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SIU professor explains how COVID variants are studied

A man in a black face mask sits in a lab.
Mark St. George
Associate Professor of Biochemistry Keith Gagnon's lab has been sequencing COVID-19 throughout the pandemic.

As more cases of the omicron variant are found, scientists are trying to determine what it will mean for the COVID 19 pandemic.

SIU Associate Professor of Biochemistry Keith Gagnon sat down with WSIU to discuss how research into new variants works.

WSIU: Gagnon says understanding a new variant starts with examining its mutations.

Gagnon: Yes, so let's say we sequence a variant variant's genome. We first look to see what mutations it has that match up to what we've already seen. And in the case of I'm across, of course, a number of new mutations were observed, all clustered in that spike gene.

So we're looking at the spike gene kind of mutations and not just that it has mutations. I'll say that omicron has mutations that we either haven't really seen much or haven't been well studied. So those are unknowns, but has a number of mutations which are kind of known troublemakers.

And that raises the red flag. That's why we're worried about crime because it's got lots of mutations in the spike gene that we know are troublesome, plus some new ones, and we haven't characterized it with how it's affecting patients and how it's responding to antibodies.

WSIU: And that sort of leads me to my next two questions. one is, you know, people hear a new variant and they just we want answers. Why does it take a while for scientists to kind of start getting into this and looking at the mutations and what they might mean theoretically from a lab standpoint?

Gagnon: Sure. So there's a lot of different approaches you can use that give you different levels of information, but invariably it takes several days to several weeks to tick the basic characterization of the virus, the spike protein, you have to design the spike.

You can't just take a virus — at least most labs can't, some labs have clearance to do this — but most labs can't just take the virus sample and grow it in the lab and then characterize it. We have to make our own version of the spike gene with those mutations running through those experimental assays.

The final thing I'll say is on a population level, watching how the pandemic's affecting and spreading through the world, different populations in countries that obviously has to play out over many weeks or months before we can interpret, you know, the effect of it.

WSIU : Yeah. And that leads me right to my next question, which is, you know, why people get, I think, overwhelmed by the amount of information and can talk a little bit about why the results you might find or speculate on based on your lab experience may not necessarily match up to what we then see as the real world effect of the virus.

Gagnon: Sure. So we have limited information. Even as scientists, we can look at the spike protein, for example. It's got these mutations. We've seen some of these mutations occur in the Delta variant or the Alpha variant, OK?

Those could be problematic all the way. There is these other mutations or what are they doing? So we have limited information. The other thing is, you know, the virus is not on an island on its own right. It's interacting with us, which is its host and the environment.

If it wants to infect people, it has to get around the vaccine or the immune system. There's many, many factors at play. So unfortunately, sometimes we make predictions that are not accurate and we have to be careful. Just like this on the omicron variant, we're all hoping that it turns out to not be as bad as we think, but we're bracing ourselves for what if it's pretty nasty?

WSIU: What if it is like, what is? Does this change our mitigation strategies that we've been dealing with throughout this pandemic?

Gagnon: That's a great question. So up till now, we were monitoring and tracking variants with the idea that we may have to update vaccines and just trying to watch how this virus is changing over time. But interestingly enough, it really hasn't changed our strategy or our approach. Social distance wear masks try to use common sense. Obviously, getting vaccinated reduces severe illness and disease. Try to limit travel across countries these things.

But this is what we were doing from the beginning. Question is, is it working? Do we need, I think all those things work and they help. Are we ever going to change that strategy based on changes of the virus?

I don't know. I'm not sure what else to do. I think we're doing all the right things, though at this point.

WSIU: Is there anything else you would add because you have a pretty neat, unique perspective on the pandemic from, you know, living in it like
we all are, but also being involved in this research?

Gagnon: Yeah, I don't know. I guess I'm I'm just like everybody else. I'm watching this play out in real time. I read the news too, and all we do is try to play our role that we've taken on, which is tracking it by sequencing.

You know, we feel confident that new variants will continue to emerge and just as curious as everybody else as. How are mask wearing our vaccination is going to benefit or not in the long run? I do think we're doing the right things.

We're doing what we know to do. And ultimately, I think the other thing I'm interested is what we grow to learn to live with this virus or will we have some breakthrough where we can eradicate it? It's unknown, but most likely we'll have to learn to live with it somehow, and it'll become a friend of ours for better or worse over the years.

WSIU: A frenemy, maybe.

Gagnon: A frenemy.

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Steph Whiteside is a Digital Media News Specialist with WSIU radio in Carbondale, Ill. She previously worked as a general reporter at AJ+ and Current TV.
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