In 2005, a strain of avian influenza called the H5N1 virus began spreading across Southeast Asia towards Eastern Europe. The disease was rare, but it could be fatal: Roughly 60 percent of those infected died. Experts were concerned that they could be looking at a “potentially historic event.”
At the time, Carroll was at USAID as a senior infectious disease specialist working on the organization’s response. His focus was on malaria and tuberculosis, diseases that are well-known — if not well-managed — everywhere in the world. Luckily, H5N1 did not turn into a global pandemic, but the experience changed Carroll’s perspective on the risks. In the 1960s, there were a few hundred million poultry produced in China; by the 2000s, when the country’s population had nearly doubled, China was producing billions of chickens, ducks, and turkeys every year. Carroll realized that as the human population grew, so would the odds of a deadly pandemic. “It was really a profound eye-opener for me,” he said.
Carroll suspected that there were many more viruses like the avian flu lying in wait, looking for a chance to make the jump to humans. But at the time, there was little understanding of how many dangerous viral illnesses existed. “It was an open question of what the ‘viral dark matter’ circulating in wildlife was,” he said. “Are we talking about a hundred viruses? Or something different?”
That question became the basis of PREDICT, a kind of catch-and-release project for viruses that Carroll championed from within USAID. The program, launched in 2009, included scientists and researchers from the University of California, Davis and EcoHealth Alliance — all with the singular goal of discovering new viruses before they spill over into people.
It was an enormous undertaking. With an annual budget of around $20 million, researchers identified potential viral “hotspots” around the world, contacted local governments, and surveyed key species that could be carrying novel diseases. They also began training locals in more than 30 countries around the world, including in Sierra Leone, Uganda, and Bangladesh. On-the-ground experts like Epstein, the wildlife veterinarian, taught locals to capture animals, take blood samples to test for novel viruses, and release them back into the wild.
“It’s really grunt work,” Carroll said. “This is not a technological challenge. You go out and capture bats, you go out and capture rodents.”
Based on PREDICT’s early work, Carroll and other researchers estimated that there are around 1.67 million yet-undiscovered viruses circulating in mammals and birds, the animals most likely to transmit disease to humans. Of those, between 631,000 and 827,000 have the potential to make the leap to humans.
The good news is that the proportion of those 600,000-plus viruses that could cause serious illness is very small. “Most microbial infections in people are inconsequential,” Carroll said. “They don’t have adverse effects.” So researchers don’t need to worry about all potentially zoonotic viruses — just the ones that could turn deadly.
Jonna Mazet, the organization’s global director from its inception until last year, said that PREDICT and its collaborators collected 168,000 samples from people and animals and identified more than 900 new viruses. Of those, 160 were coronaviruses — in the same family as SARS-CoV-2.
But sampling animals by climbing through trees, setting up nets on warehouse roofs, and crawling into bat-infested caves was only part of the challenge. There are about as many pathways for transmission as there are viruses. And so the group wasn’t only cataloging potential diseases. They were also searching for hidden patterns, looking for the unexpected risky behaviors that could allow a virus to spill over into humans.
The first case of the global Ebola outbreak in 2013 was traced to a toddler in the West African country of Guinea, who had been playing under a tree housing a family of bats, likely displaced by the destruction of surrounding forests by foreign mining and timber companies. (Scientists still aren’t sure exactly how close contact with those bats led to the child getting infected). In Malaysia, the first outbreak of Nipah was linked to pigs that had eaten pieces of fruit dropped by nearby bats and then spread the disease throughout industrial pig farms.
But some types of spillover are known, common, and preventable. “Let’s take, for example, live animal markets,” Epstein said. “People are still bringing wild animals, particularly bats, rodents, and non-human primates, from their natural environment into urban settings. These species not only have contact with each other, under very stressful and unhygienic conditions where there’s opportunity to trade viruses, but they’re also being handled and butchered by people.”
That close contact provides an opportunity for people to become exposed. The SARS outbreak in 2003 likely originated from a wildlife market in the Chinese province of Guangdong. And the suspected source of the novel coronavirus currently gripping the planet is a market in Wuhan.
Epstein explained that certain interventions — making wildlife markets more hygienic, or preventing wild animals from being sold at all — could dramatically lower the possibility of spillover. But he emphasized that the work has to be done in a culturally sensitive way, by building local partnerships. “This isn’t about a group of Westerners imposing their idea of what’s safe on cultures that have been doing something for generations,” he said.