaviruses hidden from the public, but "journalists took the NIH to court and a judge forced them."

He outlines his strategy to Shi: he will point Bloom to already published sequences on GenBank, and when Bloom asks for raw data, he will "ignore his requests."

Daszak justifies this by claiming that because the NIH grant is suspended, Bloom's request is "not appropriate."

This is Daszak, on record, coordinating with WIV to block independent scientific review and subvert the data-sharing requirements of the grant.

Shi replies, "I'll do what you suggest if I receive the email from Jesse Bloom" and notes that WIV is updating the (deleted) virus database for "cybersecurity" and "hope to reopen it in several months."

(5 years later, it's still offline.)

Then, on 19-24 Nov, 2021, Clare Thomas contacts Shi Zhengli again regarding "Matters Arising" (a formal mechanism used by Nature to address post-publication issues).

Clare raises concerns that the original Nature paper lacked sample source, methods, and a timeline on how the full RaTG13 genome was assembled from what began as a partial sequence, alongside the unexpectedly low bacterial reads for a purported fecal/anal swab.

Shi Zhengli gets highly defensive and agitated. She writes: "It's a pity that there are someone who is contining to doute and scruetine (sic) our work... I don't think I should answer his unreasonable questions and crazy ideas".

She is basically frustrated that Nature is entertaining legitimate queries from independent scientists.

5 days later, on 29 Nov 2021, Shi responds it was an anal swab (not fecal pellet), used High Pure Viral RNA Kit, 5' RACE sequencing was done in Sept 2020, and had low sequencing depth.

Then it gets really interesting.

In a March 2022 interview to @theintercept, Peter Daszak claims that parts of the RaTG13 genome "aren't correctly sequenced."

Jesse Bloom, confused by this statement, emails Shi Zhengli and Peng Zhou at the WIV, asking if these errors were in the Spike protein, noting his own lab found that RaTG13’s Spike does not bind well to bat ACE2 receptors.

This has always been a major anomaly: how did a bat virus that barely binds to its own host's receptors naturally evolve into a virus better optimized for human receptors?

Shi copies Daszak on this email, and gives the same reply that the RaTG13 sequencing was incomplete at the 5' and 3' ends upon initial publication. She defends the WIV's data practices, claiming they hid nothing.

To prove that RaTG13 has low ACE2 affinity, Shi casually says that the WIV tried to create a recombinant (chimeric) virus using a WIV1 backbone and the RaTG13 spike protein, but failed to rescue it.

Bloom again expresses surprise that RaTG13 doesn't even bind to R. affinis (its host bat species) ACE2.

Shi argues that low binding affinity is an evolutionary feature to allow the virus to cohabit with bats, and that high binding ability with human ACE2 is just coincidental.

Bloom then points out that RaTG13 is phylogenetically grouped with ACE2-binding viruses.

Peng Zhou(?) interjects, arguing that scientists should "move our focus out of ACE2" and theorizes there must be an "unknown receptor (let's say X)" that bat sarbecoviruses use.

Then Daszak steps in, privately warning Shi not to answer any more of Bloom's questions and urging her to avoid discussing any ongoing or past "recombinant virus work" (which the NIH had prohibited).

Doesn't that, btw, implicitly mean that WIV was conducting undisclosed recombinant (chimeric) coronavirus experiments?

Shi replies "Thanks Peter. No response to him anymore," but appreciates that Bloom is a "good scientist" and that she can "persuade him".

Then comes another googly by Daszak: "anyone who looks at the evidence.. and still thinks it came from the lab, cannot be a good, logical scientist", and calls Bloom a "racist."

"Thanks Peter, out true friend" replies Shi.

Daszak is now the de facto crisis manager for the WIV.

Now it's Nature editor Clare Thomas again, around a month later.

Clare informs Shi that "several scientists" are continuing to ask questions about the "methodological details" in Zhou et al. (RaTG13 paper), that her private explanations were insufficient and she has to make the details public.

She offers two paths: issue a formal correction to the Nature paper, or add the detailed metadata to the public genomic databases like NCBI.

Instead of gracefully agreeing to be open and transparent, as requested, Shi Zhengli forwards the email to Daszak, and explicitly asks Daszak to help draft a defense and to dig up dirt on Jesse Bloom to discredit him to the editors.

Now comes Daszak's active plotting and stonewalling to ignore requests for data.

He coaches Shi on how to comply: she should make the database additions "very short and simple," do so reluctantly, and write a "strong letter" to the editor framing the requests as inappropriate, politically motivated "attacks on the credibility of your work."

His reasoning is purely tactical: if she refuses, Nature might force a formal "correction to the paper."

He then promises to help draft this letter and insert links to discredit Bloom.

In a moment of candor, he also complains about his own experiences: "The original Lancet paper said 'no competing interests', but the editor made me draft a 380 word statement... mainly because people had written to him to complain."

(Daszak originally declared "no competing interests," hiding the fact that his organization actively funded and collaborated with the very lab. The Lancet forced Daszak to publish an addendum.)

Daszak is not just a collaborator now, but as a strategic PR shield for the WIV.

These emails provide the most explicit documentary evidence to date of how the scientific queries surrounding RaTG13 (and other legitimate inquiries) was artificially managed behind the scenes: never release data willingly, ignore requests until forced by a higher authority, and when forced, release the absolute minimum while playing the victim. 

Think about it: the WIV had to be forced by journal editors to release basic raw data, metadata, and methodological details about the most important virus on earth after SARS-CoV-2.

And their immediate reaction wasn't transparency, it was to smear those asking for the data. 

It is also striking to see how Jesse Bloom, who was polite, purely data-driven, and always framed his questions scientifically, was treated by Shi and Daszak as part of a "conspiracy" threat to be neutralized. 

But in the end, this is also incredibly validating. It proves that open independent peer review works. That Nature took the "Matters Arising" seriously enough to pressure Shi for answers, and that relentless pressure is what finally forced the WIV to put it in public record (or at least some of it). 

In public, Daszak preached "open scientific collaboration" with WIV. In private, he was managing the fallout, working as an ally of the WIV while helping keep key details of its bat coronavirus research hidden from the public during the worst pandemic in a century. 

We may never know the full inventory of viruses held at the WIV before 2019, or whether it included viruses closer to SARS2 than RaTG13. But we now know that Daszak, the head of a EcoHealth, and the WIV were explicitly plotting how to withhold that information. 

Proponents of the zoonosis theory often point to WIV's published papers as proof of their transparency.

These emails shatters that defense - if it ever was a credible one to begin with.

Much thanks to @RandPaul for making these emails public.