An American nonprofit received millions of dollars from the U.S. government during the Obama and Trump administrations to identify unknown viruses in bats that could infect humans and cause a global pandemic.

Now, as the world faces one such pandemic, the New York City-based EcoHealth Alliance has found itself at the center of a political maelstrom, with one of its major federal grants suddenly axed.

The reason: Its longtime Chinese partner in identifying unknown bat viruses, the Wuhan Institute of Virology, is fending off allegations from President Donald Trump and some of his top aides that the pathogen causing COVID-19 escaped from its lab.

The story of how EcoHealth became a target in the Trump administration’s effort to deflect criticism and focus blame on China illustrates the promise and perils of international cooperation on public health research between two superpowers that are increasingly at odds.

Beijing has led an authoritarian crackdown on information about the initial coronavirus outbreak, while Washington has demonstrated a cavalier willingness to fuel theories about a Chinese lab accident without presenting any evidence. Caught in the middle are scientists from both countries, facing questions about their research and doubts about whether their yearslong collaboration can continue amid escalating geopolitical tension.

After a CBS News “60 Minutes” segment detailed EcoHealth’s research and defunding on Sunday, Trump accused the show of defending China.

EcoHealth’s work in China first gained national attention during the pandemic when Trump, at a news conference in mid-April, pledged to pull its grant from NIH. Days later, the president’s personal attorney, Rudy Giuliani, assailed the grant in a tweet. Neither Trump nor Giuliani mentioned the nonprofit organization by name, instead focusing on its partners in Wuhan.

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Late last month, NIH followed through on Trump’s promise and abruptly pulled more than $3 million in funding over five years that was awarded in 2019. NIH gave the nonprofit organization little reason for doing so, writing in a letter that the project didn’t align with “program goals and agency priorities.”

“This idea that it doesn’t fit the goals and objectives — there must be more to it,” EcoHealth Alliance President Peter Daszak said in a May 1 interview. “You can’t apply for money from the NIH unless it’s within the goals and objectives of the organization. They review that when you submit a proposal.”

NIH confirmed in a statement that EcoHealth’s grant was terminated and acknowledged that the Wuhan Institute of Virology was a “sub-awardee.” Asked why the funding was pulled, NIH said it does not discuss “the details of the decision-making process regarding specific grant awards.”

Daszak, who said the grant’s termination will force EcoHealth to lay off employees, says cooperation with Chinese scientists is important because the next bat-derived virus threatening humans is likely to emerge from the region. Already, two appear to have caused pandemics in less than 20 years.

“Viruses emerge from places where wildlife carry them and people interact with the wildlife,” Daszak said. “If you have a place with a high diversity of bats and lots of people hunting and eating bats like in Southeast Asia and China, that’s where you need to go.”

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Some of the bat coronaviruses EcoHealth identified with the Wuhan Institute of Virology, Daszak said, were used at the University of North Carolina at Chapel Hill to test the effectiveness of remdesivir, the antiviral medication the United States recently approved as a therapy for COVID-19 patients.

“COVID-19 is [the result of] a bat-origin coronavirus from China,” Daszak said. “Our grant is called understanding the risk of the emergence of bat-origin coronaviruses. The place we were doing it is China. We were right to be doing that.”

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EcoHealth Alliance and the Wuhan Institute of Virology’s cooperation took their researchers to the front lines of infectious disease.

Scouring China, the scientists hunted the rare bat virus that would infect humans and cause the next severe acute respiratory syndrome, or SARS. The hope: find the virus and develop a vaccine in advance.

The quest led them to a remote bat cave in China’s Yunnan province. There and elsewhere, over many years, the researchers took blood and fecal samples from bats, used those samples to identify the genetic sequence of unknown viruses and experimented with the material in the Wuhan lab.

Over the years, the collaboration yielded considerable results.

In the aftermath of SARS, Daszak and Wuhan Institute of Virology scientist Shi Zhengli, now referred to in some Chinese media as “bat woman,” were among a group of scientists who in 2005 demonstrated that the virus most likely originated in horseshoe bats. Later, their researchers found evidence that bat coronaviruses could infect humans directly and don’t need other animals as intermediary hosts.

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The joint research involved risks. Researchers in protective equipment interacted with potentially infectious wildlife. Back in the lab, they cultured a live coronavirus from a bat on at least one occasion and tested its potential to infect human cells. Using what are known as “reverse genetics,” they took the spike proteins of new viruses that they identified and inserted them into a uniform SARS-like virus to understand which was most infectious to humans. Some experiments involved humanized mice.

Theoretically, an accident during such activities could prompt an outbreak. If researchers, for example, had found SARS-CoV-2, the virus that causes COVID-19, and cultured the virus in the lab, it could have infected humans as the result of a mishap.

No evidence of that nature has emerged. Shi has said SARS-CoV-2 wasn’t among the bat coronaviruses that her institute identified or possessed. Daszak dismissed such theories outright.

“We have worked with this lab for 15 years,” Daszak said. “They didn’t have the virus. I have never heard anything suspicious from this lab. It’s a preposterous idea.”

Along with other scientists, Daszak has argued that the COVID-19 pandemic almost certainly arose naturally, namely through the “spillover” of the SARS-CoV-2 virus from bats to humans, possibly through an intermediary species, in a process similar to what caused the SARS outbreak in 2002.

“People hunt bats, eat bats, use bat feces for Chinese medicine and put it on their vegetable gardens, every day,” he said. “We have actual evidence, real evidence, that between one [million] and seven million people a year are getting [exposed to or] infected by bat coronaviruses in Southeast Asia.”

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Anthony Fauci, who runs the part of the National Institutes of Health that awarded EcoHealth’s grant and later terminated it, hasn’t commented on why his institute, the National Institute of Allergy and Infectious Diseases, terminated the EcoHealth grant. He said in an interview with National Geographic that the available scientific evidence points to a virus that “evolved in nature and then jumped species.”

Such an outbreak could easily happen in any Chinese city with an animal market selling species that could carry the virus from bats to humans. Many of the initial patients in Wuhan, which has a population of more than 11 million, were connected to one such market.

But questions about exactly how and where the natural spillover took place, coupled with China’s refusal so far to allow an independent investigation into the origins of the pandemic, have bred suspicion about whether the institute could be to blame. So has the coincidence that both the bat coronavirus research and the outbreak took place in the city of Wuhan.

The Trump administration has amplified the suspicion. Senior administration officials told U.S. intelligence agencies to scour their records and look for new information that might show that the Wuhan lab was the source of the virus, current and former officials familiar with those efforts said. Those agencies have not found evidence to support the theory, according to those people, who spoke on the condition of anonymity to discuss internal intelligence efforts.

The U.S. intelligence community agrees with the scientific consensus that the virus was not man-made or genetically modified, the Office of the Director of National Intelligence said in a statement in late April. It also said U.S. intelligence agencies will continue examining information “to determine whether the outbreak began through contact with infected animals or if it was the result of an accident at a laboratory in Wuhan.”

Trump and his top aides have been fueling the lab-origin theory for weeks. Asked at an April 30 news conference whether he had seen any evidence that the pathogen causing COVID-19 originated at the Wuhan Institute of Virology, Trump said he had but then declined to elaborate.

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“There is enormous evidence that that’s where this began,” Secretary of State Mike Pompeo said in a May 3 interview with ABC News, when asked whether there was evidence that the outbreak began in the lab. He has not presented that evidence.

Scientists have analyzed SARS-CoV-2 and asserted that it has the makings of a naturally derived virus. And they have emphasized that the spillover of coronaviruses from animals to humans is a common occurrence, especially in a place like China.

Kristian Andersen, a microbiology professor at the La Jolla, California-based Scripps Research Institute, who co-authored a March paper in the journal Nature arguing that the virus wasn’t lab-created, said the lab-accident theory was not a plausible explanation, but rather a “possible explanation — with an extremely low likelihood of being true.”

Science alone, however, cannot definitively disprove the lab-accident scenario, said Simon Wain-Hobson, a virologist at the Pasteur Institute in Paris, in part because of the challenge of proving a negative. He said to do so would require full knowledge of the Wuhan institute’s samples and activities leading up to the outbreak.

“The only way to know is we would seek the collaboration of our colleagues at the Wuhan Institute of Virology, and this would need the collaboration of the Chinese government — and given the relationship, it seems unlikely that we are going to know,” Wain-Hobson said. Trump’s actions, he said, reduce the chances even further.

“Given available data, I subscribe to the natural-virus-origin thesis,” he said. “There may be a twist.”

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For years, the raison d’être for EcoHealth’s research in China and elsewhere has been “bio-surveillance.”

The aim, Daszak said, is “to find out which of the viruses in the wild even possibly could infect people so we know where they are and we can stop them from emerging.”

“It’s a little bit like if you listen to phone calls from Afghanistan. To find the terrorists, you have to listen to all the phone calls,” Daszak said. “Only when you’ve heard the phone call do you then go in and find out who these people are and disrupt those networks.”

The nonprofit organization partnered for years with a USAID program called Predict. Launched in 2009, the program took tens of thousands of wildlife samples and identified hundreds of new viruses that could pose a threat to humans in order to create an “early-warning system” for the next pandemic. The Trump administration declined to renew the program’s funding late last year. Its work has continued through an initiative called the Global Virome Project, for which Daszak is the secretary and treasurer.

Critics of the “early-warning system” approach say it would be onerous and costly to identify all of the world’s zoonotic viruses, let alone figure out which ones will enjoy the exact alignment of circumstances to spill over and cause the next pandemic.

Andersen said the scientific research that EcoHealth and its partners in China have been doing is very important to better understand coronaviruses and how they work — but he takes issue with the panacean rationale.

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“I feel the claim they are making that you can prevent the next pandemic by doing this type of work is preposterous,” Andersen said. “If you could, given they worked in Wuhan for so long specifically, you would have thought they could have prevented the current pandemic, and they didn’t.”

Daszak, however, points out that one of his colleagues, Ralph Baric, a virologist at the University of North Carolina at Chapel Hill, worked with Gilead Sciences to develop the antiviral drug remdesivir and used virus strains that EcoHealth and its Chinese partners identified in the process, putting the United States ahead of the curve.

In a statement, Baric said that it is critical to learn what viruses exist in nature so potential drugs can be tested against them in a laboratory setting. His lab already had been working on bat coronaviruses, including at least one discovered by EcoHealth and the Wuhan institute, before testing remdesivir.

“It is because of our early work that the United States was in a position to quickly find the first successful treatment for SARS-CoV-2,” Baric said in a statement. “It is unfortunate that research that could help humans prepare for and fight disease is now viewed as questionable.”

EcoHealth and its partners regularly sounded alarm bells about a bat coronavirus spilling over into humans and becoming the next pandemic. The nonprofit said it found more than 700 novel coronaviruses during its work in China.

Still, it did not identify or prevent the pathogen causing COVID-19. Despite seeking to find “spillover-risk hot spots,” the virus emerged in the very city their partners worked.

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Shi told Scientific American that when the outbreak of a mysterious illness emerged in Wuhan late last year, she left a conference in Shanghai and returned home. If coronaviruses were indeed the culprit, she wondered, according to the magazine, “could they have come from our lab?”

After scouring her lab’s records for possible evidence of an accident, Shi told Scientific American that she breathed a sigh of relief when the genetic sequences from the new virus came back and didn’t match those her team sampled; the closest shared 96% of its genetic material.

“That really took a load off my mind,” she told the magazine. “I had not slept a wink for days.”

Suspicion of her institute grew anyway. Rumors circulated that she had defected, that she had been shut up by China’s Communist Party in a cover-up. In a social media post in February, she promised “on her life” that the virus had nothing to do with the lab. She declined to comment for this story.

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Shi’s research partners in the United States, including Daszak, have rushed to her defense, describing her as a highly professional scientist and her lab as one of China’s best. Nevertheless, her claims have been treated with suspicion in a Washington where distrust of the Chinese government is at a decades-long high. Her institute is part of the Chinese Academy of Sciences.

Attention soon shifted to her collaboration with U.S. scientists under NIH grants.

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Starting in 2008, Daszak received the first of three multiyear grants from the National Institute of Allergy and Infectious Diseases to study bat viruses. The second grant, which began in 2014 and, according to EcoHealth, amounted to approximately $3.1 million over five years, placed the nonprofit in formal collaboration with the Wuhan Institute of Virology as a sub-recipient.

About $100,000 a year went to the institute in Wuhan to pay for the genetic sequencing of viruses under that grant, Daszak said.

Daszak received the third grant in 2019, worth about $3.2 million over five years, according to EcoHealth. The Wuhan Institute of Virology was a sub-awardee, as were East China Normal University in Shanghai, the Institute of Pathogen Biology in Beijing and Duke-NUS Medical School in Singapore, according to NIH.

Daszak said he received a letter from NIH in late April saying that the agency had decided to suspend the Wuhan Institute of Virology from federal grants pending investigation. NIH asked whether EcoHealth had sent money to the lab under the current grant, and Daszak wrote to say it had not and would not. He said NIH suggested that the rest of the grant’s work would resume.

Shortly thereafter, though, Daszak said he received another letter saying that the grant had been terminated. He wrote to NIH asking to have a conversation about the rationale for the termination. So far, he has not received a reply.

NIH would have screened the Wuhan Institute of Virology with input from the State Department as an acceptable foreign partner before issuing the grant, Daszak said. He said NIH was aware of all the work being done under the grant and never registered an objection.

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Recipients are also required to file regular status updates for review by a panel of experts. NIH and EcoHealth declined to release those reports.

Regardless of whether the funding is restored, Daszak said EcoHealth would continue its work, much of which still relies on federal funding from agencies such as the Defense Department.

“We are just going to get on with our mission,” he said. “We just move on. We have to.”