@article{1f197d463cec46d4bba0bd0a371c0183,
title = "High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States",
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.",
keywords = "COVID-19, SARS-CoV-2, coronavirus, mutational landscape, next-generation sequencing, single-nucleotide variations, testing by sequencing",
author = "McNamara, {Ryan P.} and Carolina Caro-Vegas and Landis, {Justin T.} and Razia Moorad and Pluta, {Linda J.} and Eason, {Anthony B.} and Cecilia Thompson and Aubrey Bailey and Villamor, {Femi Cleola S.} and Lange, {Philip T.} and Wong, {Jason P.} and Tischan Seltzer and Jedediah Seltzer and Yijun Zhou and Wolfgang Vahrson and Angelica Juarez and Meyo, {James O.} and Tiphaine Calabre and Grant Broussard and Ricardo Rivera-Soto and Chappell, {Danielle L.} and Baric, {Ralph S.} and Blossom Damania and Miller, {Melissa B.} and Dittmer, {Dirk P.}",
note = "Funding Information: This work was funded by NIH public health service grants CA016086 , CA019014 , and CA239583 to D.P.D. Funding was also provided by the University Cancer Research Fund and the UNC School of Medicine . This project was supported by the North Carolina Policy Collaboratory at UNC with funding from the North Carolina Coronavirus Relief Fund established and appropriated by the North Carolina General Assembly. The authors would like to thank all the members of the Damania and Dittmer labs, Corbin Jones, and Nicole Fischer for critical reading, comments, and suggestions. We also thank the participants and the nurses and physicians at the UNC Pulmonary Intensive Care Unit and Department of Infectious Diseases who, in addition to their heroic patient care, ensure that de-identified excess samples are available for discovery research and rapidly validating novel diagnostic approaches. Publisher Copyright: {\textcopyright} 2020 The Author(s)",
year = "2020",
month = nov,
day = "3",
doi = "10.1016/j.celrep.2020.108352",
language = "English (US)",
volume = "33",
journal = "Cell Reports",
issn = "2211-1247",
publisher = "Cell Press",
number = "5",
}
