Particles of a coronavirus, seen under a transmission electron microscope.Credit: AMI Images / Science Photo Library
Virologists are debating whether to establish a 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 a standardized system. But others say that now is not the time to engage in academic discussion about naming conventions, when virologists focus on fighting the pandemic.
Virologists currently name species, the most basic taxonomic range, in various ways, often depending on where the virus is found, the animals that harbor it, or the disease it causes. Many argue that the lack of conventions is frustrating for researchers who regularly identify new viruses. It also creates confusion when the common name of the virus is the same as the name of its species, as occurs with the variola virus (Variola virus), which causes smallpox.
The International Committee on Virus Taxonomy (ICTV), a body that oversees the naming of virus taxa, has proposedone a naming system, to be voted on in October. If a system is implemented, it could change the way almost all of the more than 6,500 known viral species are named.
“Obviously it is good and correct to have a standardized classification scheme for naming virus species, as the current ‘system’ is completely chaotic and a major source of frustration for those of us who regularly identify new viruses,” says Edward Holmes, a virologist at the University of Sydney in Australia. But the effort “can hardly be classified as ‘urgent’ compared to a global pandemic,” he says.
Other researchers think that now is the perfect time for such an exercise. There has been an acceleration in the number of viruses and species that have been identified in the past 15 years, thanks to genome sequencing technology, says Eric Delwart, a virologist at the 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 topic: how to classify the tens of thousands of genomes from SARS-CoV-2, the virus that causes COVID-19, which is being sequenced worldwide. Evolutionarily related groups of 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. ICTV sets rules only down to the species level, but Holmes and other independent ICTV virologists have proposedtwo A method of naming the SARS-CoV-2 lineages.
Time pressure
Currently, the only requirements for the name of a viral species are that it be in italics (with the first word capitalized) and unambiguous, and that it use as few words as possible, although some names are long, such as Tomato yellow leaf curl virus Indonesia. On December 3, members of the ICTV executive committee released a documentone in Virology files proposing a new format in which the names of the species would be limited to two words.
The first word would be gender (ending in –virus), which is defined as a group of species that share some common characteristics. The document 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 to any character set. Therefore, existing names would be condensed into a single word, potentially Latinized, or into a number or letter.
The document, which is the result of several years of public deliberation, asked investigators to provide their comments before June 30, before a decision at the next committee meeting in October. That decision would be voted on by all ICTV members.
But several virologists say they didn’t notice the role at the time, and were later swept up in the coronavirus response. “In an ideal world, we would all be looking at these magazines, but the amount of literature we have to continue has increased,” says Katherine Spindler, a virologist at the University of Michigan at Ann Arbor and secretary-treasurer of the American Society for Virology (ASV). : one of the largest virology communities in the world, with more than 3,000 members in some 20 countries. “The taxonomy does not affect what I do. It only appears when I write an article, ”says Spindler, who learned of the consultation after the June 30 deadline. She and the rest of the ASV executive committee wrote to the ICTV committee on July 9, stating that its members had not had enough time to consider the matter.
The Australian Virology Society (AVS), which represents some 700 members in Australia and New Zealand, sent its own letter to ICTV on July 4. “We believe that 2020, the year of COVID-19, is not an appropriate time to undertake a major change in the naming of virus species. Our members stretch themselves to the limit with other tasks, and many have not had time to properly consider this matter, ”the letter said.
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 ICTV’s agenda for almost two years, but he hopes that the committee consider all relevant factors at its meeting. “I agree that these are unusual times,” he says.
Learn Latin
In their letters, the ASV and AVS also state that they are opposed to the idea of requiring Latinized names, because that would require virologists to learn Latin grammar, and would be difficult to implement. Both groups prefer the option in which any word like the name of the species can be used, although the main preference of the AVS would be to maintain the status quo, its letter says. “There is no need to overhaul the entire 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 Center for Integrated Research in Fort Detrick, Maryland, and a member of the ICTV executive committee. The Latin terms would also be universal and would not require translation in documents published in languages other than English, he says.
SARS-CoV-2 Diversity
Virologists have fewer conflicts over the urgent need for consistency in naming the many SARS-CoV-2 lineages, which are labeled ad hoc. “Clearly we are going to end up with over 100,000 complete sequences from the SARS-CoV-2 genome, which is amazing. Obviously, it is important to devise a simple, rational and widely adopted scheme to classify all this diversity, “says Holmes.
No official body decides how to name viral lineages. “We have stepped in to try to resolve this. Whether people will adopt it is another matter: It really depends on the users, “says Holmes.
He and his colleagues have proposed a dynamic method that prioritizes the lineages of names that have sown an epidemic. Lineages would be labeled as active, unobserved, or inactive depending on how recently they have been isolated; These labels would be reevaluated regularly, depending on whether the lineages are still spreading. The method was describedtwo in Microbiology nature on July 15 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 facilitate monitoring of lineages with unique pathogenic properties when they emerge, says Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham and a member of the ICTV executive committee.
