What is a COVID-19 variant and how do they form?



The discovery of the Omicron coronavirus variant has sparked basic questions for people who are exhausted by quarantines and mitigation efforts brought about by Delta and the earlier variants. Dr. Monica Gandhi, infectious disease specialist and professor of medicine at the University of California San Francisco, spoke with Yahoo News about how these variants come about.

Video Transcript


MONICA GANDHI: What is a virus variant? Essentially what it means, at least in terms of COVID-19, is that they’re changes that occur across the spike protein of the virus.

What’s the spike protein? It is that little piece of the virus that sticks out and sticks to you as the host cell.

Influenza has two spike proteins, and it’s why we call these spike proteins H and N, and we say things like H2N2 or H9N9. These are basically pieces of protein that stick out from the virus, stick to the cell, and they can develop changes across their surface from the original strain that was first described. And so for COVID-19, it’s the spike protein, and we have different variants where the spike protein has developed mutations across its surface that look different from the ancestral strain.

The way the virus variants occur is that, you know, this virus has been transmitting now since probably way before even January of 2020 and lots of transmission of a virus. Basically it’s going through human hosts, and it likes to change. And where does it change the most? It changes the most in the piece that sticks out and sticks onto your host cell because that’s the part that’s most vulnerable to change.

And we have seen many variants that have emerged in this spike protein from that original ancestral strain that was originally described in Wuhan, China, and we’ve seen alpha and beta and gamma and delta and now omicron. We’ve seen many others besides, actually.

And all of these mean that just because the virus is transmitting through the human population, it’s going to develop mutations across its surface. And it’s really important to figure out if those mutations make it more transmissible– so goes more into humans. It goes faster from human to human. Does it make humans more sick? And the third thing always to know is does the mutations across the surface of the spike protein that defines a variant make it that the vaccines don’t work? Can they evade vaccine-induced immunity? Those are the three things we need to know.

In terms of the terms viral strain or mutation or variant, essentially this is all the same virus, so we should not be calling it different strains. Different strains of a virus are much different than a variant. A variant just means it’s the original viral strain, but across this particular piece of the virus that sticks out, you just develop mutations.

What do viral mutations mean? Well, the ancestral strain that was first described in Wuhan, China, had a certain sequence in its proteins. Basically amino acids line up, and that defines the proteins. And all those amino acids just looked exactly like the wild-type strain, and then sometimes you could develop mutations where an amino acid has changed into another amino acid.

And, for example, the alpha variant had about 13 mutations across its surface. Beta had more across the spike protein. Gamma had less. Mu had more. Lambda had more. And now with omicron, which is our latest variant that’s been described, which has 32 mutations, so 32 places across the spike protein where the amino acids are different than the one in the ancestral strain.

Do variants occur in other viruses? Well, they absolutely do, and influenza is sort of the classic RNA virus that changes a lot. It’s partially because it has two spike proteins, the H and the N protein, that stick to the host cell, so there’s more places for it to mutate.

And also the way that the influenza RNA virus replicating machinery works is it’s very what’s called leaky. It really has a high mutational rate. So influenza changes a lot. It’s actually why we need new influenza vaccines every year until we can get to a universal flu vaccine, which we need to get. So that changes a lot.

OK, what about HIV? HIV is a virus that I’ve worked on for decades, and HIV is a virus that is not exactly an RNA virus. It’s an RNA that actually converts into DNA inside the host cell, and that goes inside your chromosome, and so it’s called a retrovirus. And it also is very changeable, very mutable. It can change a lot. And, in fact, because we use antiviral medications to fight HIV, to give people living with HIV, it can actually change in response to seeing an antiretroviral medication.

And, in general, what we’ve seen is that it changes to try to avoid an antiviral medication, but that usually makes it less fit, less virulent. The person doesn’t replicate the HIV viruses quickly if it’s mutated from the wild type or ancestral strain.

And then finally let’s look at just one other RNA virus that’s common, which is measles. And the reason I choose measles is measles actually looks more like SARS-COV-2. It’s an RNA virus, and it doesn’t change as much as influenza does. It changes as fast as SARS-COV-2, which causes COVID.

And remember, the measles vaccine was developed in 1963, and there’s been plenty of measles since 1963. We’ve never had to update the vaccine because when variants of measles occur, the vaccine works just fine against it. So we’ve never changed the vaccine for that in years.


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