Scientists change the ways they hunt the vast virosphere

When a team of virologists named SARS-CoV-2, they had to move the virus to the head of a very, very long line.

In recent years, scientists have discovered that the world of virus diversity — what they sometimes call the virosphere — is unimaginably vast. They have uncovered hundreds of thousands of new species that have yet to be named. And they suspect that there are millions, perhaps even trillions, of species waiting to be found. "Suffice to say that we have only sampled a minuscule fraction of the virosphere," said Edward Holmes of the University of Sydney in Australia.

With the discovery of viruses in the late 1800s, scientists soon recognized that different species caused different diseases — rabies and influenza, for example. Later, virologists learned how to recognize new kinds of viruses by growing them in labs, where subtler biological features emerged.

After decades of this painstaking work, virologists have officially named 6,828 species of viruses. That's a paltry count when you consider that entomologists have named 380,000 species of beetles alone.

But in recent years, virologists have changed the way they hunt. Now they look for bits of genetic material in samples — water, mud, blood — and use sophisticated computer programs to recognize viral genes.

Matthew Sullivan, a virologist at Ohio State University, has used this method to search for viruses that infect life in the ocean. He and his colleagues analyzed genetic material in seawater collected from around the world. Some genes belonged to species known to science. But many were new. In 2016, Sullivan and his colleagues reported more than 15,000 viruses, each representing a new species.

That was more than twice as many species as all the previously identified viruses. And with that, Sullivan thought he and his colleagues had pretty much finished off the diversity of viruses in the sea. But they went on collecting more water, and invented new ways to search it for the genetic material of viruses. In 2019, they reported finding a total of 200,000 species.

Other researchers are discovering thousands of new viruses as well. "Right now, we are in the exponential phase," said Dr. Jens H. Kuhn, lead virologist at the Integrated Research Facility at Fort Detrick in Maryland. "If someone gives me a million dollars and I go out and sample sea cucumbers, I will present you with 10,000 new viruses."

The viruses that infect humans are the best understood. But only about 250 species of viruses choose us as their host — "an insignificant fraction of the virosphere infect humans," Holmes said.

While hundreds of thousands of new species await their own names, virologists believe that far more await discovery. Holmes estimates that the viruses infecting animals, plants, fungi and protozoans (a group called eukaryotes) number 100 million species.

Bacteria and other single-celled microbes belong to a group called prokaryotes. In a paper published March 4 in Microbiology and Molecular Biology Reviews, Kuhn and his colleagues argued that there are, at minimum, 100 million species of viruses that infect prokaryotes.

But some researchers suspect there are many more species of prokaryotes — which would mean many more species of viruses. The true figure might be as high as 10 trillion.

Scientists who study animals and plants can rely on the classification system established by Carl Linnaeus in the 1700s. Our species belongs to the class Mammalia, for instance, and, above that, the animal kingdom. Virologists have struggled to figure out the classes and kingdoms of the virosphere. Viruses have a penchant for trading genes with other species, making it hard to draw bright lines between groups of them.

And very often, a new virus simply makes no sense. An extreme example came to light in February when scientists found a new virus they named Yaravirus. Of Yaravirus' 74 genes, 68 are unlike any ever found in any virus.

In recent years, Kuhn and his colleagues have sought to tame this chaos. They have developed what they call a "megataxonomy" to classify viruses based on whether they carried one or more of a few "hallmark genes." They also looked for groups of species that trade genes among each other, and less so with other groups.

"A coherent account of the global organization of the virus world is now within reach," they wrote in their new paper.