How NIH-funded research in China could have led to the COVID-19 pandemic

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A multimillion-dollar bat coronavirus research grant, funded by the National Institutes of Health (NIH), was made public last week, revealing that researchers based in Wuhan, China had manipulated coronaviruses in ways that led to increased severity of infection, employing platforms that tested the ability of bat coronaviruses to use human receptors.

The grant documents underscore the perils of the collection of and experimentation on potentially pathogenic viruses, and shed new light on U.S.-funded coronavirus experiments in Wuhan, China for five years prior to the COVID-19 pandemic.

The new information disclosed in the grant proposal and its interim reports do not establish that the research led to the pandemic. But they do suggest that it was possible.

The NIH-funded, five-year grant was awarded in 2014 to the U.S.-based EcoHealth Alliance, with EcoHealth President Peter Daszak as “principal investigator” in collaboration with several researchers in China, including two working at China’s Wuhan Institute of Virology (WIV).  A key collaborator on the grant was Ralph Baric, of the University of North Carolina, providing expertise in mouse models for coronavirus infections. The grant was renewed in 2019 but then cancelled in 2020 as the pandemic set off panic around the globe.

A copy of the research plan and interim reports, titled “Understanding the Risk of Bat Coronavirus Emergence,” was obtained through litigation against the NIH and publicly released by The Intercept. The documents show that the NIH grant was for $3.1 million, of which $599,000 went to the WIV and to researcher Zhengli Shi, who specialized in the study of severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1) and similar viruses, called SARS related (SARSr)-CoVs.

Many scientists have posited a possible lab origin of SARS-CoV-2, and suggested the WIV as a possible source for the origin of the novel coronavirus SARS-CoV-2, which causes COVID-19.

Coronaviruses (CoVs) emerging from wildlife are a “significant threat to global health,” the grant claims, with bats considered a “natural reservoir of these viruses.” With that in mind, the authors said that the purpose of their research was to “examine the risk of future coronavirus…emergence from wildlife” using a range of research techniques and to understand “what factors increase the risk of the next CoV emerging in people…” The work involved screening more than 30 species of bats for CoVs and then developing strategies for assessing the potential spillover of coronaviruses from bats to humans, according to the grant documents.

But it is possible that, in seeking to learn how to avoid spillover events, the work actually caused one.

How it could have happened

How might the EcoHealth Alliance grant have caused, or contributed to, the pandemic? Here are some possible scenarios based on a close reading of the grant.

  • During fieldwork, collection, and containment of bat SARSr-CoV samples, people could have been accidentally infected. The research involved collecting samples from bats in four Chinese provinces: Yunnan, Guangdong, Guangxi and Fujian. The researchers explained their prolific sampling of Chinese bats and identification of new coronaviruses: “We have identified sequences from 268 novel bat-CoVs (140 from China alone),” they wrote in the grant. “We have an additional 5000+ clinical samples from free-ranging bats and rodents from Guangdong province.”

The grantees acknowledged that their work had serious implications, writing in the grant documents that “some SARSr-CoVs currently circulating in bats in southern China are likely able to infect and replicate within people.” [Emphasis in original].

In fact, the most closely related virus to SARS-CoV-2 identified to date was found by WIV scientists in a mineshaft in Mojiang (Yunnan Province). In 2012-2013, six miners experienced acute respiratory distress syndrome after exposure to bat feces in this mineshaft, and three died.

  • There is evidence of lax bat-handling practices and minimal use of personal protective equipment (PPE) at WIV and Wuhan University, where parts of the research were conducted. By their own admission, the researchers noted, this work could be dangerous. “Fieldwork involves the highest risk of exposure to SARSr-related or other bat CoVs, while working in caves with high bat density overhead and the potential for fecal dust to be inhaled,” according to the grant documents.

The grant documents state that “Tyvek suits and HEPA-filtered Powered Air Purifying and Supplied Air Respirator Systems (PAPRs) will additionally be worn in cave systems where there is a higher risk of contact with aerosolized bat feces.”

If any of those bat samples contained a close relative of SARS-CoV-2 infectious to humans, an accidental infection during the course of fieldwork, subsequent lab procedures, or containment could have led to a transmissible SARSr-CoV with greater similarity to SARS-CoV-2 than the currently reported strains. In fact, analysis of some early strains of SARS-CoV-2 shows that they may be more similar to bat coronaviruses than previously thought, based on evidence recovered from viral sequences deleted from NIH sequence archives.

  • During lab experimentation with the bat coronaviruses, it is possible that a novel virus was produced with greater similarity to SARS-CoV-2 than those reported in the NIH grant. The researchers stated in the grant that they developed an in vivo model, that is, mice genetically engineered to carry human angiotensin-converting enzyme 2 (hACE-2), the receptor for SARS-CoV-1 and SARS-CoV-2. The research group also reported that they were successful in generating new SARS-like coronaviruses. They did this by splicing the RNA sequences of the novel spike proteins they discovered into the viral ‘backbone’ of known lab strains.  This kind of novel virus is called a chimera because it consists of genetic elements from different viruses.

In this way, the researchers created three chimeric viruses, each with a different spike protein, from bats.

  • Though the grant does not mention a virus similar enough to SARS-CoV-2 to be a direct progenitor, it is possible that other chimeric viruses were tested in this model, but were not reported in the grant. The researchers had access to troves of novel coronaviruses collected during fieldwork, including unreported bat viruses. It is common for researchers to present some but not all data in interim grant reports. The research described in the grant established a platform that could have easily been used to study other chimeric viruses more closely related to SARS-CoV-2 than those mentioned in the grant.

There are indications of this within the grant documents. While results from infection of hACE-2 mice with three chimeric viruses were presented, the researchers wrote in the grant, “[w]e cannot anticipate exactly how many viruses we will find that are candidates for experimental models…and that we will identify approximately 20 viruses that will be used for mouse infection experiments.”  It is possible that the researchers generated a novel chimeric virus with more similarity to SARS-CoV-2 than those reported.

Experiments on human ACE-2 mice

The NIH grant describes important research on mice with human ACE-2 receptors.

The researchers infected the hACE-2 mice with the chimeric SARS-like bat coronaviruses to see how sick they would get, and whether they would shed infectious virus compared to the original viral strain. They found that hACE-2 mice infected with some of the chimeric viruses lost more body weight and shed more virus in the lungs than those infected by the original viral strain at certain time points. This research resulted in chimeric viruses that gained infectious and pathogenic properties.

“We’ll infect them [hACE-2 mice] with cultured bat coronaviruses and determine which organs become infected and whether these mice are capable of shedding infectious virus”, the grant proposed. The grant aimed to study tissues of the chimeric virus-infected hACE-2 mice for virus replication.

The grant proposed testing different transmission routes in which the mice could be infected, comparing nasal infection versus other routes. The grant outlines, “[W]e will perform in vivo infection experiments in humanized mice modified to carry human ACE2…gene in the Wuhan Institute of Virology BSL-3 animal facility…[t]his work will provide information about viral pathogenicity, tissue tropism, transmission route, and infection symptom.”

An outstanding question is whether the chimeric viruses can be transmitted between the hACE-2 mice. Whether the scientists explicitly reported on this is not the question, but rather, was a novel chimeric bat virus engineered that was also transmissible between hACE-2 mice?  While the grant does not discuss repeated passage of viruses in hACE-2 mice, the platform also sets up biosafety concerns about this possibility.

A weakness in the prominent “proximal origin” paper?

Some scientists who have argued against a lab origin for SARS-CoV-2 contend that the virus has a signature of it being adapted in an animal host with an intact immune system, for which no such appropriate laboratory model has been described.

One of these arguments against a lab origin of SARS-CoV-2, advanced by scientist Kristian Andersen and colleagues, and published as an influential correspondence in Nature Medicine, was “[s]ubsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described.” [Emphasis ours.]

However, the grant shows this is not correct; the experimentation on the hACE-2 mice establish such a model.

Infection of hACE-2 mice with the novel chimeric bat coronaviruses could have supported new viruses with sequence changes that make them better able to infect human cells. These could be more similar in sequence to SARS-CoV-2 than the original chimeric virus infecting strains.  The hACE-2 expressing mice could have enabled some human adaptation of the chimeric SARS-like bat coronaviruses in vivo, generating viruses with more similarity to SARS-CoV-2 than those reported to date.  This is another possible explanation for how NIH-funded research in China could have led to the COVID-19 pandemic.

The bottom line

In addition to searching for spillover events, the research outlined in the grant had the potential to generate a spillover event. This could have occurred as an accidental infection during fieldwork and laboratory handling of bat SARSr-CoVs; during containment or storage of them; or during the laboratory engineering of novel chimeric bat coronaviruses; or, after these novel viruses were used to infect hACE-2 mice, leading to a more infectious, transmissible, and/or pathogenic virus that was a precursor to SARS-CoV-2. The possibility of a lab leak or lab-acquired infection with any of these novel coronaviruses during lab experimentation raises serious biosafety concerns.

Though the bat coronavirus grant project has concluded, it is entirely possible that other studies using this platform were performed or are now being performed, including those related to viral transmission. It is noteworthy that it took civil litigation to bring these grant documents to light, even though the research itself was paid for by U.S. taxpayers. It is also noteworthy that EcoHealth Alliance has received nearly $40 million in multiple grants from the Department of Defense, and DOD grant data is often considered classified and withheld from the public.

And though the 5-year bat coronavirus research grant was only renewed for one additional year, a $7.5 million NIH grant, titled “Understanding Risk of Zoonotic Virus Emergence in EID Hotspots of Southeast Asia,” was awarded to EHA in 2020 to expand on the platforms established in the 2014 grant.

This newer grant, with Daszak again as principal investigator, was also made public last week by the Intercept. The new grant is a consortium grant that adds more collaborators and lab sites where the research will be performed, including a BSL-4 facility in Boston.  Funding is approved for the budget cycle of June 17, 2020 through May 31, 2025.

The bottom line is this: It is unclear whether the work performed under the 2014 bat coronavirus NIH grant played a role in the COVID-19 pandemic. But the EcoHealth Alliance and WIV collection and storage of SARS-related bat coronaviruses, and the creation and use of chimeric novel bat coronaviruses with human ACE-2 expressing mouse platforms, could have sparked the pandemic.

Congress should launch an investigation into U.S. government funding of this type of risky research as part of a full and thorough investigation of the origins of the pandemic.

U.S. Right to Know believes transparency in science is essential to protection of public health, including preventing future pandemics.

Dr. Shannon Murray is a staff scientist at U.S. Right to Know. She received her Ph.D. in the Molecular and Cellular Biology Program at the Fred Hutchinson Cancer Research Center from the University of Washington. She was a postdoctoral fellow at the National Institute of Allergy and Infectious Diseases at the National Institutes of Health.

(Editing by Carey Gillam)

Scientists who authored article denying lab engineering of SARS-CoV-2 privately acknowledged possible lab origin, emails show

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Four prominent U.S. virologists who published a widely cited commentary strongly rebutting the theory that SARS-CoV-2, the novel coronavirus that causes COVID-19, might have been engineered in a lab privately acknowledged that they could not “rule out the possibility” of a lab leak, according to emails obtained by U.S. Right to Know.

The emails discuss the need for careful wording of the commentary titled “No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2,” which was published in the journal Emerging Microbes & Infections (EMI) on February 26, 2020.

Published at a time when countries were grappling with the rapid spread of COVID-19, the commentary, which concluded that “SARS-CoV-2 shows no evidence of laboratory origin,” was shared widely in the scientific community. By the end of 2020, it had been downloaded 75,000 times and was the third most popular article in 2020 for academic publisher Taylor & Francis.

It and another influential statement denying a lab origin were published less than two months after the identification of SARS-CoV-2, when the importance of scientific studies to limit the spread and find treatments for COVID-19 were crucial. The communications within these emails, as well as others obtained and shared publicly by U.S. Right to Know, indicate involvement by individuals with undisclosed conflicts of interest; limited peer-review; and a lack of even-handedness and transparency regarding the consideration of lab-origin theories within the scientific community.

Lab leak possibility cited

The newly released emails contain discussions between scientists Shan-Lu Liu and Linda Saif, both with Ohio State University; Susan Weiss, of the University of Pennsylvania; and Lishan Su, who at the time was employed by the University of North Carolina. Some correspondence includes EMI editor Shan Lu, of the University of Massachusetts.

The published EMI commentary outlined multiple arguments as to why SARS-CoV-2 was not the result of laboratory engineering, arguing it was “more likely” the virus originated “in nature between a bat CoV and another coronavirus in an intermediate animal host.”

The authors stated in the article: “there is currently no credible evidence to support the claim that SARS-CoV-2 originated from a laboratory engineered CoV.” They wrote that despite “speculations, rumours and conspiracy theories that SARS-CoV-2 is of laboratory origin,” there was in fact “no evidence of laboratory origin.”

However, in a Feb. 16, 2020 email, Liu wrote to Weiss “we cannot rule out the possibility that it comes from a bat virus leaked out of a lab.”

Liu suggested changing the title of the commentary from “SARS-CoV-2: no evidence of laboratory origin” to downplay a focus on the origin issue.  The title Liu suggested, according to the email, should “emphasize that the new virus is not laboratory engineered.” That suggested title – “SARS-CoV-2: no evidence for laboratory engineering” – later was finalized to contain a subtle caveat: “No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2”.

The emails reveal other questionable details behind the commentary.  On Feb. 11, EMI’s Lu wrote to Su and Liu about suggested changes to the commentary, “…It is better not going to too much science/tech details as it can only confuse people and provide more room for people to raise more questions.”

Emails show EMI solicited and expedited publication of the commentary and waived fees normally associated with publication.  EMI’s Lu wrote to authors Liu and Su, “Yes, just a secret to you two and not share with others. When I put a super fast review and accept (basically no review), the JEO [Journal Editorial Office] of T&F, became very suspicious and wanted her boss to check and approve.”

Su replied: “Thanks for speeding it up, bro!”

“Frightening to think it may have been engineered“

An important part of the debate over the origin of SARS-CoV-2 is the existence of a furin cleavage site (FCS) at the junction between the SARS-CoV-2 spike protein domains, S1 and S2. SARS-CoV-2 belongs to a group of viruses known as betacoronaviruses lineage B. The FCS, however, does not appear in any of the other coronaviruses in this group. One argument in support of the lab origin hypothesis is that the FCS within the SARS-CoV-2 spike protein could be a result of laboratory manipulation.

The EMI commentary does not address the existence of the FCS, even though it is widely considered one of the strongest pieces of evidence of lab engineering. Evidence supports the importance of the FCS in the ability of SARS-CoV-2 to infect human cells and tissues. Engineering FCS within coronaviruses is a well-known practice in coronavirus research labs.

Email exchanges between the co-authors show that though their commentary did not address the issue, they discussed the troubling implications.

In one Feb 16 email Weiss wrote: “I don’t think it is likely that bat virus leaked into humans in the lab- is there any evidence that someone from the Wuhan lab is infected? …– lineage B Bat viruses generally do not have the furin site…I doubt very much it was engineered in[,] in the lab. Doesn’t make sense.”

Five days later, however, Weiss wrote to Liu: “I find it hard to imagine how that sequence got into the spike of a lineage b betacoronavirus- not seen in SARS or any of the bat viruses.”

Liu wrote back: “I completely agree with you, but rumor says that furin site may be engineered…”

Weiss replied: “I have been speculating- how can that site have appeared at S1/S2 border- I hate to think to was engineered- among the MHV [mouse hepatitis virus] strains, the cleavage site does not increaser [sic] pathogenicity while it does effect entry route (surface vs endosome). [S]o for me the only significance of this furin site is as a marker for where the virus came from- frightening to think it may have been engineered.”

Weiss wrote in another email: “I remain concerned about the insertion of the furin site.”

Other questionable revelations

The emails also show the commentary included the involvement of coronavirus expert Ralph Baric of the University of North Carolina (UNC) and Chinese virologist Shi Zhengli, of the Wuhan Institute of Virology (WIV).

Baric and Shi have been central figures in ongoing inquiries regarding the potential origins of SARS-CoV-2 and whether or not there is a connection between the virus and gain-of-function research collaborations between UNC and WIV.  Such collaborations have been funded in part by the USAID-EPT-PREDICT program through an organization called EcoHealth Alliance. 

The emails show the authors of the EMI commentary asked Baric and Shi to review the EMI commentary before its publication, and included some of their comments in revisions. Neither Shi nor Baric were listed as co-authors or acknowledged as contributing.

EMI’s Lu wrote to the authors, “We don’t want to appear that we are defending Ralph even though he did nothing wrong.”

Over the last year and a half, a few scientists have privately expressed concerns about signatures of lab engineering seen in the SARS-CoV-2 genome but later authored commentaries arguing against a lab origin of SARS-CoV-2.

Documents show that Kristian Andersen, a virologist with the Scripps Research Institute, emailed Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, early in 2020 expressing concerns about possible genetic engineering of the virus.

Andersen had a conference call with Fauci and other scientists in February 2020, and shortly after led the authoring of a high profile article, published as a correspondence in the journal Nature Medicine, specifically arguing against any possible laboratory engineering of the virus.

U.S. Right to Know obtained the emails about the EMI commentary from an Ohio Public Records Act request to Ohio State University for emails of Professor Shan-Lu Liu.

U.S. Right to Know believes transparency in science is critical for understanding the origins of SARS-CoV-2, determining control and treatment of the virus, regulating research involving dangerous pathogens, and preventing future pandemics.

(Editing by Carey Gillam)

For more information

Ohio State University Professor Shan-Lu Liu’s emails, which U.S. Right to Know obtained through an Ohio Public Records Act request, can be found here: Shan-Lu Liu emails: Ohio State University (488 pages)

U.S. Right to Know is posting documents from our public records requests for our biohazards investigation. See: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Background page on U.S. Right to Know’s investigation into the origins of SARS-CoV-2.

Altered datasets raise more questions about reliability of key studies on coronavirus origins

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Revisions to genomic datasets associated with four key studies on coronavirus origins add further questions about the reliability of these studies, which provide foundational support for the hypothesis that SARS-CoV-2 originated in wildlife. The studies, Peng Zhou et al., Hong Zhou et al., Lam et al., and Xiao et al., discovered SARS-CoV-2-related coronaviruses in horseshoe bats and Malayan pangolins.

The studies’ authors deposited DNA sequence data called sequence reads, which they used to assemble bat- and pangolin-coronavirus genomes, in the National Center for Biotechnology Information (NCBI) sequence read archive (SRA). NCBI established the public database to assist independent verification of genomic analyses based on high-throughput sequencing technologies.

U.S. Right to Know obtained documents by a public records request that show revisions to these studies’ SRA data months after they were published. These revisions are odd because they occurred after publication, and without any rationale, explanation or validation.

For example, Peng Zhou et al. and Lam et al. updated their SRA data on the same two dates. The documents don’t explain why they altered their data, only that some changes were made. Xiao et al. made numerous changes to their SRA data, including the deletion of two datasets on March 10, the addition of a new dataset on June 19, a November 8 replacement of data first released on October 30, and a further data change on November 13 — two days after Nature added an Editor’s “note of concern” about the study. Hong Zhou et al. have yet to share the full SRA dataset that would enable independent verification. While journals like Nature require authors to make all data “promptly available” at the time of publication, SRA data can be released after publication; but it is unusual to make such changes months after publication.

These unusual alterations of SRA data do not automatically make the four studies and their associated datasets unreliable. However, the delays, gaps and changes in SRA data have hampered independent assembly and verification of the published genome sequences, and add to questions and concerns about the validity of the four studies, such as:

  1. What were the exact post-publication revisions to the SRA data? Why were they made? How did they affect the associated genomic analyses and results?
  2. Were these SRA revisions independently validated? If so, how? The NCBI’s only validation criterion for publishing an SRA BioProject– beyond basic information such as “organism name”– is that it cannot be a duplicate.

For more information

The National Center for Biotechnology Information (NCBI) documents can be found here: NCBI emails (63 pages)

U.S. Right to Know is posting documents from our public records requests for our biohazards investigation. See: FOI documents on origins of SARS-CoV-2, hazards of gain-of-function research and biosafety labs.

Background page on U.S. Right to Know’s investigation into the origins of SARS-CoV-2.

No peer review for addendum to prominent coronavirus origins study?

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The journal Nature did not assess the reliability of important claims made in a November 17 addendum to a study on the bat-origins of the novel coronavirus SARS-CoV-2, correspondence with Nature staff suggests.

On February 3, 2020, Wuhan Institute of Virology scientists reported discovering the closest known relative of SARS-CoV-2, a bat coronavirus called RaTG13. RaTG13 has become central to the hypothesis that SARS-CoV-2 originated in wildlife.

The addendum addresses unanswered questions about the provenance of RaTG13. The authors, Zhou et al., clarified they found RaTG13 in 2012-2013 “in an abandoned mineshaft in Mojiang County, Yunnan Province,” where six miners suffered acute respiratory distress syndrome after exposure to bat feces, and three died. Investigations of the symptoms of the sickened miners could provide important clues about the origins of SARS-CoV-2. Zhou et al. reported finding no SARS-related coronaviruses in stored serum samples of the sick miners, but they did not support their claims with data and methods about their assays and experimental controls.

The absence of key data in the addendum has raised further questions about the reliability of the Zhou et al. study. On November 27, U.S. Right to Know asked Nature questions about the addendum’s claims, and requested that Nature publish all supporting data that Zhou et al. may have provided.

On December 2, Nature Head of Communications Bex Walton replied that the original Zhou et al.  study was “accurate but unclear,” and that the addendum was an appropriate post-publication platform for clarification. She added: “With regards to your questions, we would direct you to approach the authors of the paper for answers, as these questions pertain not to the research that we have published but to other research undertaken by the authors, upon which we cannot comment” (emphasis ours). Since our questions related to research described in the addendum, the Nature representative’s statement suggests Zhou et al.’s addendum was not evaluated as research.

We asked a follow up question on December 2: “was this addendum subjected to any peer-review and/or editorial oversight by Nature?” Ms. Walton did not answer directly; she replied: “In general, our editors will assess comments or concerns that are raised with us in the first instance, consulting the authors, and seeking advice from peer reviewers and other external experts if we consider it necessary. Our confidentiality policy means we cannot comment on the specific handling of individual cases.”

Since Nature considers an addendum to be a post-publication update, and does not subject such post publication addenda to the same peer-review standards as original publications, it seems likely that the Zhou et al. addendum did not undergo peer-review.

Authors Zhengli Shi and Peng Zhou did not respond to our questions about their Nature addendum.