Virologists are discussing whether to set up a virus naming system later this year. Some scientists argue that the current way of labeling viruses is disorganized and that there is an urgent need for a standardized system. But others say now is not the time to engage in an academic discussion on naming conventions as virologists focus on fighting a pandemic.
Virologists currently name a species ̵1; the most basic taxonomic rank – in several ways, often based on the location of the virus, the animals that host it, or the disease it causes. Many argue that the lack of conventions is frustrating for researchers who regularly identify new viruses. It also causes confusion when the common name of the virus is the same as its generic name, as is the case with smallpox virus (Smallpox virus), which causes smallpox.
The International Committee on Virus Taxonomy (ICTV), the body that oversees the naming of viral taxa, has proposed1 naming system to be voted on in October. If implemented, the system could change the way almost all of the more than 6,500 known virus species are named.
“It’s obviously good and right to have a standardized classification scheme for naming virus types, because the current ‘system’ is completely chaotic and a major source of frustration for those of us who regularly identify new viruses,” said virologist Edward Holmes at the University of Australia in Australia. However, the effort “compared to a global pandemic can hardly be described as” urgent “.
Other scientists think this is the right time for such an exercise. Virus and species identification has accelerated over the past 15 years with genome sequencing technology, says Eric Delwart, a virologist at the University of California, San Francisco. “This is the golden age of virus discovery. It’s time to start organizing the flood of viral genomes, “he says.
The debate comes amid discussions on another naming issue: how to classify the tens of thousands of genomes of SARS-CoV-2, the COVID-19-causing virus that is sequencing around the world. Groups of evolutionarily related viruses of the same species are often described as lines. It is important to monitor them if mutations occur that make the virus more infectious or dangerous. The ICTV only sets rules at the species level, but Holmes and other virologists independent of the ICTV have suggested2 the method of naming the SARS-CoV-2 lines.
Currently, the only requirements for a virus species name are italic (with the first letter capitalized) and reasonably unambiguous, and that it uses as few words as possible – although some names are long, e.g. Tomato yellow curl virus Indonesia, Members of the ICTV Executive Committee published a paper on 3 December1 in Virology archives proposes a new format in which species names 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 characteristics. The article suggests three options for the second word. One possibility is to always use the Latin term in accordance with similar rules for naming biological organisms, such as homo sapiensThe second option would limit the second word to numbers or letters, as in Alfacoronavirus 1and the third would open any set of characters. Thus, existing names would be condensed into a single, possibly Latinized word or number or letter.
The document, which is the result of several years of public deliberations, called on scientists to provide feedback by 30 June before the decision at the next committee meeting in October. This decision would then be voted on by all ICT members.
However, several virologists claim that they did not notice the paper at the time, and then were swept away in response to the coronaviruses. “In an ideal world, we would all look at these journals, but the amount of literature we need to keep up has expanded,” said Katherine Spindler, virologist at the University of Michigan in Ann Arbor and treasury secretary of the American Society for Virology (ASV) – one one of the largest virological communities in the world with more than 3,000 members in about 20 countries. “The taxonomy has no effect on what I do. It only happens when I write a document, “says Spindler, who learned about the consultation after June 30. Together with the rest of the ASV Executive Committee, she wrote to the ICTV Committee on 9 July, stating that their members did not have enough time to deal with the issue.
The Australasian Virology Society (AVS), which represents approximately 700 members in Australia and New Zealand, sent its own letter to ICTV on July 4. “We are convinced that 2020, the year of COVID-19, is not the right time to make a significant change in the naming of virus species. “Our members are fulfilling other tasks to the limit, and many have not had time to give due consideration to this issue,” the letter said.
Responding to timing concerns, ICTV President Andrew Davison, a virologist at the University of Glasgow in the UK, says the version of the proposal has been on the ICTV agenda for almost two years, but expects the committee to consider all relevant factors at its meeting. “I agree that these are unusual times,” he says.
ASV and AVS also argue in their letters that they oppose the idea of commissioning Latin names, as this would require virologists to learn Latin grammar and make implementation cumbersome. Both groups prefer the possibility that any word can be used as a species name, although the highest preference for AVS would be to maintain the status quo, the letter states. “There’s no need to redesign the whole system,” said 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 an integrated research facility in Fort Detrick, Maryland, and a member of the ICTV executive committee. Latin terms would also be universal and would not require translation into documents published in languages other than English.
Virologists are less in conflict with the urgent need for coherence in naming many SARS-CoV-2 families, which are labeled in an ad hoc manner. “We will clearly end up with more than 100,000 complete SARS-CoV-2 genomic sequences, which is amazing. Obviously, it is important to come up with a simple, rational and widely accepted system for classifying this diversity, ”says Holmes.
No official body decides how to name viral lines. “It simply came to our notice then. Whether people learn it is another thing: it’s really up to the users, “says Holmes.
He and his colleagues have proposed a dynamic method that favors the naming of families who have deployed an epidemic. Line lines would be marked as active, unmonitored, or inactive depending on how recently isolated; these labels would be regularly reassessed based on whether the lines are still spreading. The method has been described2 in Nature Microbiology July 15 and seems to have gained support among virologists. The team has also developed online tools to help users determine which line their sequence belongs to.
Such a system could make it easier to monitor genera with unique pathogenic traits when they occur, says Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham and a member of the ICTV executive committee.