Predicting the next pandemic: New online tool ranks viruses' potential to infect humans

A Mexican long-tongued bat is held by Mexico's National Autonomous University, UNAM, Ecology Institute Biologist Rodrigo Medellin after it was briefly captured for a study at the university's botanical gardens, amid the new coronavirus pandemic in Mexico City, Tuesday, March 16, 2021. (AP Photo/Marco Ugarte)

After the novel coronavirus made the leap from animals to humans and upended the world in the process, scientists are trying to prevent that from happening again with a new online tool that ranks viruses’ potential to become zoonotic.

The “Spillover: Viral Risk Ranking” application is an open-source risk assessment tool developed by scientists at the UC Davis in California, which includes contributions from experts all over the world.

It’s the first web application to rank the risk of zoonotic spillover and pandemic potential for newly-discovered viruses, according to a press release.

“SARS-CoV-2 is just one example of many thousands of viruses out there that have the potential to spill over from animals to humans,” said Zoe Grange, who led the development of SpillOver as a postdoctoral researcher with the UC Davis One Health Institute.

“We need to not only identify but also prioritize viral threats with the greatest spillover risk before another devastating pandemic happens. Our SpillOver Viral Risk Ranking tool is the starting point for building proactive solutions.”

The scientists said the online tool can serve as a “watch list” for newly discovered viruses to help policymakers and health scientists “prioritize them for further characterization, surveillance, and risk-reducing interventions.”

Grange said governments can filter by country in order to see which viruses may pose a risk and view the hosts the virus has been found in.

“They could use that kind of watch list within their country to inform their own disease surveillance, their own prioritization within their government and policy decisions,” she told CTVNews.ca during a telephone interview from Scotland on Thursday. 

In addition to the online tool, the scientists published a study in the journal PNAS, in which they ranked the spillover potential of 887 wildlife viruses using data from testing more than 500,000 samples from 74,635 animals collected as part of a virus discovery project and public records.

To do this, they created a “credit-like score” for viruses based on 31 key risk factors about the virus and hosts, such as the number of species the virus is known to infect and the risk of human interaction with an animal host.

Grange said the risk factors can be divided into three broad categories, which include information about the host, the virus, and the environment.

“Why we have so many risk factors is that it's very complicated,” she explained. “Not one of them would potentially cause a virus to spill over, it can be a combination of all of them.”

The tool was also designed to be adaptable, Grange said, so they can change, update, remove, and add risk factors as they learn more about the viruses.

SPILLOVER RISK

According to their findings, the top 12 viruses on the list were known human pathogens with the Lassa virus taking the top spot, followed by SARS-CoV-2, and the Ebola virus ranked in third place.

The animal vector for the Lassa virus is primarily rats. For Ebola, the animal source is believed to be bats or nonhuman primates, such as chimpanzees and apes. The animal origin for SARS-CoV-2 is still unknown, but it’s been detected in minks, lions, and tigers.

While it may seem surprising that SARS-CoV-2 was ranked second on the list given that it has already caused a pandemic, the researchers explained this is because there is less data available for it than other known viruses.

“At the time of publication, we do not yet have key information about the natural wildlife host(s) that would have allowed the tool to more accurately estimate the spillover risk of SARS CoV-2, including number and range of host species, geographic distribution of hosts, and types of environments in which the hosts live,” the study noted.

The researchers said they expect SARS-CoV-2 to rank higher on the list as more information becomes available.

Regardless, the scientists said the point of the tool is to identify viruses that have not yet resulted in a pandemic, but may have the capacity to do so in the future.

“So the tool is designed really for newly discovered viruses, we've put in zoonotic viruses kind of just as a comparison, as a validation,” Grange explained. “We expected that we would see the zoonotic viruses at the top because they’ve already gone from wildlife to humans.”

As for the ones that haven’t spilled over yet, a couple of top-ranking viruses include two severe acute respiratory syndrome (SARS)-related coronaviruses that have been detected in bats: SARS-related betacoronavirus Rp3 and SARS-related bat coronavirus RsSHC014.

The tool’s developers said the rankings may change as more data is inputted from other researchers around the world.

The web application allows scientists to contribute data on existing viruses as well as assess the risk of new viruses using the “Rank Your Virus” feature.

“We thought we should actually make it more useful for other people, and make it an interactive kind of resource so that the general public and policymakers and scientists around the world could view and interact with our results,” Grange said. “But not only that, they could do their own ranking and they could, if they've discovered viruses, they can enter in their information.”

The researchers hope the tool will start a global conversation about new virus threats and encourage real-time scientific collaboration around the world.

“SpillOver can help advance our understanding of viral health threats and enable us to act to reduce the risk of spillover before pandemics can catch fire,” one of the study’s authors, Jonna Mazet, a professor at the UC Davis School of veterinary medicine, said.