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Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States

Adrian A. Pater, Michael S. Bosmeny, Christopher L. Barkau, Katy N. Ovington, Ramadevi Chilamkurthy, Mansi Parasrampuria, Seth B. Eddington, Abadat O. Yinusa, Adam A. White, Paige E. Metz, Rourke J. Sylvain, Madison M. Hebert, Scott W. Benzinger, Koushik Sinha, View ORCID ProfileKeith T. Gagnon
doi: https://doi.org/10.1101/2021.01.11.426287
Adrian A. Pater
1Southern Illinois University, Chemistry and Biochemistry, Carbondale, Illinois, USA, 62901
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Michael S. Bosmeny
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Christopher L. Barkau
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Katy N. Ovington
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Ramadevi Chilamkurthy
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Mansi Parasrampuria
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Seth B. Eddington
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Abadat O. Yinusa
1Southern Illinois University, Chemistry and Biochemistry, Carbondale, Illinois, USA, 62901
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Adam A. White
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Paige E. Metz
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Rourke J. Sylvain
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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Madison M. Hebert
1Southern Illinois University, Chemistry and Biochemistry, Carbondale, Illinois, USA, 62901
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Scott W. Benzinger
1Southern Illinois University, Chemistry and Biochemistry, Carbondale, Illinois, USA, 62901
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Koushik Sinha
3Southern Illinois University School of Computing, Carbondale, Illinois, USA, 62901
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Keith T. Gagnon
1Southern Illinois University, Chemistry and Biochemistry, Carbondale, Illinois, USA, 62901
2Southern Illinois University School of Medicine, Biochemistry and Molecular Biology, Carbondale, Illinois, USA, 62901
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  • ORCID record for Keith T. Gagnon
  • For correspondence: ktgagnon@siu.edu
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Abstract

Genomic virus surveillance can lead to early identification of new variants and inform proper response during a pandemic. Using this approach, we have identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.) early in the coronavirus disease (COVID-19) pandemic and has become one of the most prevalent U.S variants. This new variant within the B.1.2 lineage referred to here as 20C-US, has not yet spread widely to other countries. The earliest 20C-US genomes can be traced to the southern U.S. in late May of 2020. A major early event was the rapid acquisition of five non-synonymous mutations. The changes carried by 20C-US include mutations to genes involved in virus particle maturation and release, processing of viral proteins, and RNA genome integrity and translation genes, all important for efficient and accurate virus production. In addition, 20C-US has since acquired two new non-synonymous mutations that highlight its ongoing evolution, one of which is a Q677H mutation in the spike protein adjacent to the furin cleavage site. We predict that 20C-US may already be the most dominant variant of SARS-CoV-2 in the U.S. 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.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 13, 2021.
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Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States
Adrian A. Pater, Michael S. Bosmeny, Christopher L. Barkau, Katy N. Ovington, Ramadevi Chilamkurthy, Mansi Parasrampuria, Seth B. Eddington, Abadat O. Yinusa, Adam A. White, Paige E. Metz, Rourke J. Sylvain, Madison M. Hebert, Scott W. Benzinger, Koushik Sinha, Keith T. Gagnon
bioRxiv 2021.01.11.426287; doi: https://doi.org/10.1101/2021.01.11.426287
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Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States
Adrian A. Pater, Michael S. Bosmeny, Christopher L. Barkau, Katy N. Ovington, Ramadevi Chilamkurthy, Mansi Parasrampuria, Seth B. Eddington, Abadat O. Yinusa, Adam A. White, Paige E. Metz, Rourke J. Sylvain, Madison M. Hebert, Scott W. Benzinger, Koushik Sinha, Keith T. Gagnon
bioRxiv 2021.01.11.426287; doi: https://doi.org/10.1101/2021.01.11.426287

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