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Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

Authors
  • Farjo, Mireille
  • Koelle, Katia
  • Martin, Michael A.
  • Gibson, Laura L.
  • Walden, Kimberly K. O.
  • Rendon, Gloria
  • Fields, Christopher J.
  • Alnaji, Fadi G.
  • Gallagher, Nicholas
  • Luo, Chun Huai
  • Mostafa, Heba H.
  • Manabe, Yukari C.
  • Pekosz, Andrew
  • Smith, Rebecca L.
  • McManus, David D.
  • Brooke, Christopher B.
Type
Published Article
Journal
Journal of Virology
Publisher
American Society for Microbiology
Publication Date
Jan 04, 2024
Volume
98
Issue
1
Identifiers
DOI: 10.1128/jvi.01618-23
Source
ASM Journals
Keywords
License
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Abstract

We detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.

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