US to revive global virus-hunting effort ended last year

A worldwide virus-hunting program allowed to expire last year by the Trump administration, just before the coronavirus pandemic broke out, will have a second life — whatever the outcome of the presidential election.

Joe Biden has promised that, if elected, he will restore the program, called Predict, which searched for dangerous new animal viruses in bat caves, camel pens, wet markets and wildlife-smuggling routes around the globe.

The expiration of Predict just weeks before the advent of the pandemic prompted wide criticism among scientists, who noted that the coronavirus is exactly the sort of catastrophic animal virus the program was designed to head off.

In a speech Thursday, Kamala Harris, the Democratic vice-presidential candidate, briefly alluded to the controversy as she attacked President Donald Trump before the last night of the Republican National Convention.

“Barack Obama and Joe Biden had a program, called Predict, that tracked emerging diseases in places like China,” she said late in her 20-minute speech. “Trump cut it.”

The government agency that let Predict die last October has quietly created a $100 million program with a similar purpose as Predict, but it has a different name. The new program, set to begin in October, will be called Stop Spillover.

Predict, which was started in 2009 as part of the Obama administration’s Emerging Pandemic Threats program, was inspired by the 2005 H5N1 bird flu scare. Predict was run by the U.S. Agency for International Development, which is an independent foreign-aid agency overseen by the State Department.

Predict was an odd fit for USAID, experts said. Unlike the Centers for Disease Control and Prevention or the National Institutes of Health, the agency is not normally a home to cutting-edge science.

The U.S. response to pandemics is strangely fragmented. The CDC investigates outbreaks, while the National Institute of Allergy and Infectious Diseases pursues vaccines. Much research into tropical diseases and bioweapons is done by the military, legacies of the Spanish-American War and the Cold War, while the State Department coordinates global campaigns against AIDS.

Some experts have called for a more centralized arrangement, a sort of Pentagon for diseases.

In the public health arena, USAID is home to programs like the President’s Malaria Initiative and campaigns to bring clean drinking water to rural villages. But those programs rely on long-established interventions, like well-drilling, mosquito nets and anti-malaria drugs.

Interviews with former Predict officials and grantees indicate that the program was not actively targeted by the White House in 2019, but that it was allowed to die by cautious administrators who were already under pressure to cut budgets and who feared running afoul of Trump’s hostility to foreign aid.

Dennis Carroll, Predict’s creator and director, retired from government service when the virus-hunting program was shut down. In an interview Friday, he said Predict was closed by “risk-averse bureaucrats who were trying to divine what the Trump administration did and didn’t want.”

Carroll, a fellow at the Bush School of Government and Public Service at Texas A&M in College Station, is now an informal adviser on global health issues to the Biden campaign.

On Friday, a USAID spokeswoman, Pooja Jhunjhunwala, denied that Predict was canceled and said it simply came to the end of its 10-year “life cycle.”

The program was then extended twice for six months, she said — first to finish some analyses, then to help other countries fight COVID-19.

In the early days of the pandemic, Predict became a target of some administration officials because of a grant to the EcoHealth Alliance, a New York-based consultancy employing field veterinarians and wildlife biologists. The alliance had used the grant money to train Chinese scientists at the Wuhan Institute of Virology to catch bats, take fecal and blood samples, and analyze them for viruses.

By then, the Wuhan institute had become the target of rumors that said it had accidentally released the lethal new coronavirus into the world. Those rumors were repeated by national security officials without evidence, and were central to the administration’s efforts to divert blame to China, rather than to Trump, for the deaths of tens of thousands of Americans from the virus.

(The rumors arose in part because one of the institute’s thousands of stored bat samples contained a virus that was a 96% match for SARS-CoV-2. But because coronaviruses mutate slowly, that figure does not describe a close relative. Most evolutionary biologists interpreted the finding to suggest that the two viruses evolved from a common ancestor 40 years ago.)

During its 10-year existence, Predict spent $207 million to train about 5,000 scientists in 30 African and Asian countries, and to build or strengthen 60 laboratories to seek out animal viruses that could endanger humans. Scientists working for Predict collected more than 140,000 biological samples and found more than 1,000 new viruses, including a new strain of Ebola.

Even after Predict ended, gene-sequencing teams that it trained in Thailand and Nepal were the first to detect COVID-19 in their countries, even before they got test kits from the World Health Organization, said Dr. Jonna Mazet, a veterinarian at the University of California, Davis, who was Predict’s global director.

Both countries rapidly contained the spread of the virus and have kept deaths from it very low, despite having cases early.

Now Predict’s five major grantees have formed a new consortium to apply for the $100 million Stop Spillover grant from USAID. The group includes the One Health Institute at UC Davis; the EcoHealth Alliance; the Wildlife Conservation Society, which runs the Bronx Zoo; the Smithsonian Institution, which manages the National Zoo in Washington; and the Center for Infection and Immunity at Columbia University in New York.

“I don’t know who our competitors are, but I’m sure we have some,” said Dr. Christine K. Johnson, associate director of the One Health Institute.

The application process for the Stop Spillover grant was unusually brief, she said. USAID first discussed it with scientists in March as a possible $50 million grant, then doubled the amount and announced May 1 that applications had to be received by June 1.

The request for applications asked for expertise in known threats like the Ebola, Nipah and Lassa viruses, she said, but it also hinted that the work could be broadened to include emerging threats. The agency sought expertise in coronaviruses, filoviruses and other viral “families” that produce novel pathogens.

Carroll said Friday that he had designed Stop Spillover years ago and intended it as a “companion piece” to Predict that would focus on spotting outbreaks of known pathogens while Predict hunted for still-unknown ones.

Predict, he had hoped, would eventually be folded into the Global Virome Project, a multibillion-dollar effort to genetically sequence up to 800,000 potentially dangerous viruses discovered in dozens of animal species.

By making Stop Spillover sound like the revival of Predict, Carroll said, USAID is “trying to create an optic that gets them out of the blowback for ending Predict.”

Although Jhunjhunwala said Stop Spillover “is not a revival of Predict, nor a follow-on project,” she said it was designed to “implement the scientific gains of Predict to reduce the risk of viral spillover.”

By coincidence, on Thursday the NIAID announced that it would spend $82 million over five years to create 11 “centers” in which American and foreign scientists would collaborate to hunt emerging diseases.

The new network, to be called the Centers for Research in Emerging Infectious Diseases, will focus more on drug and vaccine expertise than on the daring fieldwork sponsored by Predict, which involved jobs like netting bats and birds and sampling gorilla carcasses.

This $82 million grant was in the works years before Predict was eliminated, and it was created in response to the 2014 West African Ebola outbreak and the 2016 Zika epidemic, said Dr. Anthony Fauci, the NIAID’s director.

“Yes, it’s like Predict, but it wasn’t the cancellation of Predict that inspired it,” Fauci said in an interview.

The institutions receiving initial grants were the One Health Institute; the EcoHealth Alliance; the Pasteur Institute in Paris; the Scripps Research Institute in La Jolla, California; the University of Texas Medical Branch in Galveston; the University of Washington in Seattle; Washington University School of Medicine in St. Louis; RTI International in North Carolina; and Duke University in Durham, North Carolina.

In a statement to The New York Times, Biden vowed to restore many of the programs cut during the Trump administration, including Predict, that might have given the country more warning of an impending pandemic.

“As president, I will prioritize sustained long-term investments that ensure America is strong, resilient and ready in the face of new pandemic threats,” Biden said. Of the current crisis, he said: “It did not have to be this bad. That’s the greatest tragedy of all.”

Biden said he would also strengthen the military’s biological threat-reduction program, whose budget Trump proposed cutting in February, and would restore the National Security Council’s directorate for global health security and biodefense.

That directorate, established during the Obama administration, was downgraded in 2018 by John Bolton, then Trump’s national security adviser, and merged into another directorate whose chief mission was to watch out for nuclear threats.

Bolton eased out the directorate’s widely respected leader, Rear Adm. Tim Ziemer, who long led the President’s Malaria Initiative, begun under President George W. Bush. The Trump administration also sought to cut funding for fighting Ebola just as that disease was reemerging in central Africa.

Biden also promised to expand the CDC’s “disease detectives” division and rebuild its office in Beijing.

That division, the Epidemic Intelligence Service, is famous for investigating disease outbreaks, whether of Zika on Yap Island in the South Pacific or of dangerous bacteria in romaine lettuce.

In the two years before the coronavirus crisis broke out in Wuhan, China, the Trump administration cut the size of the CDC staff in Beijing to 14 people from 47, Reuters reported, and transferred home the manager of an Agriculture Department program that monitored diseases in pigs and poultry.

Recent budget cuts have shrunk the number of EIS “detectives” by about 25%, said Dr. Thomas Frieden, a former CDC director.

The current pandemic “is a once-in-a-lifetime opportunity to strengthen public health,” he said of Biden’s proposals, and that will require more funding for the World Health Organization, to which Trump has threatened to cut all U.S. funding.

Ziemer called Biden’s proposals “clear and strong” and said he supported “any science that will flush out future threats.” At the same time, he said, he did not think it made sense to “get hung up on the NSC organizational chart” or worry about which agency would run which program.

Peter Daszak, president of the EcoHealth Alliance, welcomed Biden’s plans. “Having eyes and ears on the ground in China protects America,” he said.

In his work, Daszak said, he had dealt with hunters and wildlife smugglers, and had visited farms where captive bamboo rats, civet cats and porcupines were raised in pens next to chickens and pigs.

Such situations “create a potential for another Covid-19 every 10 years,” he said. “Trying to head that off is a no-brainer. Even Republicans who think about taxpayer dollars can see that.”