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SIU Researcher Discusses New COVID Variant

A virus protein with spikes.
Daniel Roberts
The new variant is already widespread throughout the US.

SIU researchers have discovered a new variant of the coronavirus. I sat down with assistant professor of biochemistry, Keith Gagnon, whose RNA lab discovered the new strain.

Gagnon said the new variant appears to be unique and widespread.

“It has a set of mutations that are distinct and different from those that we've seen previously, including the UK variants,” Gagnon said. “So we're going to give it a different name. And it appears to have emerged in the US and spread to the US pretty widely and is now one of the most dominant forms”

Gagnon says his team wasn’t looking for the new variant.

“We've been sequencing genomes for Illinois Department of Public Health as part of a project. It's a partnership, and also an academic project,” he explained. “And we were, of course, hunting for the UK variant, like many other people, over the Christmas break and doing a lot of sequencing. When we sat down to look at our data, it sort of jumped out at us, all of a sudden, we see this new group that's popping off of the normal group. And so we decided to investigate it. And that's when we discovered these several mutations that it seems to have acquired pretty quickly.”

It’s too early for Gagnon’s team to know how the new variant might change the course of the pandemic. They are hoping to do studies to see if it might be more transmissible, but that will take time. Gagnon said it’s unlikely that this new strain will change the effectiveness of COVID vaccines.

“The questions we have is, has this variant been driving the pandemic? Is it responsible for the more cases and higher transmissibility? That's a great question, we don't know. But we would really like to know that. But the fact is that it's been here for a while, so you know, what are you gonna do? I think we need to get the vaccine as quickly as we can and just try to do the measures. We know that work. And the sooner we can, the sooner we can slow this down, the better off we'll be,” Gagnon said.

Determining whether or not this variant is more contagious isn’t an easy process, according to Gagnon.

“So there's some ways to try to predict or determine transmissibility, certainly experiments can be done, what we wanted to do is start with just cell culture, human cells in the laboratory. We can also look at epidemiology data and try to correlate that with the rise of this variant and its mutations. Eventually, you can do trials or testing in animals,” Gagnon said. “And you can also just see how things play out in the human population. So hopefully, we can learn more about the transmissibility of its variants over time, and how that changes as we change our habits. Or it acquires new mutations.”

Some places rely on modeling to determine transmissibility, which gets quicker answers.

“For example, this UK variant, where they came out right away and said, Oh, it's more transmissible. People don't understand, that was just mathematical modeling, there is no hard data that proves it's more transmissible and want to get that it does take a lot more work, testing and animal models and cell culture,” Gagnon said.

“ So all we can say is that, in the case of UK variant, it appears to be more transmissible. It's good modeling, they did good mathematical predictions and calculations, and they incorporate a lot of good epidemiology data. But still, it's not entirely clear. So this point, we can't really speculate too much about the 20CUS variant, except that it is the predominant variant right now in the US, and that coincides with lots and lots of cases,” Gagnon said, referring to the new variant.

What they do know is that this new variant spread quickly without anyone noticing.

“It was completely unnoticed, uncharacterized sort of right in our backyard. It just grew and basically took over the virus variant population, and nobody even knew and so that's sort of the take home from this, this project, that we need to do a much better job of watching this. We should not be having events that we don't know about, just come out of nowhere. We should know about these and be able to track them and follow them before they get out of hand,” Gagnon said.

Gagnon’s team is continuing to sequence the coronavirus to help track the spread of the pandemic. They are also continuing to research this new variant.

“We will continue to monitor the genome sequences globally and in the US. We will continue to generate Illinois specific genome sequences, we will be collaborating with some other research teams to do different types of experiments, which includes cell culture, hopefully testing the virus itself. And just gaining access more sequencing data so we can monitor the virus on also we'd like to incorporate more predictive tools, using the genomic data that we have available epidemiology data that we can hopefully get available, to try to see if we can learn more about the transmissibility, or potential biological impact of these mutations on us,” Gagnon concluded.

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