By Karolina Corin and Lewis Kamb

An analysis by the U.S. Defense Department’s intelligence agency concluded five years ago that the virus that caused COVID-19 could have been engineered in a Chinese laboratory and later escaped to spawn the pandemic that eventually killed millions of people, documents recently obtained by US Right to Know show.

The never-before-published analysis by the Defense Intelligence Agency (DIA) points out that the lab in question – the Wuhan Institute of Virology – was highly capable of genetic manipulation, and includes an assessment that the genome of the coronavirus strain that caused COVID-19 is “consistent with the hypothesis” that it was “a lab-engineered virus” that “escaped from containment.”

The analysis by scientists in the DIA, which is charged with collecting and analyzing medical and health intelligence as part of its operations, also concluded that the virus that became known as SARS-CoV-2 could have come from “a bank” of bat coronaviruses in the Wuhan lab that was under the research of senior virologist, Dr. Shi Zhengli.

The DIA referred questions about the analysis to the Office of the Director of National Intelligence, which did not respond to requests for comment for this story. Shi, who also did not respond to interview requests, previously denied in news reports that her lab held the virus strain that caused the pandemic.

The DIA has not publicly recognized the analysis as its official position on the matter. But, unlike other federal assessments that provide few details to back up their findings that COVID-19 likely emerged from a lab, the DIA assessment offers the most detailed U.S. agency scientific analysis made public to date supporting why such a conclusion was drawn.

The DIA analysis appears to be the work of reputable government scientists whose findings, made during the first months of the pandemic, were kept secret while a competing hypothesis that COVID-19 emerged by natural means gained traction and became widely accepted.

“The slides are highly significant because they show that a strong scientific basis supporting a potential lab leak was identified early on,” said Steve Massey, a University of Puerto Rico bioinformatics professor and researcher for DRASTIC, a group of scientists investigating COVID-19 origins. 

“Much of that basis has subsequently been fortified by new information, such as the absence of furin cleavage sites in newly sequenced coronaviruses related to SARS-CoV-2,” he added.

The DIA analysis, which is dated June 25, 2020 –  about three and a half months after COVID-19 was declared a pandemic –  has not been previously disclosed to the public. The documents consist of a 46-page slide deck and are labeled with the classification, “secret/noforn” – or, not releasable to foreign nationals. Eight pages of the analysis remain classified and were withheld from disclosure. The analysis was part of a batch of documents – some heavily redacted and one marked “top secret” – recently released to U.S. Right To Know after it filed a Freedom of Information Act request and later sued to get the records.

The DIA analysis does not prove how the pandemic began. Rather, it argues that the virus could have come from a lab, and shows that multiple features in its genome are consistent with genetic manipulation. The analysis also offers a plausible scenario for how the virus could have been made in the lab and then escaped. 

Over the past two years, U.S. agencies including the FBI, the Department of Energy and the CIA, have publicly acknowledged assessments concluding that COVID-19 could have emerged from a lab, though most intelligence agencies assess that the virus likely occurred naturally by passing from an infected animal to a human.  Neither scenario has been disproved.

In the DIA’s unpublished analysis, scientists noted that researchers at the Wuhan lab were performing the types of experiments that could lead to the creation of a virus like SARS-CoV-2, sometimes under inadequate safety conditions that could not prevent a highly transmissible virus from escaping.

While the authors of the analysis are not identified, the documents were disclosed in response to U.S. Right to Know’s FOIA request that sought records related to assessments conducted by Robert Greg Cutlip, Jean-Paul Chretien, and John Hardham –  scientists who conducted work for the National Center for Medical Intelligence, a component of the DIA.

The analysis advances a previously reported, but less detailed working paper authored by two of the scientists, Chretien and Cutlip. Their paper refuted conclusions published in The Proximal Origin of SARS-CoV-2, a highly influential paper whose authors, while acknowledging they couldn’t prove or disprove COVID-19’s origins, contended they believed no “type of laboratory-based scenario is plausible.” The Proximal Origin paper – co-authored by a group of virologists and published in the journal Nature Medicine in March 2020 – helped establish the hypothesis that COVID-19 had a natural origin during the early stages of the pandemic.

In 2023, Chretien told members of the U.S. House Select Subcommittee on the Coronavirus Pandemic that he and Cutlip held a briefing about their paper for other analysts within the agency in 2020 “that provided more detail and scientific background.”

“The thought that I had at the time was that everything we had seen … suggested that a natural origin is plausible and that a laboratory origin is plausible as well,” he told the subcommittee.

Chretien also said he didn’t know whether the findings were shared with anyone outside the DIA.

In August 2023, The Australian reported that scientists from four different intelligence agencies agreed with Chretien and Cutlip’s assessments, but government officials kept the DIA scientists’ findings out of the public eye.

Meanwhile, the theory that COVID emerged naturally gained wide acceptance. The Proximal Origin paper garnered over 3 million views within 2 weeks. It was quickly and widely cited as proof that COVID emerged naturally – even from the White House.  In turn, lab-origin hypotheses were branded as conspiracy theories.

Yet emails and Slack messages subpoenaed by Congress in 2023 showed that some Proximal Origin authors privately accepted a lab-engineered scenario as plausible.

“The lab escape version of this is so friggin’ likely to have happened because they (the Wuhan lab) were already doing this type of work and the molecular data is fully consistent with that scenario,” Kristian Andersen, a coauthor of the Proximal Origin paper, wrote in a private Slack channel with other scientists on February 1, 2020. 

The furin cleavage site: A genomic feature that could unleash a pandemic

Unlike its closest relatives, the coronavirus strain that caused the pandemic possesses a genetic feature that helps make it highly transmissible to humans, called a furin cleavage site. 

Scientists have long known that these sites can make viruses more infectious, and they have a history of adding them to viruses in the lab. The big question is, did the site in SARS-CoV-2 evolve naturally, or through experimentation in the lab?

The Proximal Origin authors argued that the site in SARS-CoV-2 probably arose naturally through the same evolutionary processes that create furin cleavage sites in influenza. They also discounted the possibility that the site in the novel coronavirus was engineered in a lab because doing so would require culturing a virus nearly identical to the pandemic virus for a long time, and no such genome or work had been published.

But when the DIA analysis compared SARS-CoV-2 to influenza and other coronaviruses with natural furin cleavage sites, they found that the site in the pandemic virus had a far different genetic makeup.  The analysis does not explain this difference, only stating that the site in SARS-CoV-2 “does not appear to be inserted via the same mechanism that drives influenza insertions.” 

The DIA analysis pointed out that Chinese researchers, including those at the Wuhan lab, had already inserted furin cleavage sites into coronaviruses. In fact, the lab’s researchers and their American collaborators proposed a project in 2018 that appeared to plan to insert cleavage sites into coronaviruses at the same spot where it exists in the genetic sequence of the virus that caused COVID-19. 

The analysis also discounted a paper that the Proximal Origin authors appeared to cite as the evidence that swayed them to conclude that COVID-19 arose naturally.

This paper reported the discovery of a new SARS-CoV-2 relative called RmYN02 that seemed to have a small section that partially resembled the furin cleavage site in SARS-CoV-2.  But the DIA analysis suggested that RmYN02 might actually be a “red herring.” This site didn’t have the components necessary to make a functional furin cleavage site, and the analysis suggests that it was located in a different spot that was near – but not the same as –  the site in the novel coronavirus.

The discovery of other close SARS-CoV-2 relatives in 2021 appeared to confirm the DIA scientist’s suspicions.

This meant that SARS-CoV-2 remained the only virus among close relatives to have a furin cleavage site inserted in its spike protein – the key feature that likely made the virus capable of unleashing a pandemic.

A central argument in Proximal Origins is that SARS-CoV-2 could not have been made in a lab because there are no published coronavirus genomes that are similar enough to use as a viral template.

The DIA analysis rejects this argument, stating that, “The absence of a published progenitor [template] virus for SARS-CoV-2 only indicates that it has not been published, not that it does not exist.”

The DIA analysis also points out that the Wuhan lab has “a large bank of Bat Coronaviruses”, and that most of the sequences have not been published.

They proceed to show two different ways that the novel coronavirus could have been constructed using a type of engineering called Golden Gate Assembly – a method the Wuhan lab had the knowledge, experience, and resources to use. 

One way could have used a curious feature of the virus’s genome – two restriction sites that are spaced at a distance along the genome that could be useful for cloning.  These sites – called BsmBI and BsaI – are commonly used in reverse genetics. Both had previously been used by the Wuhab lab to create chimeric coronaviruses, which are hybrids pieced together from sections of different coronaviruses. 

A preprint published in 2022 showed that the distances between the BsmBI and BsaI sites in SARS-CoV-2 are indeed unusual, and “extremely unlikely in wild coronaviruses and nearly universal in synthetic viruses.”

The second way uses invisible restriction sites that would leave no trace of genetic manipulation.

The DIA analysis cites a May 2020 University of Texas publication, which demonstrates how quickly virologists could synthesize an infectious SARS-CoV-2 clone using such invisible restriction sites.  Cutlip and Chretien’s working paper even stated that several labs had synthesized SARS-CoV-2 “within weeks” of its genome being published.

Both construction strategies would have been compatible with a fast and cheap reverse genetics method published by the Wuhan lab in 2016, where mutations could easily be introduced into coronaviruses.

The analysis shows that the DIA scientists suspected SARS-CoV-2 could be a chimeric – or hybrid – virus because its spike protein appeared to be stitched together from two different viruses.

Most of the spike protein is nearly identical to the spike of another bat coronavirus called RaTG13, which was previously found by Wuhan lab researchers.  

However, one small region – called the receptor binding domain – was nearly identical to a coronavirus carried by pangolins, the animals sometimes called spiny anteaters. This small section helps determine which species a coronavirus can infect. 

The DIA scientists appeared concerned that this could be a sign of genetic engineering because the size and location of the pangolin-like region correspond to a region that scientists in the Wuhan lab found could convert a coronavirus that infects bats into one that infects humans.

The DIA analysis also stated that the DNA for the pangolin-like receptor binding domain appeared to have been optimally designed for use in the lab.

The Proximal Origins paper authors claim that this “stitching” probably occurred naturally through a process called recombination, where viruses swap sections of genetic material.

The DIA analysis counters that a lab-made chimeric virus could easily be confused with a natural recombinant, and mentions suspicion that the Chinese government released fabricated studies to mislead the public about the pandemic’s origin.

The DIA analysis also questions how a pangolin virus could naturally recombine with a bat virus found 800 miles away, and noted that Wuhan scientists gathered samples from locations where both viruses were found and brought them back to the Wuhan lab.

Two years after the DIA analysis, scientists from the Pasteur Institute in France discovered multiple bat coronaviruses in Laos whose spike proteins – including the receptor binding domains – were highly similar to the novel coronavirus.  However, none had a furin cleavage site.

That finding weakened the argument that SARS-CoV-2 could be a lab-made hybrid because it showed that the region that appeared to come from pangolins could naturally occur in bat coronaviruses. But before the discovery, the DIA scientists could not dismiss the idea that the novel coronavirus was a hybrid virus created in the Wuhan lab, where scientists had the knowledge, capabilities, and experience to create such viruses.

The DIA analysis pointed out that scientists in the Wuhan lab conducted experiments with live SARS-like coronaviruses under “biosafety level 2” conditions, “which would make an accidental release” of an infectious bat coronavirus “more likely.”  

Known as “BSL2,” such safety standards are typically used for “moderate risk” organisms that have a low risk of infecting people through the air. More stringent standards, BSL3 and BSL4, are used for pathogens that are more lethal, or that can transmit easily through the air like SARS-CoV-2.

The analysis also noted that “Chinese labs have had a history of virus escapes from BSL2 laboratories.” 

The escaped viruses include SARS, which escaped Chinese labs four times, and SARS-CoV-2, which appears to have infected a Beijing lab worker early in the pandemic. 

Numerous other viruses have infected researchers or escaped from labs around the world, and possibly even started pandemics.

The discovery of bat coronaviruses highly similar to SARS-CoV-2 in Laos has since weakened the DIA analysis’s hypothesis that the pandemic virus could be a lab-made hybrid of bat and pangolin coronaviruses.    

However, the origin of the other unusual genomic features the DIA analysts noticed remains unexplained, in particular the presence of the furin cleavage site.  

The documents obtained by U.S. Right to Know, which were classified as secret, do not show why the DIA analysis or its conclusions weren’t cited in the Office of the Director of National Intelligence’s 2023 report. The report was produced by the Biden administration, which ordered federal intelligence agencies – including the DIA – to review all intelligence related to the pandemic’s origin.

Previous reporting by The Australian suggests that the DIA scientist’s contributions to the 2021 intelligence report on the pandemic’s origin were mostly deleted because they were “too technical.”

The documents used in this story were obtained through the Freedom of Information Act and litigation with the Defense Intelligence Agency. All of U.S. Right to Know’s FOI documents related to COVID-19 origins are here.