Mar. 13 2020

The Kind of Outbreak Our Scientists Knew Would Happen

“We’ve been expecting this.” These are the words of Columbia Mailman School Professor Simon Anthony, one of the world’s experts on coronavirus. Based on years of studying coronaviruses and how they spillover from animals into humans, he knew an outbreak like COVID-19 was bound to happen sooner or later.

“We didn’t know which virus would emerge or where, but the fact that it happened is no surprise at all,” says Anthony, who works in the Center for Infection and Immunity and was a key member of PREDICT, the United States Agency for International Development (USAID)-funded global program to detect and discover viruses in animal hosts with pandemic potential. The program, unfortunately, has all but ceased operations.

In October of last year, weeks before the first COVID-19 cases emerged in China, the USAID abruptly shuttered PREDICT. “USAID has been pioneering supporters of pandemic prevention, but the irony of the timing is astonishing,” Anthony observes.

As the pandemic intensifies, several prominent allies of PREDICT are questioning the program’s closing. In January, Senators Angus King (Maine) and Elizabeth Warren (Massachusetts) co-wrote a letter to USAID requesting information about the agency’s decision to close PREDICT. “Addressing and preventing the spread of coronavirus and potential pandemic disease outbreaks is a serious matter that requires adequate resources,” the lawmakers wrote in part. Days later, Senator Dianne Feinstein (California) sent her own letter that called for the program’s reinstatement citing the discovery of nearly 1,000 new viruses, including those similar to SARS-Cov-2, the virus responsible for COVID-19.

Coronavirus Discoveries

Over the years, seven coronaviruses have now been identified in humans—and all of them are thought to have spilled over from animals. Four of the coronaviruses became regular human viruses that are now among those that trigger the common cold; the remaining three are the global threats whose names are familiar to us: SARS (Severe Acute Respiratory Syndrome), MERS (Middle East Respiratory Syndrome), and SARS-Cov-2, each of which trigger respiratory disease with symptoms of fever, cough, and shortness of breath.

PREDICT launched in 2009, between the 2003 SARS outbreak and the 2012 MERS outbreak—both of which involved coronaviruses. Naturally, the virus family was among those prioritized by the scientific group (Ebola was another). Early on, the scientists established a simple yet highly effective method to look for viruses. Anthony and collaborators, including U.C. Davis, the EcoHealth Alliance, and Wildlife Conservation Society, collected and tested biological samples from wildlife in 30 countries around the world. “The result was a global dataset that is unprecedented,” he says.

Over the last decade, research by PREDICT scientists has opened a window into the natural ecology of coronaviruses and other viral threats, providing a clearer picture of where and how these coronaviruses made the jump from animals to humans—and how other new viruses could make the jump, too.

A 2017 study by Anthony and his collaborators reported that bats were the major animal reservoir for coronaviruses worldwide. Of the 100 different coronaviruses they found, more than 98 percent of the animals harboring them were bats. Extrapolating to all 1,400 bat species, they estimate a total of more than 3,700 coronaviruses are carried by these animals worldwide—most of which have yet to be detected and described.

As you might expect, the researchers discovered that areas abundant with many species of bats are also abundant with coronaviruses. The paper, which appeared in the journal Virus Evolution, provided a map highlighting these coronavirus hotspots—including areas of Africa and Southeast Asia that are predicted to be hotspots for SARS-like viruses. SARS-Cov-2 emerged in Wuhan, China, which is on the periphery of a hotspot. It is likely that patient zero was infected either directly from a bat or through an intermediary animal.

Another paper the PREDICT team published the same year described their discovery in a bat of a novel virus closely resembling MERS but which was unable to spill over to humans. While its genetics appear similar to the MERS-coronavirus, the paper in the journal mBio points to differences in its spike gene—the segment of the virus responsible for invading cells. “Coronaviruses have a propensity to change hosts,” explains Anthony. “They recombine and swap in key proteins that act as a key to get inside host cells. When they gain this ability, that’s when a spillover could happen.”

What’s Next

While there is nothing to celebrate about the pandemic, Anthony is heartened by the renewed recognition of the how significant emerging zoonotic diseases can be, and he hopes that governments and funding agencies move to invest more in pandemic prevention and research to understand how and why spillover events happen. “We are in the business of rare events,” Anthony notes. He admits it can be challenging to maintain funding for programs that require long-term investment, likening the potential for waning support to weakening antibodies after an initial immune response. We are seeing now just how disruptive pandemics can be to every corner of the world and every aspect of our lives.”

Another challenge for an expensive scientific enterprise is the lack of immediate, life-saving results. “We can’t say we stopped an outbreak from happening,” he says. “What we can do is generate the foundational knowledge necessary to make useful predictions about what virus might emerge as the next global threat.”

In the background of the COVID-19 pandemic, Anthony and his collaborators consider the specific ways the project, if reinstated, could continue to make meaningful contributions. “We have trained hundreds of field and laboratory personnel that could be surveying wildlife to identify the reservoir or reservoirs of this virus. We could also continue to look for undiscovered viruses. While the world is rightly focused on one coronavirus right now, it’s important to remember that there are likely 3,700 other coronaviruses waiting in the wings, any one of which could do the same as this outbreak or worse.”