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

The news of the Omicron variant of the coronavirus rattled markets and sparked travel bans across the world as health officials raced to determine the threat that new variant poses.

Omicron’s discovery also sparked basic questions for many people exhausted by the quarantines and destruction brought about by Delta and the earlier variants.

What causes these variants, and what is a variant, anyway? How concerned should we be? Are variants unique to the coronavirus?

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.

(Some responses have been edited for clarity.)

Yahoo News: What is a virus variant?

Dr. Monica Gandhi: Essentially what it means, at least in terms of COVID-19, is that there are 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 H2, N2, or H9, N9. 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 the surface that look different from the ancestral strain.

How does a virus variant occur?

So the way the virus variants occur is that this virus (SARS-CoV-2) has been transmitting now since, probably way before even January of 2020. And so 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 most vulnerable to change. And so 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. And 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.

Should variants be concerning?

They’ve been described as concerning just because everything about COVID-19 is so public and so out there, and we are all updated minute-to-minute on everything about COVID. But the thing about variants is [they’re natural and will happen.] We really need to understand if a variant changes any of those properties. Is it more transmissible? Does it make you more sick? And can the variant evade the vaccines? Which the reason that’s so important is [because many of the vaccines], at least six out of the nine that the [World Health Organization] is approving, involve coding for the spike protein.

What’s the difference between a strain, variant and mutation?

[In terms of] viral strain or mutation or variant, essentially, this is all the same virus (SARS-CoV2). 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 (spike protein), 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 on other viruses?

They absolutely do. And actually 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 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.

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 goes to DNA, it actually converts into DNA inside the host cell, and then 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 virus as quickly if it’s mutated from the wild type or ancestral strain.

Finally, let’s look at just one other RNA virus that’s common, which is measles. 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 pretty much 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 [measles] vaccine because when variants of measles occur, the vaccine works just fine against it. So we’ve never changed the vaccine for that many years.


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