RT Journal Article
SR Electronic
T1 High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.19.161141
DO 10.1101/2020.06.19.161141
A1 Ryan P. McNamara
A1 Carolina Caro-Vegas
A1 Justin T. Landis
A1 Razia Moorad
A1 Linda J. Pluta
A1 Anthony B. Eason
A1 Cecilia Thompson
A1 Aubrey Bailey
A1 Femi Cleola S. Villamor
A1 Philip T. Lange
A1 Jason P. Wong
A1 Tischan Seltzer
A1 Jedediah Seltzer
A1 Yijun Zhou
A1 Wolfgang Vahrson
A1 Angelica Juarez
A1 James O. Meyo
A1 Tiphaine Calabre
A1 Grant Broussard
A1 Ricardo Rivera-Soto
A1 Danielle L. Chappell
A1 Ralph S. Baric
A1 Blossom Damania
A1 Melissa B. Miller
A1 Dirk P. Dittmer
YR 2020
UL http://biorxiv.org/content/early/2020/06/19/2020.06.19.161141.abstract
AB SARS-CoV-2 is constantly evolving. Prior studies have focused on high case-density locations, such as the Northern and Western metropolitan areas in the U.S. This study demonstrates continued SARS-CoV-2 evolution in a suburban Southern U.S. region by high-density amplicon sequencing of symptomatic cases. 57% of strains carried the spike D614G variant. The presence of D614G was associated with a higher genome copy number and its prevalence expanded with time. Four strains carried a deletion in a predicted stem loop of the 3’ untranslated region. The data are consistent with community spread within the local population and the larger continental U.S. No strain had mutations in the target sites used in common diagnostic assays. The data instill confidence in the sensitivity of current tests and validate “testing by sequencing” as a new option to uncover cases, particularly those not conforming to the standard clinical presentation of COVID-19. This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S.Competing Interest StatementThe authors have declared no competing interest.