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-SotoDanielle L. Chappell, Ralph S. Baric, Blossom Damania, Melissa B. Miller*, Dirk P. Dittmer

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


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.

Original languageEnglish (US)
Article number108352
JournalCell reports
Issue number5
StatePublished - Nov 3 2020


  • COVID-19
  • SARS-CoV-2
  • coronavirus
  • mutational landscape
  • next-generation sequencing
  • single-nucleotide variations
  • testing by sequencing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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