RT Journal Article
SR Electronic
T1 Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.06.21.497047
DO 10.1101/2022.06.21.497047
A1 Mireille Farjo
A1 Katia Koelle
A1 Michael A. Martin
A1 Laura L. Gibson
A1 Kimberly K.O. Walden
A1 Gloria Rendon
A1 Christopher J. Fields
A1 Fadi G. Alnaji
A1 Nicholas Gallagher
A1 Chun Huai Luo
A1 Heba H. Mostafa
A1 Yukari C. Manabe
A1 Andrew Pekosz
A1 Rebecca L. Smith
A1 David D. McManus
A1 Christopher B. Brooke
YR 2022
UL http://biorxiv.org/content/early/2022/06/23/2022.06.21.497047.abstract
AB The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we deep sequenced saliva and nasal samples collected daily from immune and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both naïve and immune individuals appeared largely stochastic; however, we identified clear mutational hotspots within the viral genome, consistent with selection and differing between naïve and immune individuals. In rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of virus between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.Competing Interest StatementThe authors have declared no competing interest.