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SIU researchers identify new COVID-19 variant

A team led by a researcher at SIU Carbondale has discovered a new variant of the COVID-19 virus that is specific to and dominant in the United States, adding to the growing list of mutations discovered around the world.

Researchers say it might be more easily transmissible than other variants, and its impact on vaccines is uncertain.

Keith Gagnon, associate professor of chemistry and biochemistry at SIU, said work in his lab has uncovered a novel U.S.-specific coronavirus variant that accounts for about half of the cases in the country. An article detailing the discovery was submitted Monday to BioRxiv, a preprint server aimed at quickly disseminating research while it undergoes peer review.

"It's here. We found it," Gagnon said. "It's definitely home-grown and widespread, and we're the first to characterize it."

Scientists worldwide have identified multiple variants of SARS-CoV-2, the virus that causes COVID-19.

The culprit is a type of coronavirus, which encompasses a large family of viruses.

Some variants identified so far include one discovered in the United Kingdom with an unusually large number of mutations. Scientists in South Africa detected another variant in October.

The Centers for Disease Control and Prevention said last week that it had not seen the emergence of a highly contagious new U.S. variant of the coronavirus. It noted, however, that there are probably many variants emerging around the globe.

Gagnon's work traced the earliest appearance of the U.S. variant to Texas in May. The mutations it carries are in genes related to virus particle maturation and release, processing of viral proteins, and RNA genome integrity and translation, all of which are important for efficient and accurate virus production, Gagnon said.

Since then, the U.S. variant has acquired two new mutations in the spike protein that demonstrate its ongoing evolution, Gagnon said.

"We predict that 20C-US may already be the most dominant variant of SARS-CoV-2 in the U.S.," the article states. "The ongoing evolution of 20C-US, as well as other dominant region-specific variants emerging around the world, should continue to be monitored with genomic, epidemiologic, and experimental studies to understand viral evolution and predict future outcomes of the pandemic."

Gagnon said the rise of the U.S. variant coincides with the second and third wave of COVID-19 infections in the country, which might circumstantially point to it being more easily transmitted than other variants.

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

Gagnon's research team, which also included Koushik Sinha, assistant professor of computer science in the School of Computing, first noticed the possibility of the variant while looking at their own SARS-CoV-2 genome sequencing data from Illinois.

"The data kind of jumped off the page when we looked at it, so we then started looking at national data, and later worldwide genome sequence data," Gagnon said.

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

With the first vaccines still being administered in the U.S., Gagnon said it was unclear how this variant might impact its effectiveness.

"It's a great question," he said. "Based on the mutations so far, I don't think it will significantly impact the vaccine's effectiveness. The catch is that the virus continues to evolve, and since May, it has acquired three mutations, and two of them are in the spike protein, one of which might affect antibody binding. There are a lot of unknowns."