Virologists are debating whether to set up a system to name virus species later this year. Some researchers say the way viruses are currently called is disorganized and that there is an urgent need for a standardized system. But others say now is not the time to get into an academic discussion on naming conventions, when virologists are focused on fighting the pandemic.
Virologists currently mention the species ̵1; the most basic taxonomic grade – in many ways, often on the basis of where the virus is found, the animals it hosts or the disease it causes. Many argue that the lack of conventions is frustrating for researchers to identify new viruses regularly. It is also confusing when the common name of the virus is the same as the name of its species, such as smallpox virus (Smallpox virus), which causes smallpox.
The International Committee on Virus Taxonomy (ICTV), a body that oversees the designation of virus taxa, has proposed1 a system of names, to be put to the vote in October. If a system is implemented, it could change as 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 the name of 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. He says the effort “can hardly be classified as ‘urgent’ compared to a global pandemic”.
Other researchers think 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 over 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 detection. It’s a good time to start organizing the spread of viral genomes,” he continued.
The debate comes amid discussions on another name issue: how to classify the tens of thousands of genomes of SARS-CoV-2, the virus that causes COVID-19, which is sequenced across the world. world. Groups of viruses related to the evolution of the same species are often described as progeny. It is important to track them in case mutations appear that make the virus more infectious or more dangerous. The ICTV sets rules that go down only to the species level, but Holmes and other ICTV-independent virologists have proposed2 method for the SARS-CoV-2 lineage name.
Currently, the only requirements for a viral species name are that it be italicized (capitalized first word) and unambiguous, and that it use as few words as possible – although some names are long, such as Yellow-leaved leaves lower the virus of Indonesia. On 3 December, members of the ICTV executive committee published a document1 fi Virology Archives proposes a new format in which species names are limited to two words.
The first word would be gender (ending in –virus), which is defined as a group of species that have some common characteristics. The paper proposes three options for the second word. One option is always to use a Latinized term, in line with rules similar to the name of biological organisms, such as homo sapiens. The second option restricts the second word to numbers or letters, as in Alphacoronavirus 1, and the third opens it to any set of characters. Thus, existing names would be condensed either to a single word, potentially Latinized, or to a number or letter.
The document, which is the result of several years of public deliberation, asked researchers to provide feedback by June 30, before a decision is made at the next committee meeting, in October. This decision is then put to the vote by all ICTV members.
But several virologists say they did not notice the paper at the time, and then were swept away in response to the coronavirus. “In an ideal world, we would all look at these journals, but the amount of literature we have to keep with it has mushrooms,” 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 largest virology communities in the world, with more than 3,000 members in some 20 countries. “The taxonomy doesn’t affect what I do. It only happens when I was writing a document,” says Spindler, who became aware of the consultation after the June 30 deadline. She and the rest of the ASV executive committee they wrote to the ICTV committee on 9 July, stating that their members did not have enough time to consider the matter.
The Australian Virology Society (AVS), which represents around 700 members in Australia and New Zealand, sent its letter to ICTV on 4 July. “We believe that 2020, the year of COVID-19, is not an appropriate time to make a major change in the name of a virus species. Our members are stretched to the limit with other tasks, and many they did not have time to consider this issue properly, ”the letter stated.
In response to concerns over time, ICTV president Andrew Davison, a virologist at the University of Glasgow, UK, says a version of the proposal has been on ICTV’s agenda for almost two years, but expects the committee to consider the relevant factors at its meeting. “I agree that these are unusual times,” he says.
We learn Latin
In their letters, the ASV and the AVS also state that they oppose the idea of giving them Latinized names, as this would require virologists to learn Latin grammar, and would be difficult to implement. Both groups prefer the option in which any word can be used as the name of the species, although the AVS’s main preference would be to maintain the status quo, its letter states. “There is no need to reformulate the whole system,” says AVS president Gilda Tachedjian, a virologist at the Burnet Institute in Melbourne, Australia.
But when naming a species, virologists only need to know the proper Latin suffix, says Jens Kuhn, a virologist at the Integrated Research Facility in Fort Detrick, Maryland, and a member of the ICTV executive committee. He added that Latin terms would be universal and would not require translation into papers published in languages other than English.
Virologists are less conflicted about the urgent need for coherence in the name of the many SARS-CoV-2 lineages, which are being labeled ad hoc. “We will end up with more than 100,000 complete genome sequences of SARS-CoV-2, which is shocking. 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 the viral lineage. “We’ve got to try to solve this. Whether people adopt it is another matter: it’s really up to the users,” says Holmes.
He and his colleagues have proposed a dynamic method of prioritizing tying names that have sown an epidemic. The offspring are labeled active, unobserved or inactive depending on how recently they have been isolated; these labels will be re-evaluated regularly, on the basis of whether the lineage is still spreading. The method has been described2 fi Microbiology of Nature on 15 July and appears to have gained support among virologists. The team also developed online tools to help users identify which lineage belongs to their sequence.
Such a system could make it easier to monitor offspring with unique pathogenic properties when they arise, says Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham and a member of the ICTV executive committee.