A Minimum of 320,000 Mammalian Viruses Await Discovery

It’s the stuff of The Hot Zone, Outbreak and Contagion: a deadly new virus has emerged from some dark corner of the jungle. While victims succumb to a horrendous death and drop like poisoned flies, virus hunters race to identify patient zero, who turns out to have recently spent time on a pig farm. Those pigs, they discover, are exposed to fruit bat droppings, which rain down from the trees above. Another animal virus made the jump to humans. And while you probably know that such jumps have happened before, brace yourself: Scientists estimate that at least 320,000 such viruses await discovery.

The media is currently abuzz with talk of the MERS coronavirus, which might have originated in bats and then used camels as an additional host. Before that, we had SARS (from small mammals); Nipah virus (fruit bats and pigs); and swine flu. Zoonoses–or illnesses that originate in animals and cross over into humans–account for around 70 percent of all emerging viral diseases, including HIV/AIDS, West Nile and Ebola. Zoonoses originating from mammals are especially problematic. They tend to prove the most readily transmittable to people because the viruses that evolved to exploit our closest furry relatives tend to be most adept at navigating our own warm-blooded bodies. As we encroach upon new tracts of forest where dangerous pathogens may lurk, and then jet-set around the world with the pathogens hitching a ride, the rate of such emerging infectious disease outbreaks is only increasing.

Yet we know very little about “virodiversity,” or the number, types and abundance of viruses in the world. We don’t even have a handle on how many viruses may exist in any given animal species, despite those viruses potentially posing the greatest threat to our lives and economies. 

In an ambitious new study from the American Society for Microbiology’s online journal mBio, more than 20 leading virus hunters got together to try and solve this mystery. Rather than just tackle a single species, they decided to take on an entire class of animals: mammals. Collecting samples from all 5,500 known mammals wasn’t an option, so they chose a representative species, the Indian flying fox–a type of bat that is the largest flying mammal in the world and is the carrier of the Nipah virus–to supply their viral data, from which they could then extrapolate to estimate broader diversity among all mammals.

They collected nearly 2,000 samples from flying foxes trapped in Bangladesh (they let the bats go afterwards, unharmed, and wore protective gear to make sure they themselves did not become infected with the next Nipah virus), then performed nearly 13,000 genetic analyses to test for viral traces in those samples. They discovered 55 viruses from nine different families, only five of which–two bocaviruses, an adenovirus, a betacoronavirus, and a gammacoronavirus–were already known to science. Ten of the newly discovered viruses were in the same family as the deadly Nipah virus.

Additionally, a commonly used statistical test allowed the researchers to estimate that their sampling most likely missed three other, more elusive viruses, bringing the flying foxes’ tally to an estimated 58 viruses. From there, they extrapolated this figure to all mammals, calculating that, at minimum, around 320,000 viruses await discovery in these animals.

While several hundred thousand may sound like a lot, that number is much more manageable than the millions of viruses that some researchers supposed might be out there. In fact,, a species richness estimation program they used, called the Chao 2, indicated that samples from just 500 more animals would be needed to discover 85 percent of those 320,000 viruses. On the other hand, discovering the remaining 15 percent, which accounts for only the rarest of the viral bunch, would require more than ten times as many samples. The team calculated that the 85 percent effort would require about $1.4 billion in funding, which sounds like a lot but is only a fraction of the $16 billion that a single disease pandemic, SARS, has cost over the last ten years in economic impacts. Divided over a 10 year period, we could put the mystery of mammalian viruses to rest for just $140 million per year, they write.

“For decades, we’ve faced the threat of future pandemics without knowing how many viruses are lurking in the environment, in wildlife, waiting to emerge,” Peter Daszak, the study’s lead author, said in a statement. “Finally we have a breakthrough–there aren’t millions of unknown virus, just a few hundred thousand, and given the technology we have it’s possible that in my lifetime, we’ll know the identity of every unknown virus on the planet.”

The researchers did make several assumptions in their study. They assumed that 58 is a reasonable estimate for the number of viruses harbored by every mammal species. that viruses are not shared by different hosts. that mammalian viruses only belong within nine families. and that their tests for viral diversity were dependable. They acknowledge that their initial calculation is only a rough estimate, and they plan to repeat the experiment in primates in Bangladesh and bats in Mexico to add more robustness to their figure. Unfortunately, they predict that their estimate of total viral diversity will likely increase with more data.

Aside from elucidating the wondrous diversity of the natural world, discovering and classifying all of these viruses could significantly help humans. Rather than flounder for months trying to discover the origins of a virus–as scientists are still struggling to do with MERS–a central database based on extensive surveys of animals would expedite the process of identifying any new virus that emerges in humans. Knowing where a virus comes from is important for cutting off the source of infection, as demonstrated in the culling of hundreds of thousands of chickens, civets and pigs and other animals in recent viral outbreaks. But snagging the source quickly may allow animal handlers to better isolate tainted populations of animals, allowing the rest to be spared and keeping humans away from those tainted few.

Unfortunately, knowing what viruses are out there cannot prevent an emerging viral disease from striking a wide swath of people. But it can help lessen the blow, for example, by giving researchers more time to develop rapid diagnostic tests for disease intervention and control.

“To quote Benjamin Franklin, an ounce of prevention is worth a pound of cure,” said W. Ian Lipkin, director of the Center for Infection and Immunity at Columbia University’s Mailman School of Public Health and the study’s senior author. “Our goal is to provide the viral intelligence needed for the global public health community to anticipate and respond to the continuous challenge of emerging infectious diseases.” 

Rachel Nuwer | | READ MORE

Rachel Nuwer is a freelance science writer based in Brooklyn.