Emails Point to Oversight Problems With NIH Bat Coronavirus Grant

Congressional Republicans have accused the National Institutes of Health and Anthony Fauci, the head of the National Institute of Allergy and Infectious Diseases, of funding dangerous research on bat coronaviruses in Wuhan, China. The NIH has shot back that none of the experiments described in grant documents for a project it funded there could have caused the pandemic. But the agency has not been fully transparent, dribbling out documents only after The Intercept brought a lawsuit under the Freedom of Information Act and failing to explain apparent anomalies in those documents to the public. Now, the grant recipient has told The Intercept that his organization filed a key additional report that NIH has not previously acknowledged — a fact that could spark renewed scrutiny of the agency.

Peter Daszak is the head of EcoHealth Alliance, a New York-based nonprofit that partners with labs around the world to research emerging diseases. He addressed his organization’s controversial grant documents in a Zoom interview and a series of emails with The Intercept. Daszak said that EcoHealth filed a progress report to NIAID in June 2021 for a grant called “Understanding the Risk of Bat Coronavirus Emergence.” The filing of the report is supported by an agency email recently released by NIH to The Intercept following the Freedom of Information Act lawsuit. Daszak alluded to additional grant documents in a letter to NIH published by the Wall Street Journal last October, but he did not give details at the time.

NIH regulations require grant recipients to file yearly updates detailing experiments and explaining how U.S. government money was spent. EcoHealth’s progress reports have been front and center in calls for greater transparency from the agency, and in public sparring between the agency and Daszak over work conducted at the Wuhan Institute of Virology, which was a sub-awardee on the multimillion-dollar grant. Other NIH communications newly released to The Intercept add to previous evidence of oversight issues at the agency.

“They clearly demonstrate material gaps in reporting surrounding NIH grants involving research at the Wuhan Institute of Virology,” said Lawrence Gostin, faculty director of Georgetown University’s O’Neill Institute for National and Global Health Law, after reviewing several of the emails. “There is no obvious explanation for these gaps, which are deeply concerning.” NIH, he added, “has a public duty to be transparent and accountable.”

Grant documents and emails released to The Intercept in recent months have reshaped public understanding of the research done in Wuhan. But they have also contained notable omissions and inconsistencies. As NIAID Director Anthony Fauci and Sen. Rand Paul, R-Ky., have clashed over whether the work constituted so-called gain-of-function research, there is another, perhaps more important battle playing out over paperwork. This one hinges on when the grant’s progress reports were filed, why one was updated after the start of the pandemic, and why NIH has failed to release all available information about the reports to the public.

The latest salvo in that battle comes from members of the House Energy and Commerce Committee, who last week wrote to NIH acting director Lawrence Tabak asking for detailed explanations about discrepancies in the progress reports, among other alleged issues.

Daszak addressed many of those concerns in the interview. He also provided new details on the apparent paperwork anomalies.

The bat coronavirus grant initially spanned 2014 to 2019. It was renewed in July 2019 for another five-year cycle, then suspended the following year amid scrutiny of the Wuhan lab’s U.S. funding. Daszak said that the report submitted in June 2021 covers Year 6, or the first year of the grant’s renewal. “Even though we didn’t have access to the funding, we still had to file reports on it,” Daszak told The Intercept. “So we then filed the Year 6 and 7 reports. … We have tried in every possible way to be compliant.”

When asked about the Year 6 progress report, a lawyer for NIH said that the agency had looked for additional progress reports and had not found them but that the agency would review reports for possible FOIA release if located. A spokesperson for the agency said, “NIH does not comment on pending or ongoing litigation.” She declined to reply to a list of other questions about the progress reports that are unrelated to the litigation.

“These grants and their oversight have become a significant public interest issue.”

“These grants and their oversight have become a significant public interest issue,” said Filippa Lentzos, co-director of King’s College London’s Centre for Science and Security Studies. “The responsible thing for NIH to do would be to openly and frankly explain what appear to be substantial deviations from standard reviewing processes.”

Last March, members of Congress asked Francis Collins, then NIH director, for all progress reports for recent awards involving the Wuhan Institute of Virology. “If there are additional progress reports that have not been disclosed, that requires an explanation,” said Richard Ebright, a molecular biologist at Rutgers University.

FOIA Clues

The Intercept asked about the report after obtaining an automated notification email sent to an NIAID staffer describing the submission of an “RPPR,” or progress report, on June 9, 2021. In the email, which was released in Freedom of Information Act litigation, the grant number and principal investigator’s name are redacted. But The Intercept received the email after requesting from NIH all communications regarding two specific grants, and the program officer and grants management specialist named in the email match those on the bat coronavirus grant. (The second grant covered in the FOIA release was an NIAID grant to EcoHealth funding viral surveillance in Southeast Asia.) Daszak confirmed that the redacted information describes the bat coronavirus grant.

An automated NIH notification sent to grants administrators on EcoHealth Alliance’s grant suggests that the nonprofit submitted a progress report in June 2021.

Despite dozens of scientific studies, an investigation by U.S. intelligence agencies, and a fact-finding mission to China led by the World Health Organization, exactly how the novel coronavirus spread from bats to humans is still unknown. Many scientists lean toward a natural spillover from animals to humans; this camp was reinvigorated by the release in the past week of several preprints, or papers that have not undergone peer review, that describe the spread of the coronavirus at the Huanan Seafood Wholesale Market in Wuhan in late 2019 and early 2020. But others note that the preprints differ on key questions, give an incomplete picture of the early path of the virus, and do not settle the question of what animal might have harbored the virus before it jumped to humans. They remain concerned that the pandemic could have been caused by an accident during fieldwork or experiments designed to make viruses more contagious.

The Wuhan Institute of Virology in China’s central Hubei province on Feb. 3, 2021.

The Intercept has published hundreds of pages of grant documents that shed light on the EcoHealth grant. While NIH officials are correct that none of the experiments outlined in those documents could have directly led to SARS-CoV-2, the risky nature of some of the work has alarmed experts and raised questions about whether NIH and EcoHealth have been forthcoming about the research.

The initial release contained two apparent anomalies. The Year 4 progress report released by NIH was dated September 2020, over two years late. The report for Year 5 was missing entirely. Along with the first half of Year 6, those two years cover the period leading up to the pandemic. The agency subsequently released to The Intercept a second version of the Year 4 progress report that was dated April 2018, along with a Year 5 report dated August 2021, nearly two years after it was due.

Daszak told The Intercept that EcoHealth filed the Year 4 report on time in 2018, as indicated by the second version of the document, and that the late submission date was a mistake. He said that in September 2020, while working on another EcoHealth report in eRA Commons, NIH’s grant portal, EcoHealth’s chief of staff Aleksei Chmura noticed an error message attached to the human subjects section of the Year 4 report — a section unrelated to the controversial experiments — and called the portal’s help desk to try to fix it. Chmura “had been in the ERA commons system repeatedly during summer/fall 2020,” Daszak noted, and did not have notes on what grant he had been working on. During the call with the help desk, an NIH staffer later told EcoHealth, an agent opened the Year 4 report to check it, automatically resetting the submission date to the day’s date.

“This is a good example of how the very tedious and complicated process of doing science via federally funded grants can be easily misconstrued by people.”

Daszak sent The Intercept a chain of emails that partially supported this account, adding, “you should know that we made NO changes to our Yr 4 report after it was submitted and accepted by the system in 2018. … I think this is a good example of how the very tedious and complicated process of doing science via federally funded grants can be easily misconstrued by people who approach the COVID origins issue, and our work, with a mindset that we were somehow engaged in a cover-up or lack of transparency.”

The emails show that in October 2021, one day after The Intercept published the earlier Year 4 report, Chmura wrote NIH’s lead grants management analyst to note that the submission date on the Year 4 report in eRA Commons appeared as September 2020. He later followed up to explain that the routing history for the grant indicated the earlier submission date — a fact that EcoHealth also established in a proof video the organization sent to Vanity Fair contributor Katherine Eban at the time — but that the September 2020 date appeared on the downloadable document. In a reply in late December, the analyst described Chmura’s 2020 eRA Commons help desk call and said NIH had restored the 2018 submission date in the system. The analyst also said the agency had kept a copy of the original report in its files.

An email exchange, provided by EcoHealth Alliance, between EcoHealth’s chief of staff and an administrator at NIH discussing the existence of two versions of a grant progress report.

NIH has never publicly explained the reason for the two different versions of the Year 4 reports nor said how it produced the document with the earlier date.

Another question surrounding the reports has been why EcoHealth submitted the Year 5 document two years late. While scientists sometimes send in project documents after their due date, sources described the extremely late submission as unusual, especially for a grant that has come under intense scrutiny.

Daszak has repeatedly said that EcoHealth was unable to submit the Year 5 report on time because of a technical glitch. “We first uploaded this report on time, in July 2019,” he wrote in the letter to NIH published by the Wall Street Journal. “However, by the time we tried to officially submit, our R01 grant had been renewed (July 24th 2019) and the system locked us out from submitting a normal annual final Year 5 report at that point.”

In their letter last week, the House Energy and Commerce Committee members questioned that account. They noted that emails obtained by the animal rights group White Coat Waste through a FOIA request show that on July 24, 2019 — the date that Daszak implied the group was locked out — Chmura wrote to an NIAID grants management specialist acknowledging the renewal of the grant and noting that EcoHealth was able to access the system. “I see that now we may commence our Year 5 annual report in eRA Common’s RPPR,” Chmura wrote. “Peter just initiated our Year 5 report.”

Daszak maintained to The Intercept that the FOIA email supported his account of what happened. “The emails you cite from the White Coat Waste report do not challenge our explanation of what happened with respect to filing our Year 5 report, but provide some of the background on what happened,” he wrote in an email.

He sent The Intercept a screenshot from EcoHealth’s eRA Commons account in showing that the Year 5 report was initiated on July 24, 2019. To support his claim that EcoHealth had sought assistance with filing the report, he also sent additional email exchanges, including one between Chmura and the same grants management specialist from July 30, six days later. The exchanges do not mention technical problems, however. Instead, Chmura asks when the report is due. Daszak subsequently said all of the communication with NIH about the technical difficulties happened by phone.

According to Daszak, the agency never responded to several of EcoHealth’s questions. “The fact that we got the renewal funding and the fact that they never responded to our request said to us, ‘Well, there’s no problem with this. You should just carry on and do a Year 1 report on the next grant,'” he said. “And that’s what we did. Unfortunately, [the grant] got terminated, and then there were all these attacks and inquiries.”

“The relevant data had already been included in our renewal application,” he wrote in an email to The Intercept. He noted that EcoHealth had not previously had funding renewed for an NIH research project grant. As a result, he wrote, “It was unclear to us whether you have to file a final report when a grant is renewed.”

Gaps and Contradictions

Emails newly obtained by The Intercept add to the mystery of why NIH overlooked the Year 5 report for two years. During the period when the document was overdue, the FBI was conducting an inquiry that involved EcoHealth Alliance, and NIH was carrying out an internal investigation that hinged in part on the progress reports. Officials at the agency’s investigative arm exchanged a number of letters and emails with Daszak about his group’s collaboration with the Wuhan Institute. Several of these discuss progress reports, but until July 2021, none of the communications obtained by The Intercept so far note that one was in fact missing.

An April 2020 email from EcoHealth Alliance President Peter Daszak mentions the group’s progress reports. One report was overdue at the time.

When NIH terminated EcoHealth’s grant in April 2020 at the request of President Donald Trump, for example, NIH deputy director for extramural research Michael Lauer requested detailed information about EcoHealth’s work in China. Daszak responded, “Concerning the request for information on all of the sites linked to this award in China, you should be aware that these are documented in our progress reports over the course of the grant.”

A reply from NIH official Michael Lauer also leaves out mention of an overdue progress report.

Twenty minutes later, Lauer responded, “We note that … all foreign sites for the Type 1 and Type 2 awards have been documented in the progress reports submitted to NIH.” At that point, the Year 5 report was more than six months overdue.

When asked why the late report didn’t come up in this exchange, Daszak wrote in an email, “That’s a question for NIH, not EcoHealth Alliance.” He noted that Lauer’s office is typically uninvolved in the annual report process, and that it is the job of the NIAID program office to follow up on paperwork issues.

One of several weekly automated emails sent to an NIAID grants administrator in 2021.

NIAID would have had ample notice of overdue documents. The newly obtained emails show that for several months, at least, an NIAID staffer who handled paperwork for the grant was receiving automated notifications every Monday listing outstanding progress reports. “Below is a listing of Type 5 progress reports assigned to you and not yet completed,” the emails read, referring to reports for grants that have already been funded. “Please complete these reviews as soon as possible.” Most grantees filed their reports on time, the messages show. But in each weekly email, NIH redacted one or two grant numbers, along with their submission status.

As with the email indicating the submission of the Year 6 progress report, the messages were provided in response to The Intercept’s lawsuit for records from two EcoHealth Alliance grants, suggesting that at least some of the redacted information concerns EcoHealth’s progress reports.

“In any large organization, there can be errors,” said Ebright, the Rutgers molecular biologist, who has been a vocal critic of both NIH and EcoHealth. “Papers fall through the cracks. Deadlines are missed. But the number of violations in this case and the gravity of the violations in this case are so extreme that there does not appear to have been standard handling of grants.”

A July 2021 letter to EcoHealth Alliance from NIH official Michael Lauer requesting all progress reports within 30 days.

On July 23, 2021, other newly obtained emails show, Lauer demanded the Year 5 progress report within 30 days. EcoHealth complied, though Daszak told The Intercept that his group again encountered technical problems. “Even then, there was significant back-and-forth with the NIH Program Office to make the electronic system work as expected, so that we could submit the report,” he wrote in an email.

The document that EcoHealth finally submitted contains significant errors, as noted in the House Energy and Commerce Committee letter last week. In the report, Figure 8 comes directly after Figure 4, Figure 5 follows Figure 10, and Figure 7 follows Figure 13. The text says that one figure shows evolutionary transitions among a type of coronavirus, but the actual figure, which appears six pages later, in fact shows a completely unrelated measurement on MERS viruses.

“The minor inconsistencies in the figure numbers in our report are simple editing errors as we changed the order of different sections to fit the report’s narrative to the specific aims,” Daszak wrote in an email.

Cutting and pasting is common with such documents; many scientists loathe grant paperwork and reuse passages from draft or published papers in progress reports. Simon Wain-Hobson, a microbiologist at the Pasteur Institute in Paris, noted that there is a “pervasive attitude that such reports will not be read.” To test that assumption, he once pulled a sentence in German off the internet and inserted it into a French lab report to see if it would be noticed; no one caught it. Nonetheless, he added, the anomalies in the EcoHealth Year 5 report are exceptional. “Sloppiness is one thing, but this is beyond the pale,” he said. “The disconnect is amazing.”

Last fall and again in January, NIH’s Lauer requested from EcoHealth detailed lab notebook entries for the research documented in the organization’s Year 4 and Year 5 reports. (Daszak said that EcoHealth has replied to Lauer’s letter and passed on the request for lab notebook entries to the Wuhan lab.) But it is unclear whether the agency has asked for the errors in the Year 5 report to be corrected.

“They may have been human error but could be deliberate withholding of information.”

Experts are now calling on NIH to release the missing Year 6 report — and to be transparent about what happened with the other reports. “The information in these progress reports would be very much in the public interest,” said Gostin, of Georgetown University. “What we still do not know is why those gaps exist. They may have been human error but could be deliberate withholding of information. NIH should make clear the reasons for the gaps.”

Years before the coronavirus wreaked havoc on the world, NIH was caught up in controversy over risky experiments that made flu viruses more transmissible in humans. The pandemic has revived a debate over whether the agency should be regulating itself with such research. “By only communicating through litigation requests, it comes across as though they’re covering something up,” said Lentzos, of King’s College London. “And that doesn’t give anyone confidence that these high-risk projects have been adequately regulated.”

Documents published with this article: