Virologists are discussing whether to create a system for naming virus species later this year. Some researchers argue that the current way of naming viruses is disorganized and there is an urgent need for a standardized system. But others say now is not the time to engage in an academic debate on naming conventions when virologists are focused on fighting the pandemic.
Currently, virologists name species ̵1; the most important taxonomic rank – in several ways, often based on where the virus is located, the animals that receive it, or the disease it causes. Many argue that the lack of conventions upsets researchers who regularly identify new viruses. It also creates confusion when the common name of the virus is the same as its name, as in the smallpox virus (Smallpox virus), which causes smallpox.
The International Committee on Viral Systematics (ICTV), the body that oversees the naming of viral taxa, has proposed1 a system of names to be put to the vote in October. If the system is implemented, it could change the way almost all of the more than 6,500 known viral species are named.
“Obviously, it’s good and right to have a standardized classification scheme for naming virus species, because the current ‘system’ is completely chaotic and a major source of frustration for those of us who regularly identify new viruses,” said Edward Holmes, a virologist at the University of Sydney. in Australia. But the effort “can hardly be described as ‘urgent’ compared to a global pandemic,” he said.
Other researchers believe that now is the perfect time for such an exercise. Over the past 15 years, there has been an acceleration in the number of viruses and species detected through genome sequence 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 said.
The debate is taking place in the context of discussions on another naming issue: how to classify tens of thousands of genomes of SARS-CoV-2, the virus that causes COVID-19, to be sequenced around the world. Groups of evolutionarily related viruses of the same species are often described as lines. It is important to monitor them for mutations that make the virus more infectious or dangerous. ICTV sets the rules only to the species level, but Holmes and other ICTV-independent virologists have suggested2 SARS-CoV-2 line naming method.
Currently, the only requirements for the name of a viral species are that it is italicized (with the first word in capital letters) and properly unambiguous, and that it uses as few words as possible – although some names are long, e.g. Tomato yellow leaf curls Indonesia virus. On December 3, members of the ICTV executive committee released the document1 in Archives of virology proposing a new format in which species names will be limited to two words.
The first word will be genus (ending in –virus), defined as a group of species that have some common characteristics. The article offers three variants of the second word. Option one – always use the Latinized term according to similar rules for naming biological organisms, such as homo sapiens. The second option limits the second word to numbers or letters, as in Alphacoronavirus 1, and a third would open it for any character set. Thus, existing names will be reduced either to a single, potentially Latinized word, or to a number or letter.
The document, which is the result of many years of public discussion, called on researchers to provide feedback by June 30, before a decision is made at the next committee meeting in October. This decision will 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 overwhelmed by the reaction to the coronavirus. “Ideally, we would all look at these journals, but the amount of literature we have to keep up,” said Catherine Spindler, a virologist at the University of Michigan in Ann Arbor and treasurer of the American Society of Virology (DIA), one of the world’s largest. virological communities, which has more than 3,000 members in 20 countries. “Taxonomy does not affect what I do. This only happens when I write the document, “said Spindler, who learned of the consultation after June 30. On July 9, she and the rest of the ASV executive committee wrote to the ICTV committee, saying their members did not have enough time to consider the issue. .
The Australian Virological Society (AVS), which has about 700 members in Australia and New Zealand, sent its own letter to ICTV on 4 July. “We believe that 2020, the year of COVID-19, is not the right time for major changes in the name of virus species. Our members are stretched to other tasks, and many did not have time to properly consider this case, “the letter reads.
Responding to concerns about the timing, ICTV President Andrew Davison, a virologist at the University of Glasgow in the UK, says the version of the proposal has been on ICTV’s agenda for almost two years, but he expects the committee to consider all relevant factors at its meeting. “I agree that these are unusual times,” he said.
In their letters, ASV and AVS also state that they oppose the idea of banning Latinized names, as this would require virologists to study Latin grammar, and would be cumbersome to implement. Both groups prefer a variant in which any word can be used as a species name, although the main advantage of AVS would be to maintain the status quo indicated in its letter. “There is no need to overhaul the entire system,” said AVS President Gilda Tahejian, a virologist at the Burnett Institute in Melbourne, Australia.
But when naming a species, virologists only need to know the appropriate Latin suffix, says Jens Kuhn, a virologist with the Integrated Research Foundation in Fort Detrick, Maryland, and a member of the ICTV executive committee. Latin terms would also be universal without requiring translation in documents published in languages other than English, he said.
Variety of SARS-CoV-2
Virologists are less in conflict about the urgent need for consistency in the name of many SARS-CoV-2 lines, which are labeled in a special order. “Obviously, we will end up with more than 100,000 complete sequences of SARS-CoV-2 genomes, which is amazing. Obviously, it’s important to come up with a simple, rational, and widely accepted scheme for classifying all this diversity, ”says Holmes.
No official body decides what to call viral families. “We came in to try to figure it out. Whether people will accept it is another matter: it really depends on the users, ”says Holmes.
He and his colleagues proposed a dynamic method that prioritizes the naming of the lines that sowed the epidemic. Rows will be marked as active, unnoticed, or inactive depending on how recently they were selected; these labels are reviewed regularly to see if the lines are still spreading. The method was 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 can make it easier to monitor lines with unique pathogenic properties when they occur, says Elliot Lefkowitz, a virologist at the University of Alabama at Birmingham and a member of the ICTV executive committee.