Cell Reports (Nov 2020)
High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States
- Ryan P. McNamara,
- Carolina Caro-Vegas,
- Justin T. Landis,
- Razia Moorad,
- Linda J. Pluta,
- Anthony B. Eason,
- Cecilia Thompson,
- Aubrey Bailey,
- Femi Cleola S. Villamor,
- Philip T. Lange,
- Jason P. Wong,
- Tischan Seltzer,
- Jedediah Seltzer,
- Yijun Zhou,
- Wolfgang Vahrson,
- Angelica Juarez,
- James O. Meyo,
- Tiphaine Calabre,
- Grant Broussard,
- Ricardo Rivera-Soto,
- Danielle L. Chappell,
- Ralph S. Baric,
- Blossom Damania,
- Melissa B. Miller,
- Dirk P. Dittmer
Affiliations
- Ryan P. McNamara
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Carolina Caro-Vegas
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Justin T. Landis
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Razia Moorad
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Linda J. Pluta
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Anthony B. Eason
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Cecilia Thompson
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Clinical Microbiology Laboratory, UNC Medical Center, Chapel Hill, NC 27599, USA
- Aubrey Bailey
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
- Femi Cleola S. Villamor
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Philip T. Lange
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Jason P. Wong
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Tischan Seltzer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Jedediah Seltzer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Yijun Zhou
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Wolfgang Vahrson
- Basel, Switzerland
- Angelica Juarez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- James O. Meyo
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA
- Tiphaine Calabre
- École supérieure de Chimie Physique Électronique (CPE), Lyon, France
- Grant Broussard
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA
- Ricardo Rivera-Soto
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA
- Danielle L. Chappell
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Ralph S. Baric
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA; Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Blossom Damania
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
- Melissa B. Miller
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Clinical Microbiology Laboratory, UNC Medical Center, Chapel Hill, NC 27599, USA; Corresponding author
- Dirk P. Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA; Corresponding author
- Journal volume & issue
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Vol. 33,
no. 5
p. 108352
Abstract
Summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly evolving. Prior studies focused on high-case-density locations, such as the northern and western metropolitan areas of the United States. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern region of the United States by high-density amplicon sequencing of symptomatic cases. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expands with time. Four strains carry a deletion in a predicted stem loop of the 3′ UTR. The data are consistent with community spread within local populations and the larger continental United States. The data instill confidence in current testing sensitivity and validate “testing by sequencing” as an option to uncover cases, particularly nonstandard coronavirus disease 2019 (COVID-19) clinical presentations. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the United States.
