Emerging Info about New Variant

A reader asked for the genetic map for the new SARS-CoV-2 variant VUI–202012/01. With her background, she can understand that much better than I ever will. I’m not a geneticist. This isn’t the level of detail she wants, but it’s a step in the right direction from the COVID-19 Genomics UK Consortium.

Perhaps, like me, you don’t have the professional knowledge to understand that entire report. In that case, do what I did. Read the parts you can comprehend. Look up a few things if that’s what you need to help you puzzle out enough to get the gist of it. That’s plenty for those of us who don’t work with the genetics of viruses for our living. Or if you find the report too much of a bother and just want the headlines, read more of this post.

Variants and Mutations: What’s the Difference?

Each mutation is a change in the genetics of the virus. Mutations result from mistakes when the virus makes new copies of itself. Mutations happen routinely. Most of them don’t give the virus a new advantage or even put the virus at a disadvantage. Copies of the virus with those mutations die out. But once in a while, a mutation turns out to be either neutral or advantageous for the virus. When that happens, copies with the mutation thrive better than other versions of the virus, so the mutation becomes more widespread.

A variant of the virus often has multiple mutations. The specific combination of mutations is so beneficial for the virus that copies with the combination become a noticeable proportion of what is spreading. That’s what has happened in southeastern England and all over Wales. A new variant has emerged with a specific package of mutations. As you read this, don’t feel too smug if you live somewhere other than the UK. We aren’t the only country where the mutations involved have appeared. For example, South Africa seems to have a similar variant in circulation.

What Is Causing Concern About the Variant VUI–202012/01?

To me, it looks like there are two perspectives about this. Initially Westminster had to respond to the first one, the simple fact that cases are rising dramatically in London and certain nearby areas where this variant has been found. England was in national Lockdown #2 for a few weeks until early December. The R value (the average number of new infections stemming from each infected person) had dropped below one, but appeared to rise quickly and is now estimated about 1.1 to 1.2.

Although this does not prove the new variant infects people more efficiently than the previous most common variant, the government chose not to wait. If this is indeed a more contagious variant, waiting for more definite information could allow the case rate to explode, especially if people socialize as much over Christmas as the government was previously willing to allow… so everything has been clamped down considerably.

This looks sensible to me. Crucial decisions often have to be made without complete data.

As more information comes in, we can take a perspective more informed by scientific detail. From what I can understand in the report I pointed out, the combined effects of the mutations in this variant could indeed cause some trouble. They generally don’t tend to make illness more severe (although that might not be true for people with compromised immune systems), but they do look like a combination that can help it spread from person to person more easily. These effects include:

• increasing the ‘binding affinity’ for the human ACE-2 receptor, which means it more enthusiastically hooks a target cell to infect it

• ‘immune escape’ capability, an ability to evade the immune system in immunosuppressed people

• a dropout in one (but not all) of the features that tests look for to detect viral infection

Summary

We still don’t need to panic about the new variant. We shouldn’t assume southeast England is the only place with anything like it. This doesn’t look more lethal, but it may indeed be more contagious.

So what we need to do is the same as before. We need to take the precautions we know we should take. Especially through the holiday break.

CORRECTION: In the original version of this post, I mistakenly used the word strain as though it is synonymous with variant. That was incorrect. SARS-CoV-2 is a strain of coronavirus. SARS and MERS are other strains of coronavirus. Variants occur within a strain. Mutations can occur individually. Sometimes a variant has one significant mutation of a strain, although a variant often has a small handful of specific mutations. The new variant called B.1.1.7 (sometimes written B117) identified by the UK is unusual because it includes so many mutations.