Jens Kuhn wasn’t surprised people accused him, mockingly, of doing drugs. He’s used to hate mail. After all, he has the most despised job in virology: He’s a taxonomist, a categorizer of the viral world.
“We have this joke,” he said. “When you go to a nice dinner, you shall not discuss sex, politics, religion and taxonomy.”
Mostly, other researchers are content with that, regarding what Kuhn and his colleagues at the International Committee on Taxonomy of Viruses, or ICTV, do as roughly equivalent to biological stamp collecting. Recently, though, they did something so brazen, so high-handed, that outrage was unavoidable: They essentially renamed all the viruses.
The change unfolded slowly, over the course of the last four years. But it largely escaped notice until December, when the U.S. National Library of Medicine said it would change names in its databases of genes and viruses to comply with the ICTV’s new monikers.
Many new names sounded as if they’d been cooked up by a medieval monk. HIV-1 would henceforth be known as Lentivirus humimdef1. SARs-CoV-2, the virus that causes Covid, would be known as Betacoronavirus pandemicum. Ebola was now Orthoebolavirus zairense.
“Somebody needs to take away whatever drugs the committee is on,” wrote Kristian Andersen, an HIV researcher at Scripps Institute, on Bluesky. Boghuma Titanji, an HIV researcher at Emory University, chimed in: “How do I get on this committee which sounds like they do mushrooms while renaming pathogens😂?”
Angela Rasmussen, an emerging pathogens researcher at the University of Saskatchewan, seemed ready to lay siege to Kuhn’s house. “Down with the ever-tightening iron-fisted grip of taxonomic dictators,” she wrote.
Kuhn, the autocrat, mainly rolled his eyes. He hated some of the names, too. “Salt in my wounds,” he called syllabic stews like Lentivirus humimdef1. But he pointed out that only the species names had been changed, not the common name. Researchers, he said, can keep using HIV in papers the same way researchers use “mouse” and not mus musculus. (Critics argue that, with viruses, it’s not so simple, and note the new names have already tripped up such august bodies as the World Health Organization.)
And Kuhn insisted it had to be done. Viral taxonomy had to be revolutionized for the simple reason that virology itself is undergoing a revolution.
A torrent of findings in places as remote as Antarctic ponds and as near as your colon has upended researchers’ understanding of just how vast this nether kingdom of life truly is. Where scientists once counted a couple thousand known viruses, they now know there are likely billions.
The discovery of this virosphere, as researchers call it, is one of the 21st century’s unheralded breakthroughs. Only an infinitesimal percentage of viruses can infect humans, let alone cause disease. Yet collectively, the virosphere has uncharted effects on climate, ecosystems and human health; it holds keys to the origins of our most feared pathogens; and it is a bottomless trove of potential microbial tools, refined through eons spent trying to invade and subdue cells, some of which could be harnessed as the next CRISPR.
To navigate this Vernian jungle of gene and protein, some researchers argue they need a new taxonomy. Slowly, the committee (and its subcommittees) has been giving viruses new, two-part names — as have long existed for cellular organisms — that indicate both the specific species and its position in the broader viral world.
“The diversity is useless and incomprehensible without a formal taxonomy,” said Eugene Koonin, an NIH researcher who has led some of the efforts. And that taxonomy can’t just be for the new viruses. “It must be systemic and go throughout.”
Critics don’t just take issue with the sillier names. Echoing an argument dating to Darwin, they say it’s impossible to separate viruses into species, a clumsy attempt to impose human categories on a viral world that is pure blur.
Everyvirus everywhere
For over 200 years, life on Earth has been named and categorized according to a system set by the 18th century Swedish botanist Carl Linnaeus. Many of Linnaeus’ classifications have since been redrawn but the system itself stuck.
Every species is given a two-part Latinized name. The first word is the genus, a collection of connected species. The second is an “epithet” for the species itself. (As in Homo sapiens, for humans, Homo neanderthalensis for Neanderthals.) It both gives specificity and indicates placement in a larger biological world.
Virologists fought for over half a century over whether viruses should be classified by the same system.
Scientists learned of viruses in the late 1800s, finding a tobacco-wasting pathogen so minute it could pass through porcelain. Yet viruses remained a dinky sideshow beside the World’s Fair of animal, plant and bacterial life — invisible even to microscopes, hard to isolate, harder to study. In 1971, when the ICTV issued its first report, the committee could still list only 290 viruses. There were by contrast already 20,000 known species of roundworm.
Virology simply didn’t have enough evolutionary information to adopt a Linnaean system, Kuhn said.
Viruses were instead lumped into loose buckets, based on factors like their host species or the shape of their proteins. The logic of 16th century explorers prevailed: Find it, you can name it. “It was a wild, wild west,” said Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham.
Then about 20 years ago, researchers began finding viruses everywhere. The revolution came thanks to a powerful new field called metagenomics. Instead of sequencing a single organism’s genome, researchers started taking samples from nature and sequencing the vast soup of RNA and DNA. Then they used computational techniques to interpret the results, searching for similarities to known viral genes.
It was like sending flares into the microbial depths, revealing vast viral kingdoms in places, like the ocean, once thought to be barren of them. Virologists, who had been largely limited to studying viruses they could culture, often at great expense, could suddenly look through a sample of sea water and find thousands of species. The world’s driest deserts were shown to be populated with microbial Dubais. Bat guano, crayfish, and spiders contained their own Lilliputian city-states.
“We had no idea that they were everywhere, at such scale, and it happened so fast,” said F. Murilo Zerbini, a plant virologist at the Federal University of Viçosa in Brazil and head of the ICTV. He recently gave a talk titled: “Everyvirus everywhere all at once.”
It was virology’s Hubble Space Telescope moment. It set off a series of efforts to quantify, through metagenomic sequencing, the potential pandemic pathogens lurking in animals. Among taxonomists, it sparked debates about categorizing. Could you even call a genetic signature found by a computer, never isolated or photographed, a species? In 2016, the ICTV decided yes. Paleontologists don’t need a living specimen, after all.
For taxonomists like Khun, it was an opportunity to finally bring viruses in line with the rest of life.
New sequencing information would allow researchers to create a taxonomy grounded in evolutionary genetics. Ideally, the new names would convey information about structure and evolution, which could indicate, say, susceptibility to a certain antiviral. “Pity the ICTV,” one researcher wrote in 2018, assessing the task of naming tens of thousands of new species.
Order to chaos vs. ‘word salad’
There’s a reason some researchers hate taxonomy. It’s a sleepy meerkat of a scientific discipline, occasionally popping out to rename your favorite organism or say something absurd about the natural world: That there are, secretly, four species of giraffe, or that microbiologists’ had been misclassifying bacteria and fungi for decades; that humans arguably belong to the same domain as the microbes on deep sea vents; or, sheepishly, that “fish” do not exist.
All this many do for free. Being a taxonomist is often a volunteer position. Kuhn spends most of his days studying Ebola for the National Institutes of Health. Yet a childlike enthusiasm for obscure critters and a Genesis-esque desire to wrest order out of chaos has kept him traveling once a year for the 15-hour-long ICTV meetings and fighting with other virologists the rest of the time. “I am totally in love with viruses, they are absolutely awesome,” said Kuhn, who grew up reading encyclopedias to identify the birds and mice of his native Germany.
Critics are missing the point, he said: “I think the problem is that people do not seem to understand that taxonomy is not a service for them. Taxonomy is a sub-discipline of evolutionary biology. And evolutionary biology works for evolutionary biologists.”
But taxonomists don’t want to upend the tree of life with every new finding, so even they must negotiate between evolutionary biology and older, less strictly scientific sensibilities.
Humans are a textbook example. Homo sapiens and Homo neanderthalensis are still considered independent species, even though modern genetics suggest they interbred heavily and that the entire genus Homo probably shouldn’t exist — we are but a subset of monkeys. “There is always an arbitrariness to it,” Kuhn said.
With viruses it becomes even murkier. For one, there is no virus tree of life. All of cellular life emerged from a single common ancestor. But recent metagenomic analyses suggest viruses emerged repeatedly throughout history, by multiple mechanisms.
They’re tiny. They evolve quickly. Where do you draw the line between one virus and another?
Within the ICTV have been intense debates. New computationalists debated pipette-and-petri-dish virologists, in a microbial re-enactment of Moneyball.
The ICTV’s initial impulse to use only Latin drew an uproar from representatives from the U.S. and the U.K. So some committees have gone with Latinized names, as in measles (Morbillivirus hominis). Others chose strange contractions, such as HIV-1 (Lentivirus is a well-established genus, but humimdef1 contracts human immunodeficiency virus-1).
Nikos Vasilakis, a University of Texas researcher, said he led a “revolt” in 2018 at the ICTV after it decided to classify several closely related bunyaviruses, a class of rodent and insect-borne pathogens, as the same species. Vasilakis argued it was dangerous. Some of those viruses could likely cause serious hemorrhagic fevers. Others are far more benign. Classifying them all the same species could make it hard to properly write biosafety procedures.
But the harshest words have come from outside the committee, on grounds theoretical, practical and societal.
“If you have a viral ‘species’ defined and all of a sudden you discover a highly related virus that is 1% different, maybe 2% different, or maybe even 5% different — is that now a new species or is it the same species?” Andersen, the Scripps HIV researcher, wrote in an email. “What if it is 20% different, but is causing the same infections and disease? All of this gets arbitrary very quickly and as we continue to expand the viral tree, becomes very unstable.”
HIV-1 itself seems to violate the ICTV’s own rule for defining species. Species are supposed to descend from a single common ancestor, but HIV-1 arose from at least six spillovers over a century. And similar to humans, it is genetically only a small step from the vastly older simian immunodeficiency virus, or SIV. But it would’ve been awfully strange to strip one of history’s deadliest pathogens of its status.
Andersen’s hackles were raised after he encountered a World Health Organization report on potential pandemic threat pathogens, including the lassa fever viruses Andersen’s group studies. The report called them “Mammarenavirus
lassaense.” Andersen had no idea what he was reading, and he knew the public wouldn’t either. “It’s word salad,” he said. “It’s nonsense.”
Kuhn said the WHO report “did everything wrong.” Scientists, he said, should stick to common names, using species only in methods sections or at the top of an article. But Andersen predicted more confusion.
“Despite what Jens says, these new names will start to be forced onto people via publications, grants, articles, etc.,” said Andersen. “Mark my words.”
Others have seen their actual work disrupted. Gytis Dudas, a virologist at Vilnius University, said he was analyzing large amounts of genetic data from mosquitos in California, to identify novel RNA viruses. “And pretty much right in the middle of our analyses, the whole taxonomy for viruses changes on Genbank,” he said, referring to a database of genes across life. It impeded their ability to sort through the sequence data.
Then there’s the startling decision by the committee on pox viruses to, even as the ICTV rechristened thousands of species, keep the name monkeypox (full name Orthopoxvirus monkeypox). Activists and researchers had pushed to change the disease and virus to mpox, to destigmatize an infection that has now spread widely and particularly affected queer men.
“It’s mystifying,” said Rasmussen, the University of Saskatchewan virologist, noting that a name like “Orthopoxvirus mpox” would comply with ICTV’s naming rules. “There’s really no reason to keep it monkeypox…. this feels very dictatorial.”
Lefkowitz, a member of the pox subcommittee, said they “wanted to have stability in the naming.” Zerbini said he would have changed the name.
Regardless, Kuhn, Zerbini and the rest of the ICTV say they are confident the rest of the field will eventually get used to the changes, like internet users adjusting to a new website design.
“You don’t make an omelet without breaking some eggs,” said Zerbini. “A few years go by, and things will just settle and stabilize.”
Perhaps. The virosphere keeps getting bigger, and each new discovery threatens to rearrange the taxonomy. In November, using a new artificial intelligence approach, researchers in China reported they had found over 161,000 virus species. Many look nothing like a typical virus. Almost none have yet been named.