All SARS-CoV-2 infections include multiple variants: study

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Researchers have found wide genetic variation in SARS-CoV-2 viruses among 360 patients whose viral infections were genetically sequenced.

The results of a study by researchers at Case Western Reserve University (CWRU) in Cleveland, published on Thursday in PLOS Genetics, show that all individual infections include multiple variants of the virus, the authors said.

In the interest of time, reporting about the virus usually highlights a single dominant strain, but that leads to underreporting of virus genetic variation and can have serious consequences in public-health planning and response, the researchers noted.

The CWRU researchers noted that, given the multiple variations within single infections, it is important to report a more complete representation of the viral genetic sequences. That leads to an understanding of how these genetic changes can spread and potentially interact with different categories of patient conditions.

"Concentration on a majority consensus of virus variants within the global research community diverts attention from genetic variation that may contribute significantly to the continuing evolution of the COVID-19 pandemic," Peter Zimmerman, a professor in the Department of Pathology at the CWRU School of Medicine, said in a statement.

The research team performed full genome sequencing of SARS-CoV-2 viruses from 250 patients in northeastern Ohio and used similar data from another 110 patients with full genetic sequences of infecting viruses provided through international research collaborators.

These data were developed in the early days of the COVID-19 pandemic when the Alpha variant and then the Delta variant were of major concern. The work showed that mutations found in Omicron BA.1 and BA.2 were already present as relatively minor variations at least a year before Omicron and its many iterations became variants of concern., the researchers said.

"Our work brings attention to the complexity of infectious diseases that is often oversimplified when considering only the most abundant virus in an infection, and we demonstrate the importance of examining the variations that are historically considered noise," Ernest Chan, director of the bioinformatics core at the Case Western Reserve School of Medicine, said in a statement. "We see that genetic variants observed in low frequency in SARS-CoV-2 infections can be early indicators of new strains responsible for later transmission surges."

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