Thursday, November 30, 2023

All these mutant virus strains need new code names

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It’s not Tulio Oliveira’s fault that every mutated variant of the virus that causes Covid-19 has more than one name, let alone that they all read as foolproof passwords. But de Oliveira could have inspired a new international impetus to change this system.

Bioinformatician and Director of the KwaZulu-Natal Research and Innovation Sequencing Platform at the University of KwaZulu-Natal in South Africa, de Oliveira leads the team which in December identified one of those variants – a version of SARS-CoV-2 with a mutation that seemed to make it more easily passed from person to person. In a pandemic, that’s bad.

De Oliveira did what you’re supposed to do: he shared what he knows about the genetic makeup of this new variant with the thousands of scientists around the world who are trying to beat the disease. One of the best ways to do this is to understand how a given variant is evolutionarily and epidemiologically related to all the others – to understand why certain mutations might confer the ability to spread faster and easier, maybe then avoiding certain vaccine formulations. His team sequenced the genes for the viral variant and uploaded the results to a database called GISAID, the “Global Initiative on Sharing All Influenza Data”.

If you’ve heard of the viral offshoot from Oliveira’s team, it could be “the variant first identified in South Africa”. But that’s not what scientists call it. For them it was B.1.351 (pronounced “bee point one point three five one”).

This is where de Oliveira helped make things more complicated. See, UK researchers had also found a fast-spreading variant, which they had named SARS-CoV-2 VOC 202012/01, a less than happy way of saying it was the first ‘variant of concern’ identified in December 2020. Its key mutation appeared to be the same as in the variant Oliveira had found, a change technically called “N501Y”. But one way to classify variants is based on their mutations. So things were about to get confused.

But de Oliveira had land. “It became clear that the variants had a different role in the ranking,” de Oliveira tells me. He proposed that the British researchers’ variant be called 501Y.V1 (as well as B.1.1.7). De Oliveira would still be B.1.351, as well as 501.V2. You may have also heard of another variant called 501Y.V3… or one called P.1… or another called CAL.20C. Maybe you are also trying to keep track of other genetic mutations, like E484K (also called “Eeek”) or D614G, “Doug”. These are funny names that deny some bad things.

Scientists don’t like to name diseases after places or people (too stigmatizing). They prefer something more specific and more esoteric. What is called a virus is also often what it does, or its place in the family tree. Scientists argue over nomenclature, naming of things, because it’s a proxy to fight over what things are—Methodologically, objectively and philosophically. But in the midst of a pandemic, that might not be enough. “It’s too complicated,” said Maria Van Kerkhove, head of the emerging diseases unit at the World Health Organization, in a statement. Questions and answers at the end of January. “We don’t really need to name all the variants that are of interest, but we do have to name the ones that are important, those that have a potential impact on severity, on transmission and all of those that impact therapies. and vaccines. ”So with all the bigwigs in the Covid nomenclature, the WHO started trying to unravel the naming mess.

No epidemic has ever had so many people sequencing so many samples of a virus. There was bound to be a stack. “It may seem like it has burst onto the public scene. But in the scientific community, this discussion about “How do we talk about it?” What nomenclature do we use? has been brewing for a while, ”says Emma Hodcroft, molecular epidemiologist at the University of Bern and co-developer of Nextstrain, one of the main efforts to organize viral genetic sequences. “A lot of it depends on what you’re doing. Are you doing a public health intervention or a large scale evolution? “


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