Individual COVID-19 infections include multiple variants of the SARS-CoV-2 virus, study finds.

Researchers from Case Western Reserve University have discovered a large genetic variation in virus of SARS-CoV-2 in 360 patients whose viral infections were genetically sequenced, showing that all individual infections include multiple variants of the virus.

The researchers noted that reports of the virus typically highlight a single dominant strain, which leads to underreporting of genetic variation in the virus and can have serious implications for public health planning and response.

Our work draws 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 looking at variations that are historically considered noise. . We find that the genetic variants observed at low frequency in SARS-CoV-2 infections may be early indicators of new strains responsible for subsequent transmission surges. »

Ernest (Ricky) Chan, director of the bioinformatics core at the Cleveland Institute for Computational Biology at the Case Western Reserve School of Medicine.

The article, titled “COVID-19 Infection and Transmission Includes Complex Sequence Diversity,” will be published September 8, 2022 in the journal “COVID-19.” PLOS Genetics. {Embargoed for 9.8 at 2 p.m. ET).

The CWRU team performed whole genome sequencing of the SARS-CoV-2 viruses from 250 patients in northeast Ohio and used similar data from another 110 patients whose full genetic sequences of the infecting viruses were provided by international research collaborators.

These data were developed at the start of the COVID-19 pandemic, when the Alpha variant and then the Delta variant were a major concern. This work showed that the 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”. Omicron and its own variants were at the heart of a major COVID-19 resurgence last winter.

“The focus on a majority consensus of virus variants within the global research community diverts attention from genetic variations that may contribute significantly to the ongoing evolution of the COVID-19 pandemic,” said Peter Zimmerman , professor in the Department of Pathology at the Faculty of Medicine. “Focusing on majority variants is an essential first step in the development of diagnostics, therapeutics and vaccines, but the research community must quantify and report this variation, so that the public health community and the general public are better prepared and more agile in the face of this ever-evolving virus. »

Much effort continues to be made to define and track the emergence of viral lineages in the ongoing evolution of SARS-CoV-2 around the world. To save time, researchers around the world have been content to track and report the relatively dominant variations. But the CWRU researchers noted that, given the multiple variations within a single infection, it is important to report a more complete representation of viral genetic sequences to understand how these genetic changes can spread and potentially interact with different categories of patient conditions, including evasion of eradication efforts.

Source :

Journal reference:

Chan, ER, et al. (2022) COVID-19 infection and transmission comprises a complex diversity of sequences. PLOS Genetics. doi.org/10.1371/journal.pgen.1010200.

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