What We Do—And Don’t—Know About Omicron

IRA FLATOW: This is Science Friday. I’m Ira Flatow. Later in the hour, a look at the disruptive technology of quantum computing– what it is, where it is now, and where it is going. But first, the Omicron variant has been detected in the US, the first case identified this week in California.

Last week, South African researchers identified and then sequenced the variant. And since then, scientists all over the world went into overdrive trying to understand this heavily mutated new strain. And I mean Omicron has 32 mutations in the spike protein alone. More mutations don’t necessarily mean it’s more contagious than the delta variant or more likely to evade the vaccine. We just need to give scientists enough time to figure it out.

Joining me now to help us understand how scientists are compiling data on Omicron, both inside and outside of the lab, is Katelyn Jetelina, assistant professor in the University of Texas School of Public Health in Dallas. She’s also the author of the newsletter Your Local Epidemiologist. Thanks for being with us today. Welcome to Science Friday.

KATELYN JETELINA: Yeah, thanks for having me. I’m excited to be here.

IRA FLATOW: Well, now that we have seen cases in the US, wasn’t it always inevitable that Omicron would arrive here?

KATELYN JETELINA: Fortunately, we are fast, but unfortunately, still once we identify a case or a variant, that means it’s probably been circulating under our radar for a little while before. And we’ve seen that cases pop up in Europe before even the cases that were identified in South Africa. So we had a hunch it was in the United States. It was just a matter of time of us finding that needle in a haystack.

IRA FLATOW: And what is it about Omicron that has you and other scientists on such high alert? Is it the number of those mutations?

KATELYN JETELINA: Well, certainly the number of mutations got our attention because there were a lot. There are a lot compared to, for example, delta, and specifically the mutations on the spike protein. So for example, with delta, we had nine changes on the spike protein. With Omicron, we have 32.

And we pay attention to this spike protein specifically because this is the virus’s key into our cells. And if the virus changes this key or even finds a different key for a different door, we need to know about it, and really pay attention to it and figure out if that change on the spike protein, one, increases transmissibility, two, has the ability to escape our vaccine or infection-induced immunity, and/or, three, increase the severity of disease, like hospitalization or death.

IRA FLATOW: Does it share any mutations with the delta variant, in terms of giving you a hint of how it might act?

KATELYN JETELINA: Yeah, so– and this is what also kind of brought this onto our radar– so Omicron actually has a number of mutations we’ve seen on other variants of concern, like delta, like you said, but also alpha and gamma and beta. In fact, there’s nine mutations out of those 32 that we’ve seen on previous variants of concern. There’s one, in particular. It is called P681R, if anyone wants to know.

And it’s a particular mutation called a furin cleavage. And that was on delta, as well, which made it so much more transmissible, this one little change. Unfortunately, with Omicron, it has this furin cleavage, as well as a second furin cleavage. And so we’re trying to figure out what the two together really means.

IRA FLATOW: The fact that it was first detected in South Africa doesn’t necessarily mean it first appeared in South Africa, correct?

KATELYN JETELINA: Yeah, no, and it was actually first discovered in Botswana on November 11th, and then three days later discovered in South Africa. And we really owe it to the scientists in South Africa for, one, identifying it, two, telling the world so scientists, thousands of scientists could be working on this as quickly as possible, as well as being very transparent about what’s happening on the ground, really walking us through case growth, what they’re seeing at the hospitals, et cetera.

IRA FLATOW: Let’s talk about how likely it is that Omicron will evade the vaccine. What’s your take on that? Or do we not know that yet?

KATELYN JETELINA: So we don’t know that yet. We certainly have hypotheses. And really, what’s driving those hypotheses is that some of the changes on Omicron reflect the changes we saw in beta. And beta is one of the previous variants of concern that have escaped our vaccine protection the most.

Now, I think it’s really important to realize or address that immune escape isn’t a binary event. It’s not yes or no. We’re not going to start from square one. Immune escape is really more like corrosion, like picking away at the sides of our protection. So we hypothesize that this Omicron variant will have a negative impact on the level of protection we have, but not fully. We’ll still have some protection against severe disease and death. And that’s what scientists right now are trying to figure out.

IRA FLATOW: And could it be less deadly than the variants we have now?

KATELYN JETELINA: It certainly could. The variant changes and mutates randomly, and what all of the virus wants to do is survive. And if a virus is killing off their hosts, it’s not going to survive. And so there’s this balance between severity as well as immune escape. So it can outsmart vaccines, as well as a balance and tradeoff with transmissibility. Again, I feel like I keep saying this, but we don’t know yet the extent in which that will happen.

IRA FLATOW: Yeah. We like it when scientists say they don’t know, rather than faking it. Speaking of faking it, tests. The tests we take for discovering whether we have the virus or we had it before, will this new strain be picked up for the tests that are currently in our drugstores?

KATELYN JETELINA: So I’ll start with PCR tests. And we got actually some really great news from South Africa on this, that PCR tests can actually tell the lab whether it’s Omicron or not. And this typically isn’t the case. Usually, we would have get this swab of the PCR, that PCR goes to a special lab for genomic sequencing. It can take a few weeks to know which variant caused that infection. With Omicron, though, it has a really special signal. And we actually saw this before with alpha. And it has this special signal on the PCR directly.

So when a PCR is positive, it lights up three channels, typically. With Omicron, it lights up two channels, which will indicate it’s Omicron versus delta. And this is really amazing news because it means we can track the virus much easier and much quicker within the United States, and then across the world.

And that’s PCR. And so then we also have rapid antigen tests at our corner pharmacies that we can buy over the counter. Those will not tell us what variant it is, but it still can detect Omicron. We got some confirmation from the drug companies that it does still work. And that’s because those rapid antigen tests test for something other than the spike protein that hasn’t changed. And so that’s also great news, as well.

IRA FLATOW: OK, now if someone was infected with the delta variant, would that protect them against Omicron?

KATELYN JETELINA: Yeah, this is a really good question, and an important one we’re trying to answer, right? So because the United States was hit so hard, and continues to be hit so hard with delta, one great question is what does the infection-induced immunity, how does that protect against Omicron. And unfortunately, a day or two ago, the WHO came out with their briefing and said that they have preliminary evidence showing a high reinfection rate among those with infection-induced immunity.

So those that have gotten COVID-19 before, but don’t have the vaccines. And that’s really important information because it will tell us, you know, it’s been almost 90 days since our delta wave, or our main one, and that will tell us and help us predict how high the COVID-19 wave will be this winter once Omicron, or if and when Omicron enters the scene.

IRA FLATOW: How do you piece together all of the information to get a complete picture about Omicron, and where it stands with the other variants and the virus itself?

KATELYN JETELINA: Yeah, it’s hard for an individual to do. I’m trying to keep track of it. But from a scientific perspective, we really need to marry two sources of data. And these sources of data kind of come from two different angles. One is we are running lab tests right now. We call these lab studies. And what they’re doing is seeing how our antibodies attach, given Omicron’s changes, and if so, how tightly do these antibodies attach.

And to answer this, scientists actually have to develop or engineer, it’s called a pseudovirus. And so they take another virus and attach the Omicron spike protein to it, and let it grow in a lab. And this is why we keep hearing we’ll know in two weeks, we’ll know in two weeks, is that because it takes time for that to grow.

But they essentially grow a virus that mimics Omicron. And once they have enough of this sample on a Petri dish, people’s blood that had the vaccine, mix it with this pseudovirus, and see how our antibodies respond, really on a micro level. And then so this is more like lab scientists.

On the other end, we have to marry– I call it real-world data. And that’s epidemiology of what’s happening on the ground, what are we seeing was spread, how quickly is it spreading, what’s happening at the hospitals, is it severe, is it not, what is the symptomology that people are showing. And that’s really important because lab studies are very different than the real world, right?

In the lab, we have it’s temperature-controlled, everything’s sterile, we’re on a Petri dish. That doesn’t necessarily always pan out to what happens in our environment, with our genetics, et cetera. And so having those two pieces really gives us the, quote unquote, true perspective on what’s happening out there.

IRA FLATOW: Well, thank you for sharing your true perspective on what’s happening out there.

KATELYN JETELINA: Yeah, no, thanks for having me.

IRA FLATOW: Katelyn Jetelina, assistant professor in the University of Texas School of Public Health in Dallas. She’s also the author of the newsletter Your Local Epidemiologist.

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