Virologists are debating whether to establish a standardized system for naming virus species later this year. Some researchers say that the current way viruses are named is disorganized and that there is an urgent need for such a system. But others say that now is not the time to engage in an academic discussion over naming conventions, when virologists are focused on fighting the pandemic.
Virologists currently name species — the most basic taxonomic rank — in several ways, often on the basis of where the virus is found, the animals that host it or the disease it causes. Many argue that the lack of conventions is frustrating for researchers who identify new viruses regularly. It also creates confusion when the virus’s common name is the same as its species name, as with variola virus (Variola virus), which causes smallpox.
The International Committee on Taxonomy of Viruses (ICTV), a body that oversees naming of virus taxa, has proposed1 a naming system, which will be put to a vote in October. If a system is implemented, it could change how almost all of the more than 6,500 known viral species are named.
“It is obviously good and correct to have a standardized classification scheme for naming virus species, as the current ‘system’ is utterly chaotic and a major source of frustration for those of us that regularly identify novel viruses,” says Edward Holmes, a virologist at the University of Sydney in Australia. But the effort “can hardly be classed as ‘urgent’ compared to a global pandemic”, he says.
Other researchers think now is the perfect time for such an exercise. There has been an acceleration in the number of viruses and species being identified over the past 15 years, thanks to genome-sequencing technology, says Eric Delwart, a virologist at University of California, San Francisco. “This is the golden age of virus discovery. It is a good time to start organizing the deluge of viral genomes,” he says.
The debate comes amid discussions about another naming issue: how to classify the tens of thousands of genomes of SARS-CoV-2, the virus that causes COVID-19, being sequenced around the world. Groups of evolutionarily related viruses of the same species are often described as lineages. It is important to track them in case mutations emerge that make the virus more infectious or more dangerous. The ICTV sets rules only down to the level of the species, but Holmes and other virologists independent of the ICTV have proposed2 a method for naming the SARS-CoV-2 lineages.
Time pressure
Currently, the only requirements for a viral species name are that it is italicized (with the first word capitalized) and appropriately unambiguous, and that it uses as few words as possible — although some names are long, such as Tomato yellow leaf curl Indonesia virus. On 3 December, members of the ICTV’s executive committee published a paper1 in Archives of Virology proposing a new format in which species names would be limited to two words.
The first word would be the genus (ending in -virus), which is defined as a group of species that share some common characteristics. The paper proposes three options for the second word. Option one is always to use a Latinized term, in line with similar rules for naming biological organisms, such as Homo sapiens. The second option would restrict the second word to numbers or letters, as in Alphacoronavirus 1, and the third would open it up to any set of characters. So, existing names would be condensed to either a single, potentially Latinized, word, or a number or letter.
The paper, which is the result of several years of public deliberation, called on researchers to provide feedback by 30 June, ahead of a decision at the committee’s next meeting, in October. That decision would then be put to a vote by all ICTV members.
But several virologists say they did not notice the paper at the time, and were then swept up in the coronavirus response. “In an ideal world, we would all be looking at these journals, but the amount of literature we have to keep up with has mushroomed,” says Katherine Spindler, a virologist at the University of Michigan in Ann Arbor and secretary-treasurer of the American Society for Virology (ASV) — one of the world’s largest virology communities, with more than 3,000 members in some 20 countries. “Taxonomy doesn’t affect what I do. It only happens to come up when I write a paper,” says Spindler, who learnt of the consultation after the 30 June deadline. She and the rest of the ASV executive committee wrote to the ICTV committee on 9 July, stating that their members had not had sufficient time to consider the issue.
The Australasian Virology Society (AVS), representing some 700 members in Australia and New Zealand, sent its own letter to the ICTV on 4 July. “We believe that 2020, the year of COVID-19, is not an appropriate time to undertake a major change of naming virus species. Our members are stretched to the limit with other tasks, and many have not had time to properly consider this matter,” the letter stated.
In response to concerns about the timing, ICTV president Andrew Davison, a virologist at the University of Glasgow, UK, says that a version of the proposal has been on the ICTV agenda for nearly two years, but he expects the committee to consider all the relevant factors at its meeting. “I agree that these are unusual times,” he says.
Learning Latin
In their letters, the ASV and AVS also state that they oppose the idea of mandating Latinized names, because that would require virologists to learn Latin grammar, and would be cumbersome to implement. Both groups prefer the option in which any word can be used as the species name, although the AVS’s top preference would be to maintain the status quo, its letter states. “There is no need to overhaul the whole system,” says AVS president Gilda Tachedjian, a virologist at the Burnet Institute in Melbourne, Australia.
But when naming a species, virologists would only need to know the appropriate Latin suffix, says Jens Kuhn, a virologist at the Integrated Research Facility at Fort Detrick, Maryland, and a member of the ICTV executive committee. Latin terms would also be universal, not requiring translation in papers published in languages other than English, he says.
SARS-CoV-2 diversity
Virologists are less conflicted about the urgent need for coherence in naming the many SARS-CoV-2 lineages, which are being labelled in an ad hoc manner. “We are clearly going to end up with more than 100,000 complete genome sequences of SARS-CoV-2, which is staggering. It is obviously important to come up with a simple, rational and widely adopted scheme to classify all this diversity,” says Holmes.
No official body decides how to name viral lineages. “We’ve stepped in to try and sort this out. Whether people will adopt it is another matter: it’s really up to the users,” says Holmes.
He and his colleagues have proposed a dynamic method that prioritizes naming lineages that have seeded an epidemic. The lineages would be labelled active, unobserved or inactive depending on how recently they have been isolated; these labels would be reassessed regularly, on the basis of whether the lineages are still spreading. The method was described2 in Nature Microbiology on 15 July and seems to have gained support among virologists. The team has also developed online tools to help users identify which lineage their sequence belongs to.
Such a system could make it easier to monitor lineages with unique pathogenic properties when they arise, says Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham and member of the ICTV executive committee.
Virologists currently name species — the most basic taxonomic rank — in several ways, often on the basis of where the virus is found, the animals that host it or the disease it causes. Many argue that the lack of conventions is frustrating for researchers who identify new viruses regularly. It also creates confusion when the virus’s common name is the same as its species name, as with variola virus (Variola virus), which causes smallpox.
The International Committee on Taxonomy of Viruses (ICTV), a body that oversees naming of virus taxa, has proposed1 a naming system, which will be put to a vote in October. If a system is implemented, it could change how almost all of the more than 6,500 known viral species are named.
“It is obviously good and correct to have a standardized classification scheme for naming virus species, as the current ‘system’ is utterly chaotic and a major source of frustration for those of us that regularly identify novel viruses,” says Edward Holmes, a virologist at the University of Sydney in Australia. But the effort “can hardly be classed as ‘urgent’ compared to a global pandemic”, he says.
Other researchers think now is the perfect time for such an exercise. There has been an acceleration in the number of viruses and species being identified over the past 15 years, thanks to genome-sequencing technology, says Eric Delwart, a virologist at University of California, San Francisco. “This is the golden age of virus discovery. It is a good time to start organizing the deluge of viral genomes,” he says.
The debate comes amid discussions about another naming issue: how to classify the tens of thousands of genomes of SARS-CoV-2, the virus that causes COVID-19, being sequenced around the world. Groups of evolutionarily related viruses of the same species are often described as lineages. It is important to track them in case mutations emerge that make the virus more infectious or more dangerous. The ICTV sets rules only down to the level of the species, but Holmes and other virologists independent of the ICTV have proposed2 a method for naming the SARS-CoV-2 lineages.
Time pressure
Currently, the only requirements for a viral species name are that it is italicized (with the first word capitalized) and appropriately unambiguous, and that it uses as few words as possible — although some names are long, such as Tomato yellow leaf curl Indonesia virus. On 3 December, members of the ICTV’s executive committee published a paper1 in Archives of Virology proposing a new format in which species names would be limited to two words.
The first word would be the genus (ending in -virus), which is defined as a group of species that share some common characteristics. The paper proposes three options for the second word. Option one is always to use a Latinized term, in line with similar rules for naming biological organisms, such as Homo sapiens. The second option would restrict the second word to numbers or letters, as in Alphacoronavirus 1, and the third would open it up to any set of characters. So, existing names would be condensed to either a single, potentially Latinized, word, or a number or letter.
The paper, which is the result of several years of public deliberation, called on researchers to provide feedback by 30 June, ahead of a decision at the committee’s next meeting, in October. That decision would then be put to a vote by all ICTV members.
But several virologists say they did not notice the paper at the time, and were then swept up in the coronavirus response. “In an ideal world, we would all be looking at these journals, but the amount of literature we have to keep up with has mushroomed,” says Katherine Spindler, a virologist at the University of Michigan in Ann Arbor and secretary-treasurer of the American Society for Virology (ASV) — one of the world’s largest virology communities, with more than 3,000 members in some 20 countries. “Taxonomy doesn’t affect what I do. It only happens to come up when I write a paper,” says Spindler, who learnt of the consultation after the 30 June deadline. She and the rest of the ASV executive committee wrote to the ICTV committee on 9 July, stating that their members had not had sufficient time to consider the issue.
The Australasian Virology Society (AVS), representing some 700 members in Australia and New Zealand, sent its own letter to the ICTV on 4 July. “We believe that 2020, the year of COVID-19, is not an appropriate time to undertake a major change of naming virus species. Our members are stretched to the limit with other tasks, and many have not had time to properly consider this matter,” the letter stated.
In response to concerns about the timing, ICTV president Andrew Davison, a virologist at the University of Glasgow, UK, says that a version of the proposal has been on the ICTV agenda for nearly two years, but he expects the committee to consider all the relevant factors at its meeting. “I agree that these are unusual times,” he says.
Learning Latin
In their letters, the ASV and AVS also state that they oppose the idea of mandating Latinized names, because that would require virologists to learn Latin grammar, and would be cumbersome to implement. Both groups prefer the option in which any word can be used as the species name, although the AVS’s top preference would be to maintain the status quo, its letter states. “There is no need to overhaul the whole system,” says AVS president Gilda Tachedjian, a virologist at the Burnet Institute in Melbourne, Australia.
But when naming a species, virologists would only need to know the appropriate Latin suffix, says Jens Kuhn, a virologist at the Integrated Research Facility at Fort Detrick, Maryland, and a member of the ICTV executive committee. Latin terms would also be universal, not requiring translation in papers published in languages other than English, he says.
SARS-CoV-2 diversity
Virologists are less conflicted about the urgent need for coherence in naming the many SARS-CoV-2 lineages, which are being labelled in an ad hoc manner. “We are clearly going to end up with more than 100,000 complete genome sequences of SARS-CoV-2, which is staggering. It is obviously important to come up with a simple, rational and widely adopted scheme to classify all this diversity,” says Holmes.
No official body decides how to name viral lineages. “We’ve stepped in to try and sort this out. Whether people will adopt it is another matter: it’s really up to the users,” says Holmes.
He and his colleagues have proposed a dynamic method that prioritizes naming lineages that have seeded an epidemic. The lineages would be labelled active, unobserved or inactive depending on how recently they have been isolated; these labels would be reassessed regularly, on the basis of whether the lineages are still spreading. The method was described2 in Nature Microbiology on 15 July and seems to have gained support among virologists. The team has also developed online tools to help users identify which lineage their sequence belongs to.
Such a system could make it easier to monitor lineages with unique pathogenic properties when they arise, says Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham and member of the ICTV executive committee.
