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How do viral variants get their names?



20H / 501Y.V2.

VOC 202012/02.

B.1.351.

These were the charming names proposed by scientists for a new variant of the coronavirus identified in South Africa. Curved strings of letters, numbers, and dots are deeply significant to the scientists who invented them, but how was anyone else supposed to keep them straight? Even the easiest to remember, B.1.351, refers to a completely different origin of the virus if a point is missed or misplaced.

Virus naming conventions were good, as long as the options remained esoteric topics for study. But now they are a source of concern for billions of people. They need names that roll from the tongue without stigmatizing the people or places associated with them.

“The challenge is to come up with names that are different, informative, that don’t involve geographic references, and that are somehow pronounced and memorable,” said Emma Hodcroft, a molecular epidemiologist at the University of Bern, Switzerland. “It sounds kind of simple, but it’s actually a really big request to try to convey all this information.”

The solution, she and other experts said, is to come up with a unified system that everyone can use, but connect it to the more technical ones that scientists rely on. The World Health Organization has convened a working group of several dozen experts to come up with a clear and scalable way to do this.

“This new system will give concerned options a name that is easy to pronounce and call out, and will also minimize unnecessary negative effects on nations, economies and people,” the WHO said in a statement. “The proposal for this mechanism is currently under internal and external review by partners before finalization.”

So far, the leading WHO candidate, according to two members of the working group, is disarmingly simple: numbering the options in the order in which they are identified – V1, V2, V3, etc.

“There are thousands and thousands of options, and we need some way to identify them,” said Trevor Bedford, an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle and a member of the task force.

Naming diseases has not always been so complicated. Syphilis, for example, is derived from a poem from 1530 in which the shepherd Syphilis was cursed by the god Apollo. But the sophisticated microscope, invented around 1600, opened up a hidden world of microbes, allowing scientists to begin naming them after their shapes, said Richard Barnett, a British science historian.

Yet racism and imperialism have penetrated the names of diseases. In the 1800s, when cholera spread from the Indian subcontinent to Europe, British newspapers began calling it “Indian cholera,” portraying the disease as a figure in a turban and robes.

“Naming can very often reflect and extend the stigma,” said Dr. Barnett.

In 2015, the WHO published best practices for naming diseases: avoiding geographical location or the names of people, animal or food species and terms that arouse unnecessary fear, such as “fatal” and “epidemic”.

Scientists rely on at least three competing nomenclature systems – Gisaid, Pango and Nextstrain – each of which makes sense in its own world.

“You can’t trace something you can’t name,” said Oliver Peabus, an evolutionary biologist at Oxford who helped design the Pango system.

Scientists name variants when changes in the genome coincide with new foci, but they only draw attention to them if there is a change in their behavior – if, for example, they transmit more easily (B.1.1.7, the variant first seen in the UK). or if they at least partially circumvent the immune response (B.1.351, the variant found in South Africa).

Coded in scrambled letters and numbers are clues to the ancestors of the variant: “B.1”, for example, means that these variants are related to the outbreak in Italy last spring. (Once the hierarchy of variants becomes too deep to accommodate another number and point, the newer ones are given the next letter in alphabetical order.)

But when scientists announced that a variant called B.1.315 – two digits removed from the variant first seen in South Africa – was spreading to the United States, South Africa’s health minister “got quite confused” between that and B. 1,351, said Tulio de Oliveira, a geneticist at Nelson Mandela Medical School in Durban and a member of the WHO working group.

“We need to come up with a system that not only evolutionary biologists can understand,” he said.

Without easy alternatives, people resort to calling B.1.351 the “South African version.” But Dr. de Oliveira is asking his colleagues to avoid the term. (Look no further for the origins of this great virus: Calling it the “Chinese virus” or the “Wuhan virus”, fueled by xenophobia and aggression against people of East Asian descent around the world.)

The potential damage is serious enough to dissuade some countries from moving forward when a new pathogen is discovered within their borders. Geographical names are also rapidly becoming obsolete: B.1.351 is already in 48 countries, so to call it a South African version is absurd, added Dr. de Oliveira.

And practice can distort science. It is not entirely clear that the variant originated in South Africa: It was identified there largely thanks to the diligence of South African scientists, but its branding as a variant of this country may mislead other researchers to ignore their possible path to South Africa from another side that makes a sequence of fewer coronavirus genomes.

In the last few weeks, offering a new system has become something of a spectator sport. Some of the suggestions for inspiration for the names: hurricanes, Greek letters, birds, other animal names such as red squirrel or aarvarka and local monsters.

Ayn O’Toole, a PhD student at the University of Edinburgh who is part of the Pango team, suggested colors to show how different constellations of mutations are related.

“You could end up with dusty pink or purple or fuchsia,” she said.

Sometimes identifying a new variant by the characteristic mutation may be sufficient, especially when the mutations acquire bizarre names. Last spring, Ms. O’Toole and her associates began calling D614G, one of the earliest known mutations, “Doug.”

“Somehow we wouldn’t have a huge amount of human interaction,” she said. “That was our idea of ​​humor when locking №1.”

Other aliases followed: “Nelly” for N501Y, a common thread in many new variants of concern, and “Eeek” for E484K, a mutation thought to make the virus less susceptible to vaccines.

But Eeek has appeared in multiple variants simultaneously around the world, emphasizing the need for variants to have different names.

The numbering system that the WHO is considering is clear. But all new names will have to overcome the lightness and simplicity of geographical labels for the general public. And scientists will have to strike a balance between naming a variant fast enough to prevent geographical names and careful enough not to end up naming minor variants.

“What I don’t want is a system where we have this long list of options, all of which have WHO names, but in fact only three of them are important and the other 17 are not important,” Dr. Bedford said.

Whatever the final system, it will also have to be adopted by different groups of scientists, as well as by the general public.

“Unless it really becomes a lingua franca, it will make things more confusing,” Dr. Hodcroft said. “If you don’t come up with something that people can easily say and write and remember easily, they’ll just go back to using the geographical name.”




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