Virus Hunters Hobbled as Pandemic Broke Out Get Emergency Reprieve — For Now

An effort to track viruses called PREDICT was to have wrapped up at the end of March. It has gotten a six-month extension to provide emergency support to countries responding to the outbreak

A group of giant fruit bats that are hung on trees during the day in Aceh Utara, on January 31, 2020, Aceh, Indonesia. Bats are animals that are considered to contain a lot of dangerous viruses, which are also thought to be the cause of the new coronavirus.
Fachrul Reza/Barcroft Media via Getty Images

Epidemiologists are warning amid the coronavirus pandemic of other viruses that could sweep the globe — just as a decade-old program designed to identify those deadly viruses is on the chopping block.

The federally-funded program, called PREDICT, has gotten a six-month extension for the current outbreak to help with early detection and to track the animal source of the virus, but health officials say their work must continue.

PREDICT is to end after the summer even as officials warn the novel and deadly coronavirus SARS-CoV-2 could kill hundreds of thousands. PREDICT’s work in 30 countries had been focused on finding viruses with the potential to move from animals to people and to cause pandemics. It has already been central to identifying this virus, which causes the disease COVID-19, and its connection to bats.

“Even though we don’t yet know exactly which species of bats or exactly where it originated, our global surveillance work very quickly identified this as being a zoonotic virus the origins of which were very likely to be bats,” said Simon Anthony, one of the program’s key members, an expert on coronaviruses and an assistant professor in epidemiology at Columbia University in New York City,

PREDICT'S epidemiologists say this pandemic, unprecedented in our lifetimes in its scale and effect, was to be anticipated, and they fear new ones.

Christine Kreuder Johnson, a professor of epidemiology and ecosystem health and associate director of the One Health Institute in the School of Veterinary Medicine at the University of California, Davis, said to expect zoonotic viruses "to emerge at an increasing rate because we have more people on the planet than ever and we are changing the environment on the planet, the landscape more rapidly than ever.”

“It’s those activities that bring about the emergence,” she said.

With the additional $2.26 million from its funder, the U.S. Agency for International Development, PREDICT will investigate the animal source or sources of SARS- CoV-2 using data and samples collected over the past 10 years in Asia and Southeast Asia. It also will continue to provide expertise to help detect cases in Africa, Asia and the Middle East.

Its collaborating laboratories will test for SARS-CoV-2 on samples collected from the region, including from animal markets. They will analyze existing data to investigate the risks for viruses to make the jump into humans and to spread at the markets and through other high-risk animal-human encounters.

“The PREDICT-trained labs and networks have been key for detection of initial cases in their countries,” Tracey Goldstein, the pathogen detection lead for PREDICT and an associate director of the UC Davis One Health Institute, said in a statement.

PREDICT was begun in 2009 between two outbreaks involving coronaviruses: SARS in 2003 and MERS in 2012. The collaborators collected and tested biological samples from wildlife in 30 countries, resulting in a data set that was unprecedented, Anthony told a Columbia University publication. It was to have wrapped up at the end of March.

In its decade of operation, PREDICT has found more than 1,000 new viruses, among them coronaviruses similar to what has caused the current pandemic and a new strain of Ebola in healthy bats in Sierra Leone before an outbreak in humans.

Its surveillance teams in Asia and Southeast Asia collected more than 57,000 animal and human samples and identified bat families that are likely to carry viruses in the SARS group.

A 2017 study by Anthony and others found that bats were a significant reservoir for coronaviruses, representing 98% of the animals hosting the coronaviruses they had found. Areas abounding with bats also had many coronaviruses.

Anthony says that there are likely 3,700 other coronaviruses, any one of which could cause a similar outbreak or worse. Researchers need to better understand which factors lead to viruses spilling over, or making that animal-to-human jump.

“This is not going to be the only time that this happens," Anthony said. "One does not want to paint an apocalyptic or a doom and gloom scenario because on the flip side we can see that the global response to this pandemic has been phenomenal. But we also see how impactful they can be and so all I can say is that it underscores the importance to try and get better at understanding at how and where and under what sort of conditions these viruses spill over and emerge.”

From the perspective of what has been learned about the virus quickly, advances are astonishing, he said.

How Coronavirus Has Grown in Each State

This chart shows the cumulative number of cases per state by number of days since the 500th case.

Source: The COVID Tracking Project
Credit: Amy O’Kruk/NBC

“Everything from understanding the natural history of the virus, which is our territory, right up to testing medical interventions, and that’s all in matter of weeks,” he said.

Dennis Carroll, who launched PREDICT, told Inside Climate News last month that even if PREDICT were to continue, that program and others were not enough to track viral outbreaks. A worldwide response is needed, he said.

A main driver, Anthony and others said, was changes in land use, whether for farming, mining or other activities that resulted in the loss of habit for wildlife and increased interactions between animals and humans.

"When we go and modify the environment, we’re changing the ecology of the wildlife that are present and we’re changing the way that people come into contact with those animals," he said.

But researchers do not know exactly why that is, he said.

If PREDICT were fully funded, he and his collaborators would be looking for coronaviruses where wildlife, livestock and humans meet, characterizing the genome sequence of those viruses and doing experimental work to try to determine whether the viruses had the potential to infect people. That would be followed by more ecologically focused studies to find out exactly how people might come in contact with a virus and the probability of that virus actually spilling over into people.

 "For any virus to emerge as a pandemic threat, you have to have both the genetic capacity to infect people and the opportunity to do so," he said.

The cost of PREDICT, $200 million over a decade to operate in 30 African and Asian countries, pales in comparison to the $1 trillion that the United Nations’ trade and development agency says the pandemic will cost the world economy in 2020.

Asked whether there had been second thoughts about ending PREDICT considering the devastation caused by this coronavirus -- close to a million confirmed cases worldwide and nearly 50,000 deaths, as of the morning of March 2 -- USAID said in a statement that the program had made crucial progress but accounted for less than 20 percent of the agency's global health security funding.

"USAID is now in a position to begin developing and implementing interventions to reduce the risk of people being infected with high-consequence animal viruses," the statement read.

Its new STOP Spillover project, which will be awarded in August with a cost of between $50 million and $99.99 million, will focus on strengthening the capacities of select countries in Asia and Africa to monitor and analyze the risk of priority emerging zoonotic viruses spilling over from animals to people, to develop, test and implement interventions meant to reduce that risk and to mitigate the spread of those diseases in human populations.

"The agency is confident that the new STOP Spillover project – in concert with other USAID global health security investments to address emerging animal viruses – will allow countries, and the world, to mount stronger and more-effective responses to epidemics and pandemics, including COVID-19, and possibly reduce the chances of their occurrence," the statement said.

Anthony said of the multi-year funding that PREDICT had received: “This is an ongoing, long-term effort to build foundational knowledge, massive amounts of foundational knowledge, to try and move the needle on an extremely, extremely complex problem so it necessitates these long-term investments.”

Some politicians have called on USAID to explain its decision and to reverse it.

In January, Sens. Elizabeth Warren, Democrat of Massachusetts and Angus King, independent of Maine, wrote to the USAID administrator, Mark Green, asking why the program had not been renewed, how the agency planned to continue work on detecting emerging zoonotic pathogens, as it has said it would do, how much funding it was allocating to a successor project and what role PREDICT was playing in the detection of and response to the current coronavirus.

The following month, Sen. Dianne Feinstein, Democrat of California, called for PREDICT’s reinstatement. She noted that research it supported had led to the discovery of several SARS-like coronaviruses related to the one causing the pandemic, including viruses in bats that could be transmitted directly to people. Public health professionals it had trained in several countries were working to control the outbreak, she wrote.

“The current deadly viral outbreak and its quick appearance in the United States make clear that PREDICT’s contributions to zoonotic disease surveillance and forecasting must continue,” she wrote. “We simply cannot afford to go backwards and jeopardize the success we’ve seen over the last 10 years.”

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