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 common in a number of species that regularly come into contact with humans, and they have a clear history of adapting themselves to human cells.
Being aware of viruses that have similar characteristics can help us recognize threats to future pandemics. Now researchers are taking the results of a massive virus survey and releasing a public database of hundreds of viruses, all of which are being assessed for how much risk the viruses pose to humans. And any viruses we discover can be plugged into the framework they developed, so we can quickly get information or threaten them.
What’s out there?
The effort grew out of a USAID-sponsored program called PREDICT, which was part of a series of efforts focused on zoonotic diseases, those that can cross species barriers and infect humans. The PREDICT project jointly conducted a survey of animal viruses with more than half a million individual samples taken from 75,000 animals. From the data, the project has identified more than 700 new viruses and another that has never been seen in the animal in which it was found.
Knowing the genome sequence of the viruses does not tell us much about the risk that viruses pose to humans. We can determine which proteins the viruses encode, but we are not at the point where we can look at the proteins and determine if they are more likely to infect humans. And besides, it’s not just infectivity that carries a risk. If the virus normally circulates in rare animals that humans avoid, the chances of it jumping to us are slim.
Factors abound, as well as differences of opinion among experts on how important these factors are. So it was a challenge to figure out how to evaluate these new viruses.
To find out what is important, the researchers got 150 virology and public health experts to consider 50 different potential risk factors, ranging from the host species that transported it to where it was found, to its evolutionary relationship to known viruses. The experts were asked to rank the importance of each of these risk factors, and the PREDICT team weighed each of its ratings based on the person’s expertise in each issue. (Thus, for example, the opinion of a virologist may count less on issues related to how often the host animal interacts with humans.)
Some of the key risk factors that were consistently highly rated were obvious: the frequency of interactions with humans and our livestock, the ability to infect a variety of hosts, and transmission methods. However, not every factor was considered very important, and seven of those evaluated were considered important. But we simply do not have enough data on most viruses to enable its evaluation.
Score leftover
The net result is a surplus score, the best estimate of the risk that each of these viruses poses to humans, uncomfortably rated on a score of 1 to 155 (this is what happens when you start with 50 factors that score 1-5 be, weigh it in varying degrees, and then discard some of it). As a test of its validity, the researchers looked at the top characterization of viruses; it was already known that all the first dozen people were infected.
SARS-CoV-2 was between two viruses that caused several outbreaks of hemorrhagic fever in Africa: Lassa and Ebola. It did not come out on top because the other viruses caused several outbreaks (SARS-CoV-2 only had one but made it count). We also know a lot more about their normal hosts, while we did not identify the species that was SARS-CoV-2 before it entered humans.
All the analyzes are made available via the Spillover website, which contains a list of all the viruses that have been analyzed so far. A quick overview of each divides the risk into three categories (based on the host in which it occurs, the environment of that host and the genetics of the virus). A detailed overview outlines each factor that we have enough data to evaluate.
In addition to the data available on these new viruses, Spillover is also a flexible sharing platform. Flexibly, as we learn more about what makes a virus a zoonotic threat, the researchers promise to update the analyzes for all the viruses in the database. And share, because the PREDICT team hopes the research community will add new viruses to judge as it is discovered. It is possible to create a risk score with as few as half a dozen viral properties.
Although these many new viruses are a good start, there are some obvious limitations. Because the researchers are already intensively detected, the researchers do not add flu viruses to their database. Second, although it represents a lot of work, the hundreds of viruses described here are a drop in the bucket compared to the 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 coming our way.
Yet the project is a valuable start. Several of the viruses that have not been described before are considered more threatening than viruses that we already know can make the leap in humans. Clearly, the target on those for study and closer supervision may have the potential for a significant payout, especially when compared to the global cost of the COVID-19 pandemic.
PNAS, 2021. DOI: 10.1073 / pnas.2002324118 (About DOIs).