by Mara Hvistendahl, Sharon Lerner
The Intercept
October 1 2021, 10:11 a.m.
A PROGRESS REPORT detailing controversial U.S.-funded research into bat coronaviruses in China was filed more than two years after it was due and long after the corresponding grant had concluded. The U.S.-based nonprofit the EcoHealth Alliance submitted the report to its funder, the National Institutes of Health, in September 2020, while the group was engulfed in controversy surrounding its work with partners in China. The Intercept obtained the report, along with the grant proposal and other documents, through a Freedom of Information Act lawsuit.
Scientists consulted by The Intercept described the late date as highly unusual and said it merited an explanation, given the controversy surrounding the EcoHealth Alliance’s work at the time that the report was submitted. The scientists spoke under the condition of anonymity due to the sensitivity of the topic with the NIH, the world’s leading funder of biomedical research.
The annual report described the group’s work from June 2017 to May 2018, which involved creating new viruses using different parts of existing bat coronaviruses and inserting them into humanized mice in a lab in Wuhan, China. The work was overseen by the NIH’s National Institute of Allergy and Infectious Diseases, which is headed by Anthony Fauci.
Neither the NIH nor the EcoHealth Alliance offered an explanation for the date of the report or responded to questions from The Intercept about whether another version of the report had been submitted on time and, if so, in what ways that version may have been altered.
The Intercept is seeking any missing progress reports, among other documents, through ongoing litigation against the NIH.
The agency has been criticized for withholding information that might relate to the origins of the coronavirus pandemic, which is now responsible for more than 4.5 million deaths around the world. “NIH has a public responsibility to be fully transparent on why it gave funding to the EcoHealth Alliance, whether it considered the potential of a possible accidental leak of dangerous bat viruses, and the ethics of approving the study,” said Lawrence Gostin, a professor at Georgetown University’s school of law and director of the World Health Organization Collaborating Center on National and Global Health Law. “Overall, it is important to fund good basic research on bat viruses, but the project has been shrouded in uncertainty and lacks full transparency.”
The progress report and other documents were released by the NIH over a year after The Intercept and others requested them. “What [the NIH] really needs to do is not just react to FOIA requests. They need to be proactive and say, ‘OK, here’s the process, and here’s the outcome.’ And they haven’t done that,” said Gregory Koblentz, director of the Biodefense Graduate Program at George Mason University. “That just raises questions about why they’re dragging their heels. They should have provided all relevant information months ago.”
The EcoHealth Alliance and its longtime partner the Wuhan Institute of Virology have come under intense scrutiny in the search for the pandemic’s origins. The two groups are at the center of the lab-origin hypothesis, the idea that the coronavirus could have emerged through a lab accident, the collection and storage of thousands of bat coronavirus samples, or through divisive research that makes viruses more transmissible in order to study how they evolve.
There has been no shortage of unsubstantiated ideas in circulation about SARS-CoV-2, the coronavirus that causes the respiratory illness Covid-19, several of which continue to be used as political wedges by former President Donald Trump and the far right. But EcoHealth Alliance President Peter Daszak helped organize scientists to tar any discussion of a possible lab origin, even if it was science-based, as a conspiracy theory.
In February 2020, the medical journal The Lancet published a statement decrying the spread of “rumours and misinformation” around the origins of the pandemic. “We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” read the letter. Emails later obtained by U.S. Right to Know showed that Daszak had orchestrated the effort. Daszak has also served on two international committees tasked with investigating the origins of the pandemic, despite having a clear conflict of interest. (Last weekend, the Wall Street Journal reported that one of these committees, a task force convened by The Lancet, would be disbanded.)
For months, Daszak continued to push the notion that a lab origin was preposterous. “They’re coming at this with the belief system that there’s a cabal of mysterious international folks who are trying to kill people,” he said in an online seminar in October 2020, of those who believe it’s possible that the virus that causes Covid-19 emerged from a lab. “They come at it with a belief system. So logic jumps out the window.”
The unusually dated EcoHealth Alliance progress report adds to a string of missing, incomplete, or disappeared information that could be relevant to the origins of the pandemic.
The report describes work done in year four of the five-year, $3.1 million NIH grant “Understanding the Risk of Bat Coronavirus Emergence.” It was due in April 2018. The version released by the NIH was submitted over two years later, after The Intercept had filed a public records request seeking the bat coronavirus and other NIH grants to the EcoHealth Alliance.
The NIH sends out automatic reminders ahead of key due dates and makes the distribution of new funding contingent upon receipt of the previous years’ annual reports. According to an NIH instruction manual, submission dates are automatically generated, meaning that the date could not be a typo.
Adding to the evidence that the annual update was submitted in 2020 are references to studies that were published after 2018, when the update was due. NIH progress reports include a section in which researchers list any papers that have been published or accepted for publication. In the EcoHealth Alliance progress report, the section lists papers published in 2019 and 2020.
Many researchers say the experiment that involved infecting humanized mice with altered bat coronaviruses described in the annual report qualifies as “gain-of-function research of concern.” None of the viruses described in the experiment are related to SARS-CoV-2 closely enough to have evolved into it. But scientists said the odd submission date raises questions about whether information in an earlier draft of the report had been altered — or omitted — amid controversy over the EcoHealth Alliance’s work in Wuhan.
Early on, several groups, media outlets, and individuals requested the grant documents and communications surrounding them, an effort that apparently irked Daszak. “Conspiracy-theory outlets and politically motivated organizations have made Freedom of Information Act requests on our grants and all of our letters and e-mails to the NIH,” he told Nature in August 2020. “We don’t think it’s fair that we should have to reveal everything we do.”
The Intercept requested the grant documents from the NIH on September 3 of that year. The anomalous progress report was submitted less than two weeks later, on September 16.
The documents released to The Intercept are also missing a year-five progress report, covering the crucial period of June 2018 to May 2019, which was due in September 2019, according to NIH guidelines. Scientists said that NIH program officers sometimes overlook reports for the final reporting period, but taken together with the odd date on the year-four report, the omission raises questions that the agency should answer.
Federal funding documents are routinely released under the Freedom of Information Act. In this case, public interest in the origins of the pandemic should have led to a timely and full release of documents, transparency experts say. “The presumption of disclosure is all the more crucial when dealing with documents that are squarely in the public interest,” said Gunita Singh, a staff attorney with the Reporters Committee for Freedom of the Press. “And records about how the pandemic may have originated and where our taxpayer dollars have been spent are clearly worthy of public observation and scrutiny and debate.”
“Records about how the pandemic may have originated and where our taxpayer dollars have been spent are clearly worthy of public observation and scrutiny and debate.”
The origins of the pandemic remain hotly debated. In August, President Joe Biden announced that a three-month inquiry into the matter by U.S. intelligence agencies was inconclusive. Many scientists lean toward a natural origin, but in recent months an increasing number of prominent researchers have gone on record as saying that a lab origin deserves thorough investigation.
The progress report is just one of many missing puzzle pieces that could shed light on the question. In June, evolutionary biologist Jesse Bloom reported that key data from Wuhan had been deleted from an NIH database, a move allowed by NIH rules but that is nonetheless unusual. From a Google Cloud server, he recovered 13 partial viral sequences collected from people in the city in the early days of the pandemic. These added to evidence that the coronavirus was circulating in the city long before the December 2019 outbreak at the city’s Huanan seafood market, which was a major focus of the recent WHO report on the origins of the pandemic. It turned out that researchers from Wuhan University had emailed the NIH in June 2020 to request that the sequences be deleted.
Then in July, after the Washington Post reported on other discrepancies in early WHO data, the WHO changed the virus sequence IDs associated with three early patients described in the joint report.
There are also important gaps in what we know about the history of RaTG13, a relative of SARS-CoV-2, which was sequenced and written about by scientists at the Wuhan Institute of Virology. Last summer, Shi Zhengli, director of the Center for Emerging Infectious Diseases of the Wuhan Institute of Virology, admitted to Science magazine that RaTG13 was a renamed version of a virus found in a Chinese mineshaft where miners fell ill in 2012. But that admission only came following pressure from independent scientists.
Also unresolved are questions about revisions made to public databases of viruses that infect pangolins and about a database that the Wuhan Institute of Virology took offline in September 2019, claiming that it had been hacked.
In 2019, the NIH renewed the EcoHealth Alliance bat coronavirus grant for a second five-year period. The Trump administration suspended funding in April 2020. (The NIH reinstated the grant in July 2020, under strict terms that Daszak said his group could not meet.) It is unclear whether the EcoHealth Alliance would have been required to file a progress report for the final year of the grant, given that it was terminated.
Correction: October 3, 2021
A previous version of this article incorrectly stated that Peter Daszak did not sign a February 2020 letter in The Lancet. Although Daszak had originally suggested keeping his name off the letter, in the end he did in fact sign it.
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Leaked Grant Proposal Details High-Risk Coronavirus Research. The proposal, rejected by U.S. military research agency DARPA, describes the insertion of human-specific cleavage sites into SARS-related bat coronaviruses.
by Sharon Lerner, Maia Hibbett
The Intercept
September 23 2021, 11:16 a.m.
A GRANT PROPOSAL written by the U.S.-based nonprofit the EcoHealth Alliance and submitted in 2018 to the Defense Advanced Research Projects Agency, or DARPA, provides evidence that the group was working — or at least planning to work — on several risky areas of research. Among the scientific tasks the group described in its proposal, which was rejected by DARPA, was the creation of full-length infectious clones of bat SARS-related coronaviruses and the insertion of a tiny part of the virus known as a “proteolytic cleavage site” into bat coronaviruses. Of particular interest was a type of cleavage site able to interact with furin, an enzyme expressed in human cells.
The EcoHealth Alliance did not respond to inquiries about the document, despite having answered previous queries from The Intercept about the group’s government-funded coronavirus research. The group’s president, Peter Daszak, acknowledged the public discussion of an unfunded EcoHealth proposal in a tweet on Saturday. He did not dispute its authenticity.
Since the genetic code of the coronavirus that caused the pandemic was first sequenced, scientists have puzzled over the “furin cleavage site.” This strange feature on the spike protein of the virus had never been seen in SARS-related betacoronaviruses, the class to which SARS-CoV-2, the coronavirus that causes the respiratory illness Covid-19, belongs.
The furin cleavage site enables the virus to more efficiently bind to and release its genetic material into a human cell and is one of the reasons that the virus is so easily transmissible and harmful. But scientists are divided over how this particular site wound up in the virus, and the cleavage site became a major focus of the heated debate over the origins of the pandemic.
Many who believe that the virus that caused the pandemic emerged from a laboratory have pointed out that it is unlikely that the particular sequence of amino acids that make up the furin cleavage site would have occurred naturally.
Adherents of the idea that SARS-CoV-2 emerged from a natural spillover from animal hosts have argued that it could have evolved naturally from an as-yet undiscovered virus. Further, they argued, scientists were unlikely to have engineered the feature.
“There is no logical reason why an engineered virus would utilize such a suboptimal furin cleavage site, which would entail such an unusual and needlessly complex feat of genetic engineering,” 23 scientists wrote earlier this month in an article in the journal Cell. “There is no evidence of prior research at the [Wuhan Institute of Virology] involving the artificial insertion of complete furin cleavage sites into coronaviruses.”
But the proposal describes the process of looking for novel furin cleavage sites in bat coronaviruses the scientists had sampled and inserting them into the spikes of SARS-related viruses in the laboratory.
“We will introduce appropriate human-specific cleavage sites and evaluate growth potential in [a type of mammalian cell commonly used in microbiology] and HAE cultures,” referring to cells found in the lining of the human airway, the proposal states.
The origin of SARS-CoV-2 that we propose below is based on the case histories of these miners and their hospital treatment. This simple theory accounts for all the key features of the novel SARS-CoV-2 virus, including ones that have puzzled virologists since the outbreak began.
The theory can account for the origin of the polybasic furin cleavage site, which is a region of the viral spike protein that makes it susceptible to cleavage by the host enzyme furin and which greatly enhances viral spread in the body. This furin site is novel to SARS-CoV-2 compared to its near relatives (Coutard, et al., 2020). The theory also explains the exceptional affinity of the virus spike protein for human receptors, which has also surprised virologists (Letko et al., 2020; Piplani et al, 2020; Wrapp et al., 2020; Walls et al., 2020). The theory further explains why the virus has barely evolved since the pandemic began, which is also a deeply puzzling aspect of a virus supposedly new to humans (Zhan et al., 2020; van Dorp et al., 2020; Chaw et al., 2020). Lastly, the theory neatly explains why SARS-CoV-2 targets the lungs, which is unusual for a coronavirus (Huang et al., 2020).
-- A Proposed Origin for SARS-CoV-2 and the COVID-19 Pandemic [W/Comments], by Jonathan Latham, PhD and Allison Wilson, PhD
How I Learned to Start Worrying
Oh, come on. Lab-made? Nonsense! Back in January, that was my knee-jerk reaction when ideas that Covid-19 is caused by a laboratory leak had just surfaced. Bioweapon? Well, that is just Flat Earth crazies territory. Thus, whenever I kept hearing anything about non-natural origins of SARS-CoV-2, I brushed it aside under similar sentiments. So what if there is a virology institute in Wuhan? Who knows how many of those are sprinkled throughout China.
At some point, it became necessary to brush such theories aside in a substantiated manner, as their proponents began to back up their theses about the possible artificial nature of the virus with arguments from molecular biology, and when engaging them in debate, I wanted to smash their conspiracy theories with cold, hard scientific facts. Just like that Nature paper (or so I thought).
So it was then, in pursuit of arguments against the virus’s lab-madeness, that I got infected by the virus of doubt. What was the source of my doubts? The fact that the deeper you dive into the research activities of coronavirologists over the past 15–20 years, the more you realize that creating chimeras like CoV2 was commonplace in their labs.
And CoV2 is an obvious chimera (though not necessarily a lab-made one), which is based on the ancestral bat strain RaTG13, in which the receptor binding motif (RBM) in its spike protein is replaced by the RBM from a pangolin strain, and in addition, a small but very special stretch of 4 amino acids is inserted, which creates a furin cleavage site that, as virologists have previously established, significantly expands the “repertoire” of the virus in terms of whose cells it can penetrate. Most likely, it was thanks to this new furin site that the new mutant managed to jump species from its original host to humans.
Indeed, virologists, including the leader of coronavirus research at the Wuhan Institute of Virology, Shi Zhengli, have done many similar things in the past — both replacing the RBM in one type of virus by an RBM from another, or adding a new furin site that can provide a species-specific coronavirus with an ability to start using the same receptor (e.g. ACE2) in other species. In fact, Shi Zhengli’s group was creating chimeric constructs as far back as 2007 and as recently as 2017, when they created a whole of 8 new chimeric coronaviruses with various RBMs. In 2019 such work was in full swing, as WIV was part of a $3.7 million NIH grant titled Understanding the Risk of Bat Coronavirus Emergence. Under its auspices, Shi Zhengli co-authored a 2019 paper that called for continued research into synthetic viruses and testing them in vitro and in vivo...
A Killer Intro
It is impossible to ignore the introduction of a PRRA insert between S1 and S2: it sticks out like a splinter. This insert creates the furin cleavage site, which I mentioned at the very beginning. Let me explain what a furin site is....
-- Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function Research, by Yuri Deigin
IV. “Is It a Complete Coincidence?”
Even so, in January and February of 2020, there were thoughtful people who were speaking up, formulating their perplexities.
One person was Sam Husseini, an independent journalist. He went to a CDC press conference at the National Press Club on February 11, 2020. By then, 42,000 people had gotten sick in China and more than a thousand had died. But there were only 13 confirmed cases in the U.S. Halfway through the Q&A period, Husseini went to the microphone and asked the CDC’s representative, Anne Schuchat, where the virus had come from. His head was spinning, he told me later.
“Obviously the main concern is how to stop the virus,” Husseini said; nonetheless, he wanted to know more about its source. “Is it the CDC’s contention,” he asked, “that there’s absolutely no relation to the BSL-4 lab in Wuhan? It’s my understanding that this is the only place in China with a BSL-4 lab. We in the United States have, I think, two dozen or so, and there have been problems and incidents.” (A BSL-4 laboratory is a maximum-security biosafety-level-four facility, used to house research on the most dangerous known pathogens. New York has confirmed there are at least 11 BSL-4 facilities currently operating in the U.S.) Husseini hastened to say that he wasn’t implying that what happened in Wuhan was in any way intentional. “I’m just asking, Is it a complete coincidence that this outbreak happened in the one city in China with a BSL-4 lab?”
Schuchat thanked Husseini for his questions and comments. Everything she’d seen was quite consistent with a natural, zoonotic origin for the disease, she said.
That same month, a group of French scientists from Aix-Marseille University posted a paper describing their investigation of a small insertion in the genome of the new SARS-2 virus. The virus’s spike protein contained a sequence of amino acids that formed what Etienne Decroly and colleagues called a “peculiar furin-like cleavage site” — a chemically sensitive region on the lobster claw of the spike protein that would react in the presence of an enzyme called furin, which is a type of protein found everywhere within the human body, but especially in the lungs. When the spike senses human furin, it shudders, chemically speaking, and the enzyme opens the protein, commencing the tiny morbid ballet whereby the virus burns a hole in a host cell’s outer membrane and finds its way inside.
The code for this particular molecular feature — not found in SARS or any SARS-like bat viruses, but present in a slightly different form in the more lethal MERS virus — is easy to remember because it’s a roar: “R-R-A-R.” The letter code stands for amino acids: arginine, arginine, alanine, and arginine. Its presence, so Decroly and his colleagues observed, may heighten the “pathogenicity” — that is, the god-awfulness — of a disease.
Botao Xiao, a professor at the South China University of Technology, posted a short paper on a preprint server titled “The Possible Origins of 2019-nCoV Coronavirus.” Two laboratories, the Wuhan Center for Disease Control and Prevention (WHCDC) and the Wuhan Institute of Virology, were not far from the seafood market, which was where the disease was said to have originated, Xiao wrote — in fact, the WHCDC was only a few hundred yards away from the market — whereas the horseshoe bats that hosted the disease were hundreds of miles to the south. (No bats were sold in the market, he pointed out.) It was unlikely, he wrote, that a bat would have flown to a densely populated metropolitan area of 15 million people. “The killer coronavirus probably originated from a laboratory in Wuhan,” Xiao believed. He urged the relocation of “biohazardous laboratories” away from densely populated places. His article disappeared from the server.
And late in the month, a professor at National Taiwan University, Fang Chi-tai, gave a lecture on the coronavirus in which he described the anomalous R-R-A-R furin cleavage site. The virus was “unlikely to have four amino acids added all at once,” Fang said — natural mutations were smaller and more haphazard, he argued. “From an academic point of view, it is indeed possible that the amino acids were added to COVID-19 in the lab by humans.” When the Taiwan News published an article about Fang’s talk, Fang disavowed his own comments, and the video copy of the talk disappeared from the website of the Taiwan Public Health Association. “It has been taken down for a certain reason,” the association explained. “Thank you for your understanding.”
-- The Lab-Leak Hypothesis For decades, scientists have been hot-wiring viruses in hopes of preventing a pandemic, not causing one. But what if …?, by Nicholson Baker
“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.
Comparing the rival scenarios of SARS2 origin.
The evidence above adds up to a serious case that the SARS2 virus could have been created in a lab, from which it then escaped. But the case, however substantial, falls short of proof. Proof would consist of evidence from the Wuhan Institute of Virology, or related labs in Wuhan, that SARS2 or a predecessor virus was under development there. For lack of access to such records, another approach is to take certain salient facts about the SARS2 virus and ask how well each is explained by the two rival scenarios of origin, those of natural emergence and lab escape. Here are four tests of the two hypotheses. A couple have some technical detail, but these are among the most persuasive for those who may care to follow the argument.1) The place of origin. Start with geography. The two closest known relatives of the SARS2 virus were collected from bats living in caves in Yunnan, a province of southern China. If the SARS2 virus had first infected people living around the Yunnan caves, that would strongly support the idea that the virus had spilled over to people naturally. But this isn’t what happened. The pandemic broke out 1,500 kilometers away, in Wuhan.
Beta-coronaviruses, the family of bat viruses to which SARS2 belongs, infect the horseshoe bat Rhinolophus affinis, which ranges across southern China. The bats’ range is 50 kilometers, so it’s unlikely that any made it to Wuhan. In any case, the first cases of the COVID-19 pandemic probably occurred in September, when temperatures in Hubei province are already cold enough to send bats into hibernation.
What if the bat viruses infected some intermediate host first? You would need a longstanding population of bats in frequent proximity with an intermediate host, which in turn must often cross paths with people. All these exchanges of virus must take place somewhere outside Wuhan, a busy metropolis which so far as is known is not a natural habitat of Rhinolophus bat colonies. The infected person (or animal) carrying this highly transmissible virus must have traveled to Wuhan without infecting anyone else. No one in his or her family got sick. If the person jumped on a train to Wuhan, no fellow passengers fell ill.
It’s a stretch, in other words, to get the pandemic to break out naturally outside Wuhan and then, without leaving any trace, to make its first appearance there.
For the lab escape scenario, a Wuhan origin for the virus is a no-brainer. Wuhan is home to China’s leading center of coronavirus research where, as noted above, researchers were genetically engineering bat coronaviruses to attack human cells. They were doing so under the minimal safety conditions of a BSL2 lab. If a virus with the unexpected infectiousness of SARS2 had been generated there, its escape would be no surprise.
2) Natural history and evolution. The initial location of the pandemic is a small part of a larger problem, that of its natural history. Viruses don’t just make one time jumps from one species to another. The coronavirus spike protein, adapted to attack bat cells, needs repeated jumps to another species, most of which fail, before it gains a lucky mutation. Mutation — a change in one of its RNA units — causes a different amino acid unit to be incorporated into its spike protein and makes the spike protein better able to attack the cells of some other species.
Through several more such mutation-driven adjustments, the virus adapts to its new host, say some animal with which bats are in frequent contact. The whole process then resumes as the virus moves from this intermediate host to people.
In the case of SARS1, researchers have documented the successive changes in its spike protein as the virus evolved step by step into a dangerous pathogen. After it had gotten from bats into civets, there were six further changes in its spike protein before it became a mild pathogen in people. After a further 14 changes, the virus was much better adapted to humans, and with a further four, the epidemic took off.
But when you look for the fingerprints of a similar transition in SARS2, a strange surprise awaits. The virus has changed hardly at all, at least until recently. From its very first appearance, it was well adapted to human cells. Researchers led by Alina Chan of the Broad Institute compared SARS2 with late stage SARS1, which by then was well adapted to human cells, and found that the two viruses were similarly well adapted. “By the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV,” they wrote.
Even those who think lab origin unlikely agree that SARS2 genomes are remarkably uniform. Baric writes that “early strains identified in Wuhan, China, showed limited genetic diversity, which suggests that the virus may have been introduced from a single source.”
A single source would of course be compatible with lab escape, less so with the massive variation and selection which is evolution’s hallmark way of doing business.
The uniform structure of SARS2 genomes gives no hint of any passage through an intermediate animal host, and no such host has been identified in nature.
Proponents of natural emergence suggest that SARS2 incubated in a yet-to-be found human population before gaining its special properties. Or that it jumped to a host animal outside China.
All these conjectures are possible, but strained. Proponents of a lab leak have a simpler explanation. SARS2 was adapted to human cells from the start because it was grown in humanized mice or in lab cultures of human cells, just as described in Daszak’s grant proposal. Its genome shows little diversity because the hallmark of lab cultures is uniformity.
Proponents of laboratory escape joke that of course the SARS2 virus infected an intermediary host species before spreading to people, and that they have identified it — a humanized mouse from the Wuhan Institute of Virology.
3) The furin cleavage site. The furin cleavage site is a minute part of the virus’s anatomy but one that exerts great influence on its infectivity. It sits in the middle of the SARS2 spike protein. It also lies at the heart of the puzzle of where the virus came from.
The spike protein has two sub-units with different roles. The first, called S1, recognizes the virus’s target, a protein called angiotensin converting enzyme-2 (or ACE2) which studs the surface of cells lining the human airways. The second, S2, helps the virus, once anchored to the cell, to fuse with the cell’s membrane. After the virus’s outer membrane has coalesced with that of the stricken cell, the viral genome is injected into the cell, hijacks its protein-making machinery and forces it to generate new viruses.
But this invasion cannot begin until the S1 and S2 subunits have been cut apart. And there, right at the S1/S2 junction, is the furin cleavage site that ensures the spike protein will be cleaved in exactly the right place.
The virus, a model of economic design, does not carry its own cleaver. It relies on the cell to do the cleaving for it. Human cells have a protein cutting tool on their surface known as furin. Furin will cut any protein chain that carries its signature target cutting site. This is the sequence of amino acid units proline-arginine-arginine-alanine, or PRRA in the code that refers to each amino acid by a letter of the alphabet. PRRA is the amino acid sequence at the core of SARS2’s furin cleavage site.
Viruses have all kinds of clever tricks, so why does the furin cleavage site stand out? Because of all known SARS-related beta-coronaviruses, only SARS2 possesses a furin cleavage site. All the other viruses have their S2 unit cleaved at a different site and by a different mechanism.
How then did SARS2 acquire its furin cleavage site? Either the site evolved naturally, or it was inserted by researchers at the S1/S2 junction in a gain-of-function experiment.
Consider natural origin first. Two ways viruses evolve are by mutation and by recombination. Mutation is the process of random change in DNA (or RNA for coronaviruses) that usually results in one amino acid in a protein chain being switched for another. Many of these changes harm the virus but natural selection retains the few that do something useful. Mutation is the process by which the SARS1 spike protein gradually switched its preferred target cells from those of bats to civets, and then to humans.
Mutation seems a less likely way for SARS2’s furin cleavage site to be generated, even though it can’t completely be ruled out. The site’s four amino acid units are all together, and all at just the right place in the S1/S2 junction. Mutation is a random process triggered by copying errors (when new viral genomes are being generated) or by chemical decay of genomic units. So it typically affects single amino acids at different spots in a protein chain. A string of amino acids like that of the furin cleavage site is much more likely to be acquired all together through a quite different process known as recombination.
Recombination is an inadvertent swapping of genomic material that occurs when two viruses happen to invade the same cell, and their progeny are assembled with bits and pieces of RNA belonging to the other. Beta-coronaviruses will only combine with other beta-coronaviruses but can acquire, by recombination, almost any genetic element present in the collective genomic pool. What they cannot acquire is an element the pool does not possess. And no known SARS-related beta-coronavirus, the class to which SARS2 belongs, possesses a furin cleavage site.
Proponents of natural emergence say SARS2 could have picked up the site from some as yet unknown beta-coronavirus. But bat SARS-related beta-coronaviruses evidently don’t need a furin cleavage site to infect bat cells, so there’s no great likelihood that any in fact possesses one, and indeed none has been found so far.
The proponents’ next argument is that SARS2 acquired its furin cleavage site from people. A predecessor of SARS2 could have been circulating in the human population for months or years until at some point it acquired a furin cleavage site from human cells. It would then have been ready to break out as a pandemic.
If this is what happened, there should be traces in hospital surveillance records of the people infected by the slowly evolving virus. But none has so far come to light. According to the WHO report on the origins of the virus, the sentinel hospitals in Hubei province, home of Wuhan, routinely monitor influenza-like illnesses and “no evidence to suggest substantial SARSCoV-2 transmission in the months preceding the outbreak in December was observed.”
So it’s hard to explain how the SARS2 virus picked up its furin cleavage site naturally, whether by mutation or recombination.
That leaves a gain-of-function experiment. For those who think SARS2 may have escaped from a lab, explaining the furin cleavage site is no problem at all. “Since 1992 the virology community has known that the one sure way to make a virus deadlier is to give it a furin cleavage site at the S1/S2 junction in the laboratory,” writes Steven Quay, a biotech entrepreneur interested in the origins of SARS2. “At least 11 gain-of-function experiments, adding a furin site to make a virus more infective, are published in the open literature, including [by] Dr. Zhengli Shi, head of coronavirus research at the Wuhan Institute of Virology.”
4) A question of codons. There’s another aspect of the furin cleavage site that narrows the path for a natural emergence origin even further.
As everyone knows (or may at least recall from high school), the genetic code uses three units of DNA to specify each amino acid unit of a protein chain. When read in groups of 3, the 4 different kinds of DNA unit can specify 4 x 4 x 4 or 64 different triplets, or codons as they are called. Since there are only 20 kinds of amino acid, there are more than enough codons to go around, allowing some amino acids to be specified by more than one codon. The amino acid arginine, for instance, can be designated by any of the six codons CGU, CGC, CGA, CGG, AGA or AGG, where A, U, G and C stand for the four different kinds of unit in RNA.
Here’s where it gets interesting. Different organisms have different codon preferences. Human cells like to designate arginine with the codons CGT, CGC or CGG. But CGG is coronavirus’s least popular codon for arginine. Keep that in mind when looking at how the amino acids in the furin cleavage site are encoded in the SARS2 genome.
Now the functional reason why SARS2 has a furin cleavage site, and its cousin viruses don’t, can be seen by lining up (in a computer) the string of nearly 30,000 nucleotides in its genome with those of its cousin coronaviruses, of which the closest so far known is one called RaTG13. Compared with RaTG13, SARS2 has a 12-nucleotide insert right at the S1/S2 junction. The insert is the sequence T-CCT-CGG-CGG-GC. The CCT codes for proline, the two CGG’s for two arginines, and the GC is the beginning of a GCA codon that codes for alanine.
There are several curious features about this insert but the oddest is that of the two side-by-side CGG codons. Only 5 percent of SARS2’s arginine codons are CGG, and the double codon CGG-CGG has not been found in any other beta-coronavirus. So how did SARS2 acquire a pair of arginine codons that are favored by human cells but not by coronaviruses?
Proponents of natural emergence have an up-hill task to explain all the features of SARS2’s furin cleavage site. They have to postulate a recombination event at a site on the virus’s genome where recombinations are rare, and the insertion of a 12-nucleotide sequence with a double arginine codon unknown in the beta-coronavirus repertoire, at the only site in the genome that would significantly expand the virus’s infectivity.
“Yes, but your wording makes this sound unlikely — viruses are specialists at unusual events,” is the riposte of David L. Robertson, a virologist at the University of Glasgow who regards lab escape as a conspiracy theory. “Recombination is naturally very, very frequent in these viruses, there are recombination breakpoints in the spike protein and these codons appear unusual exactly because we’ve not sampled enough.”
Robertson is correct that evolution is always producing results that may seem unlikely but in fact are not. Viruses can generate untold numbers of variants but we see only the one-in-a-billion that natural selection picks for survival. But this argument could be pushed too far. For instance, any result of a gain-of-function experiment could be explained as one that evolution would have arrived at in time. And the numbers game can be played the other way. For the furin cleavage site to arise naturally in SARS2, a chain of events has to happen, each of which is quite unlikely for the reasons given above. A long chain with several improbable steps is unlikely to ever be completed.
For the lab escape scenario, the double CGG codon is no surprise. The human-preferred codon is routinely used in labs. So anyone who wanted to insert a furin cleavage site into the virus’s genome would synthesize the PRRA-making sequence in the lab and would be likely to use CGG codons to do so.
“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.
-- The origin of COVID: Did people or nature open Pandora’s box at Wuhan?, by Nicholas Wade
The new proposal, which also described a plan to mass vaccinate bats in caves, does not provide conclusive evidence that the virus that caused the pandemic emerged from a lab. And virus experts remain sharply divided over its origins. But several scientists who work with coronaviruses told The Intercept that they felt that the proposal shifted the terrain of the debate.
Tipping the Scales
“Some kind of threshold has been crossed,” said Alina Chan, a Boston-based scientist and co-author of the upcoming book “Viral: The Search for the Origin of Covid-19.” Chan has been vocal about the need to thoroughly investigate the possibility that SARS-CoV-2 emerged from a lab while remaining open to both possible theories of its development. For Chan, the revelation from the proposal was the description of the insertion of a novel furin cleavage site into bat coronaviruses — something people previously speculated, but had no evidence, may have happened.
“Let’s look at the big picture: A novel SARS coronavirus emerges in Wuhan with a novel cleavage site in it. We now have evidence that, in early 2018, they had pitched inserting novel cleavage sites into novel SARS-related viruses in their lab,” said Chan. “This definitely tips the scales for me. And I think it should do that for many other scientists too.”
Richard Ebright, a molecular biologist at Rutgers University who has espoused the possibility that SARS-CoV-2 may have originated in a lab, agreed. “The relevance of this is that SARS Cov-2, the pandemic virus, is the only virus in its entire genus of SARS-related coronaviruses that contains a fully functional cleavage site at the S1, S2 junction,” said Ebright, referring to the place where two subunits of the spike protein meet. “And here is a proposal from the beginning of 2018, proposing explicitly to engineer that sequence at that position in chimeric lab-generated coronaviruses.”
“A possible transmission chain is now logically consistent — which it was not before I read the proposal.”
Martin Wikelski, a director at the Max Planck Institute of Animal Behavior in Germany, whose work tracking bats and other animals was referenced in the grant application without his knowledge, also said it made him more open to the idea that the pandemic may have its roots in a lab. “The information in the proposal certainly changes my thoughts about a possible origin of SARS-CoV-2,” Wikelski told The Intercept. “In fact, a possible transmission chain is now logically consistent — which it was not before I read the proposal.”
But others insisted that the research posed little or no threat and pointed out that the proposal called for most of the genetic engineering work to be done in North Carolina rather than China. “Given that the work wasn’t funded and wasn’t proposed to take place in Wuhan anyway it’s hard to assess any bearing on the origin of SARS-CoV-2,” Stephen Goldstein, a scientist who studies the evolution of viral genes at the University of Utah, and an author of the recent Cell article, wrote in an email to The Intercept.
Other scientists contacted by The Intercept noted that there is published evidence that the Wuhan Institute of Virology was already engaged in some of the genetic engineering work described in the proposal and that viruses designed in North Carolina could easily be used in China. “The mail is filled with little envelopes with plasmid dried on to filter paper that scientists routinely send each other,” said Jack Nunberg, director of the Montana Biotechnology Center at the University of Montana.
Vincent Racaniello, a professor of microbiology and immunology at Columbia University, was adamant that the proposal did not change his opinion that the pandemic was caused by a natural spillover from animals to humans. “There are zero data to support a lab origin ‘notion,’” Racaniello wrote in an email. He said he believed that the research being proposed had the potential to fall in the category of gain-of-function research of concern, as did an experiment that was detailed in another grant proposal recently obtained by The Intercept. The government funds such research, in which scientists intentionally make viruses more pathogenic or transmissible in order to study them, only in a narrow range of circumstances. And DARPA rejected the proposal at least in part because of concerns that it involved such research.
While Racaniello acknowledged that the research in the DARPA proposal entailed some danger, he said “the benefits far, far outweigh the risk.” He also said the fact that the viruses described in the proposal were not known pathogens mitigated the concern. “This is not SARS,” he said, referring to SARS-CoV-1, the virus that caused a 2003 outbreak. “It’s SARS-related.”
But SARS-CoV-2 is not a direct descendant of that virus — it’s a relative.
In fact, the viruses described in the grant proposal, which was first posted online by the research group DRASTIC, were not known pathogens. And the authors of the grant proposal make the case that because the scientists would be using SARS-related bat viruses, as opposed to the SARS virus that was known to infect humans, the research was exempt from “gain-of-function concerns.” But according to several scientists interviewed by The Intercept, the viruses presented a threat nevertheless.
“The work describes generating full-length bat SARS-related coronaviruses that are thought to pose a risk of human spillover. And that’s the type of work that people could plausibly postulate could have led to a lab-associated origin of SARS-CoV-2,” said Jesse Bloom, a professor at Fred Hutchinson Cancer Research Center and director of the Bloom Lab, which studies the evolution of viruses. Bloom pointed out that the scientists acknowledge the risk to humans in their proposal. “It’s an explicit goal of the grant to identify the bat SARS-related coronaviruses that they think pose the highest risk.”
Stuart Newman, a professor of cell biology who directs the developmental biology laboratory at New York Medical College, also said the fact that the viruses weren’t known to be dangerous didn’t preclude the possibility that they might become so. “That’s really disingenuous,” Newman said of the argument. “The people that are claiming natural emergence say that it begins with a bat virus that evolved to be compatible with humans. If you use that logic, then this virus could be a threat because it could also make that transition.” Newman, a longtime critic of gain-of-function research and founder of the Council for Responsible Genetics, said that the proposal confirmed some of his worst fears. “This is not like slightly stepping over the line,” said Newman. “This is doing everything that people say is going to cause a pandemic if you do it.”
While the grant proposal does not provide the smoking gun that SARS-CoV-2 escaped from a lab, for some scientists it adds to the evidence that it might have. “Whether that particular study did or didn’t [lead to the pandemic], it certainly could have,” said Nunberg, of Montana Biotechnology Center. “Once you make an unnatural virus, you’re basically setting it up in an unstable evolutionary place. The virus is going to undergo a whole bunch of changes to try and cope with its imperfections. So who knows what will come of it.” The risks of such research are profound and irreversible, he said. “You can’t call back the virus once you release it into the environment.”
DARPA, a division of the Department of Defense, said regulations prevented it from confirming that it had reviewed the proposal. “Since EcoHealth Alliance may or may not be the direct source of the material in question, and we are precluded by Federal Acquisition Regulations from divulging bidders or any associated proposal details, we recommend that you reach out to them to confirm the document’s authenticity,” a DARPA spokesperson wrote in an email to The Intercept. The British Daily Telegraph reported that it had confirmed the document’s legitimacy with a former member of the Trump administration.
The Telegraph story erroneously reported that the scientists proposed to inoculate bats with live viruses. In fact, they hoped to inoculate them with chimeric S proteins, which were proposed to be developed through a subcontract in the grant in Ralph Baric’s lab at the University of North Carolina at Chapel Hill, not in Wuhan. Baric did not respond to The Intercept’s request for comment.
Conflict of Interest
Many questions remain about the proposal, including whether any of the research described in it was completed. Even without the DARPA funding, there were many other potential ways to pay for the experiments. And scientists interviewed for this article agreed that often researchers do some of the science they describe in proposals before or after they submit them.
“This was a highly funded group of researchers that wouldn’t let one rejection halt their work,” said Chan, the “Viral” author.
Perhaps the most troubling question about the proposal is why, within the small group of scientists who have been searching for information that could shed light on the origins of the pandemic, there has apparently been so little awareness of the planned work until now. Peter Daszak and Linfa Wang, two of the researchers who submitted the proposal, did not previously acknowledge it.
Daszak, the EcoHealth Alliance president, has actively sought to quash interest in the idea that the novel coronavirus originated in a lab. In February 2020, as the pandemic began to grip major cities in the U.S., he began organizing scientists to write an open letter that was published in the Lancet addressing the origins of the virus. “The rapid, open, and transparent sharing of data on this outbreak is now being threatened by rumours and misinformation around its origins,” read the statement signed by Daszak and 26 co-authors. “We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin.”
Daszak directed and gathered signatures for the letter, all the while suggesting that he and his collaborators on the proposed DARPA project, Baric and Wang, distance themselves from the effort.
“I spoke with Linfa [Wang] last night about the statement we sent round. He thinks, and I agree with him, that you, me and him should not sign this statement, so it has some distance from us and therefore doesn’t work in a counterproductive way,” Daszak wrote to Baric in February 2020, just weeks before it appeared in the journal, according to an email surfaced a year later by public health investigative research group U.S. Right to Know. “We’ll then put it out in a way that doesn’t link it back to our collaboration so we maximize an independent voice.” Ultimately, Daszak did sign the letter.
“I also think this is a good decision,” Baric replied. “Otherwise it looks self-serving and we lose impact.”
Baric and Wang — a professor in the emerging infectious diseases program at Duke-NUS Medical School, Singapore — did not respond to inquiries from The Intercept about their decision not to sign the letter in the Lancet.
Daszak was also a member of the joint team the World Health Organization sent to China in February 2020 to investigate the origins of the pandemic, which concluded that it was “extremely unlikely” that the virus had been released from a laboratory. (In March, WHO called for further investigation of the origins of the virus and stated that “all hypotheses remain open.”)
“I find it really disappointing that one of the members of the joint WHO-China team, which is essentially the group of scientists that were tasked as representatives of both the scientific community and the World Health Organization of investigating this, are actually on this proposal, knew that this line of research was at least under consideration, and didn’t mention it all,” said Bloom, of Fred Hutch. “Whatever information that relates to help people think about this just needs to be made transparently available and explained.”
Correction: September 24, 2021
A previous version of this article stated incorrectly that the EcoHealth Alliance proposal had been featured on Sky News Australia.
Correction: September 23, 2021, 3:30 p.m.
A previous version of this article stated incorrectly that Linfa Wang was a member of the WHO-China team.