High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States
Public Deposited- Creator
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McNamara, R.P.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Caro-Vegas, C.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Landis, J.T.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Moorad, R.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Pluta, L.J.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Eason, A.B.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Thompson, C.
- Affiliation: School of Medicine, Department of Pathology and Laboratory Medicine
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Bailey, A.
- Other Affiliation: Kuopio Center for Gene and Cell Therapy
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Villamor, F.C.S.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Lange, P.T.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Wong, J.P.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Seltzer, T.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Seltzer, J.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Zhou, Y.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
- Vahrson, W.
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Juarez, A.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Meyo, J.O.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Calabre, T.
- Other Affiliation: École supérieure de Chimie Physique Électronique (CPE)
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Broussard, G.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Rivera-Soto, R.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Chappell, D.L.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Baric, R.S.
- Affiliation: N.C. Cancer Hospital, UNC Lineberger Comprehensive Cancer Center
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Damania, B.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
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Miller, M.B.
- Affiliation: School of Medicine, Department of Pathology and Laboratory Medicine
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Dittmer, D.P.
- Affiliation: School of Medicine, Department of Microbiology and Immunology
- Abstract
- 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.
- Date of publication
- 2020
- Keyword
- DOI
- Identifier
- Resource type
- Article
- Rights statement
- In Copyright
- License
- Attribution 3.0 United States
- Journal title
- Cell Reports
- Journal volume
- 33
- Journal issue
- 5
- Page start
- 108352
- ISSN
- 2211-1247
Relations
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