@article{1fe6571849c642438afda96eaa268113,
title = "Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection",
abstract = "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 sequenced saliva and nasal samples collected daily from vaccinated 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 unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants 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.",
keywords = "KEYWORDS SARS-CoV-2, genetic compartmentalization, viruses, within-host evolution",
author = "Mireille Farjo and Katia Koelle and Martin, {Michael A.} and Gibson, {Laura L.} and Walden, {Kimberly K.O.} and Gloria Rendon and Fields, {Christopher J.} and Alnaji, {Fadi G.} and Nicholas Gallagher and Luo, {Chun Huai} and Mostafa, {Heba H.} and Manabe, {Yukari C.} and Andrew Pekosz and Smith, {Rebecca L.} and McManus, {David D.} and Brooke, {Christopher B.}",
note = "This work has been generously supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health award 3U54HL143541-02S2) through the RADx-Tech program to D.D.M., L.L.G., and C.B.B. as well as additional funds generously provided by the Carl R. Woese Institute for Genomic Biology and the Department of Microbiology at the University of Illinois at Urbana-Champaign. HHS | NIH | National Heart, Lung, and 3U54HL143541-02S2 Laura L. Gibson Blood Institute (NHLBI) Yukari C. Manabe Andrew Pekosz Christopher B. Brooke Gloria Rendon Christopher J. Fields Rebecca L. Smith Heba H. Mostafa Katia Koelle Fadi G. Alnaji Michael A. Martin Kimberly K. O. Walden Nicholas Gallagher Chun Huai Luo David D. McManus Mireille Farjo",
year = "2024",
month = jan,
doi = "10.1128/jvi.01618-23",
language = "English (US)",
volume = "98",
journal = "Journal of virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "1",
}