We did not know about the SARS-CoV-2 virus until it appeared in humans. But previous experience with other coronaviruses that have jumped into humans (SARS and MERS) has told us that something like COVID-19 can pose a risk. Coronaviruses are prevalent in a number of species that have frequent contact with humans and have a clear history of being able to adapt to human cells.
Awareness of viruses that have similar properties can help us identify threats to future pandemics. Now researchers are taking the results of a massive survey of viruses and publishing a public database with hundreds of viruses, all of which have assessed how much risk viruses pose to humans. And any viruses we detect can be included in the framework they’ve developed so we can get quick information on whether it’s threatening.
What’s out there?
The effort stemmed from a USAID-sponsored program called PREDICT, and was part of a series of efforts focused on zoonotic diseases, those that can cross species barriers and infect humans. Together, the PREDICT project conducted a massive study of animal viruses, using over half a million individual samples taken from 75,000 animals. From that data, the project identified over 700 new viruses and another that was never seen in the animal in which it was found.
Knowing the genomic sequence of a virus doesn’t tell us much about the risk that viruses pose to humans. We can understand which proteins viruses encode, but we are not in a place where we can look at those proteins and determine if a virus is more likely to infect humans. And besides, risk is not just contagious. If the virus circulates normally in rare animals that avoid humans, the chances of it jumping to us are slim.
There are plenty of factors, as well as disagreements among experts about how important these factors are. So discovering how to evaluate these new viruses was a challenge.
To understand what’s important, the researchers got 150 virology and public health experts to consider 50 different potential risk factors, ranging from the type of host that transmitted it to where it was found, to evolutionary links to known viruses. Experts were asked to rank the importance of each of these risk factors, and the PREDICT team weighed each of their assessments based on the expertise of the person in each issue. (Thus, for example, the opinion of a virologist might be less likely to count on questions about how often his host animal communicates with humans.)
Obvious were some of the important risk factors that were consistently highly rated: the frequency of interactions with humans and our livestock, the ability to infect various hosts, and the modes of transmission. But not every factor was rated as very significant, and seven of those rated were rated as important. But we just don’t have enough data on most viruses to be able to evaluate them.
The net score is the result of the spillover, the best risk assessment that each of these viruses poses to humans, clumsily rated at a score of 1 to 155 (this happens when you start with 50 factors with scores of 1-5, weigh them in varying degrees, and then throw out some of them). As a test of its validity, the researchers looked at the best virus scores; all the top ten were already known to have infected people.
SARS-CoV-2 ranked exactly between the two viruses that caused multiple outbreaks of hemorrhagic fever in Africa: Lassa and Ebola. It didn’t break out at the top because those other viruses caused multiple outbreaks (SARS-CoV-2 had only one, but it counted). We also know a lot more about their normal hosts, although we did not identify the type of SARS-CoV-2 before it migrated to humans.
All analyzes are available through the Spillover website, which includes a ranked list of all viruses analyzed so far. A quick review of each divides the risk into three categories (based on the host in which it is located, the environment of that host, and the genetics of the virus). The detailed breakdown breaks down each individual factor for which we have sufficient data to estimate.
In addition to making information about these new viruses available, Spillover is also a flexible sharing platform. Flexible, because as we learn more about what makes a virus a zoonotic threat, researchers promise to update analyzes for all viruses in the database. And sharing, because the PREDICT team hopes the research community will add new viruses that will be evaluated as they are discovered. It is possible to create a risk assessment with only half a dozen viral properties.
While so many new viruses are a great start, there are a few obvious limitations. First of all, because they are already intensively monitored, researchers do not add flu viruses to their database. Second, while representing a lot of work, the hundreds of viruses described here are down from an estimated 1.7 million viruses that infect mammals and birds. We have a lot more work to do if we really want to avoid the next pandemic creeping up on us.
Still, the project is a worthwhile start. Several viruses that have not been described before have been rated as more dangerous than viruses that we already know can make a leap into humans. Obviously directing those to studies and more careful monitoring is the potential for significant payouts, especially compared to the global cost of the COVID-19 pandemic.
PNAS, 2021. DOI: 10.1073 / pnas.2002324118 (About DOIs).