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SIU researchers identify new variant of the coronavirus unique to the U.S., could spread more easily

SIU researchers identify new variant of the coronavirus unique to the U.S., could spread more easily

Coronavirus U.S. variant identified by SIU

Koushik Sinha, assistant professor of computer science in SIU Carbondale’s School of Computing, left, and Keith Gagnon, associate professor of chemistry and biochemistry in the College of Agricultural, Life and Physical Sciences, after receiving a one-year $360,000 grant last fall from the Walder Foundation to study and track the COVID-19 virus as it moves through the population. Photo by Yenitza Melgoza for SIU.

CARBONDALE — Researchers out of Illinois have identified a variant of the coronavirus that is unique to and dominant in the United States and appears to be more transmissible than other variants, according to the findings released Thursday.

Southern Illinois University Carbondale submitted the study this week to the public server BioRxiv, which aims to quickly disseminate research while it undergoes the lengthy peer-review process required to publish in medical journals.

The new variant adds to the growing list of mutations of the virus such as those discovered in the United Kingdom and South Africa that have raised alarms because they are more easily spread. They don’t appear to be any more lethal, however.

Keith Gagnon, associate professor of chemistry at SIU, said the U.S.-specific variant first appeared early in the pandemic and has become one of the most prevalent in the U.S., accounting for about half of the cases in the country.

“It’s here. We found it,” Gagnon said in a press release. “It’s definitely home-grown and widespread, and we’re the first to characterize it.”

Viruses change and evolve as they move through populations. Scientists worldwide have identified multiple variants of SARS-CoV-2, the virus that causes COVID-19. Sometimes variants disappear shortly after they emerge, while others hang around.

Gagnon’s lab studied the genome of coronavirus samples collected across the country and world. His team traced the earliest appearance of the U.S. variant to Texas in May.

The variant’s unique mutations are in the genes that are important for efficient and accurate virus production, Gagnon stated.

Since May, the U.S. variant — referred to as 20C-US — continued to circulate unnoticed and evolve, acquiring to new mutations.

The rise of the U.S. variant coincides with the second and third wave of COVID-19 infections in the country, which suggests that it spreads more easily than other variants, Gagnon said.

“There are hundreds of variants floating around, so for this one to rise to prominence suggests it might be more transmissible,” he said.

The researchers found that the U.S. variant had not spread significantly beyond the country’s borders and that it was most highly prevalent in the Upper Midwest.

“It should be a shock that it was able to basically overtake all the other variants in the U.S.,” Gagnon said. “It’s now possibly the major dominant variant in the U.S., and it was right underneath our noses.”

Identifying mutations can give clues to the way a virus spreads and what it might do next. Scientists can now track the newly discovered variant and look for increases in transmission, more severe illness or increases in death.

“It has very different mutations than the other variants that are out there in the world,” Gagnon said. “So, we get to determine what that means, let’s just hope it turns out to be mundane and not another big story.”

The U.S. Centers for Disease Control and Prevention is working to learn more about the variants and whether they act as “escape mutants” with the ability to evade immunity provided by the vaccine.

“There is no evidence that this is occurring, and most experts believe escape mutants are unlikely to emerge because of the nature of the virus,” the CDC website states.

Strain surveillance has recently been ramping up in the U.S. State health departments and other public health agencies have since November been regularly sending test samples of the coronavirus to the CDC for genome sequencing.

As of Dec. 29, the CDC has partnered with labs across the country to sequence 1,750 samples a week, the CDC website states.

Gagnon said that while he’s happy to see the recent efforts, the U.S. is “woefully behind” other countries in sequencing the genomes of the coronavirus circulating within their borders.

“I think we are answering the call. It was a little too late for this variant,” he said, “but now that we know it’s here, we can watch it closely.”

Gagnon said based on the mutations he’s seen in the U.S. variant, he does not think it will significantly impact the vaccine’s effectiveness.

But that could change.

“The catch is that the virus continues to evolve, and since May, it has acquired three mutations …,” he said. “There are a lot of unknowns.”

Updated at 6 p.m.(tncms-asset)485a597e-567e-11eb-ab5d-00163ec2aa77[1](/tncms-asset)(tncms-asset)ea7f12f4-55c4-11eb-8c9b-00163ec2aa77[2](/tncms-asset)

Michele Munz • 314-340-8263 @michelemunz on Twitter

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