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Virologists shared plans to change the rules for naming viruses during a pandemic

Orange and green spots with prickly protrusions on a blue background.

Coronavirus particles visible through a transmission electron microscope.Credit: AMI Images / Science Photo Library

Virologists are debating whether to create a system of virus species naming later this year. Some researchers say the current way of naming viruses is messy and that a standardized system is urgently needed. But others say now is not the time to start an academic debate on naming conventions when virologists focus on fighting a pandemic.

Virologists currently identify a species as a major taxonomic rank in several ways, often depending on where the virus was found, the animals that keep it, or the disease it causes. Many argue that the lack of conventions frustrates researchers who regularly detect new viruses. This also causes confusion when the common name of the virus is the same as its species name as for the variola virus (Variola virus), which causes smallpox.

The International Committee on Viral Taxonomy (ICTV), the body responsible for overseeing the identification of viral taxa, has proposed1 naming system, which will be voted on in October. If the system is installed, it could change the way almost all of the more than 6,500 known types of viruses are named.

“Obviously, it is good and right to have a standardized classification scheme for virus species names, because the current ‘system’ is completely chaotic and very frustrating for those of us who regularly identify new viruses,” says virologist Edward Holmes. University of Sydney, Australia. But the effort “can hardly be described as” urgent “compared to a global pandemic,” he says.

Other researchers believe that now is the best time for such exercises. Genome sequencing technology has increased the speed of virus and species identification over the past 15 years, 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 destruction of viral genomes, “he says.

Discussions are taking place during a debate on another naming issue: how to classify tens of thousands of SARS-CoV-2, the genomes of the virus that causes COVID-19, being tracked around the world. Groups of evolutionarily related viruses of the same species are often described as lines. It is important to follow them if mutations occur that make the virus more contagious or dangerous. ICTV sets rules only at the species level, but Holmes and other virologists independent of ICTV have suggested2 method for naming SARS-CoV-2 lines.

Time pressure

Currently, the only requirements for the name of a viral species are that it be italicized (with the first word in capital letters) and properly unambiguous, using as few words as possible – although some names are long, e.g. Tomato yellow leaf curls Indonesian virus. December 3 Members of the ICTV Executive Committee published the document1 to Virology archives propose a new format in which species names are limited to two words.

The first word would be tribe (ending invirus), which is described as a group of species with certain common characteristics. The article offers three possibilities for the second word. The first option is to always use the Latin term, following similar biological organisms such as homo sapiens. The second option would limit the second word to numbers or letters as indicated 1 alpha coronavirus, and the third would open it to any character set. So the existing names would be condensed into one, possibly Latin word, number, or number.

This document, which was the result of several years of public deliberation, invited researchers to comment by 30 June, before taking a decision at the next committee meeting in October. All ICTV members will then vote in favor of this decision.

However, several virologists say they did not notice the paper at the time and were then greeted in response to the coronavirus. “In an ideal world, we would all look at these journals, but there is still a lack of literature we need to keep,” says Katherine Spindler, a virologist and secretary-treasurer at Ann Arbor University of Michigan. The American Society of Virology (ASV) is one of the largest communities of virologists in the world, with more than 3,000 members in about 20 countries. “Taxonomy doesn’t affect what I do. It only happens when I am writing a document, ”says Spindler, who learned of the consultation after June 30th. July 9 She and the rest of the U.S. executive committee wrote to the ICTV committee stating that their members did not have enough time to address the issue.

The Australian Society of Virologists (AVS), representing around 700 members in Australia and New Zealand, on 4 July. Sent his letter to ICTV. “We believe that 2020, the year of COVID-19, is not the right time to fundamentally change the naming of virus species. Our members are being extended to other tasks, and many have not had time to consider the matter properly, ”the letter said.

Responding to concerns about time, ICTV President Andrew Davison, a virologist at the University of Glasgow (UK), says the version of the proposal has been on the ICTV agenda for almost two years, but he hopes the committee will consider all relevant factors at its meeting. “I agree it’s unusual times,” he says.

Learn Latin

In their letters, the U.S. and AVS also state that they oppose the idea of ​​legalizing Latin names, as this will require virologists to learn Latin grammar and make it difficult to implement. Both groups prefer the option of using any word as a species name, although the EMS favors maintaining the status quo, according to its letter. “There is no need to redesign the entire system,” said GSD President Gilda Tachedjian, a virologist at the Burnet Institute in Melbourne, Australia.

But when you name the species, virologists will only need to know the appropriate Latin suffix, says Jens Kuhn, a virologist and member of the ICTV Executive Committee at the Integrated Research Center in Fort Detroit, Maryland. He says Latin terms would be universal and would not require translation into documents published in languages ​​other than English.

SARS-CoV-2 diversity

Virologists are less likely to argue about the urgent need for compatibility, naming many SARS-CoV-2 lines that are labeled on an ad hoc basis. “Clearly, we will have more than 100,000 SARS-CoV-2 genome sequences, which is staggering. It is obvious that it is important to come up with a simple, rational and widely used scheme to classify all this diversity, ”says Holmes.

No official body decides how to name viral lines. “We started trying to figure it out. Whether people will accept it is another question: it really depends on the consumers, ”says Holmes.

He and colleagues proposed a dynamic approach that prioritized the emergence of an epidemic. Lines will be marked as active, unattended, or inactive, depending on how recently they were singled out; these labels would be re-evaluated regularly to see if relatives are still spreading. The method was described2 to Natural microbiology July 15 and seems to have received the support of virologists. The team has also developed online tools to help users determine which sequence they belong to.

Such a system could facilitate the monitoring of lines with unique pathogenic properties as they appear, says Elliot Lefkowitz, a virologist at the University of Alabama in Birmingham and a member of the ICTV executive committee.

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