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

Mireille Farjo, Katia Koelle, Michael A. Martin, Laura L. Gibson, Kimberly K.O. Walden, Gloria Rendon, Christopher J. Fields, Fadi G. Alnaji, Nicholas Gallagher, Chun Huai Luo, Heba H. Mostafa, Yukari C. Manabe, Andrew Pekosz, Rebecca L. Smith, David D. McManus, Christopher B. Brooke

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
JournalJournal of virology
Issue number1
StatePublished - Jan 2024


  • genetic compartmentalization
  • viruses
  • within-host evolution

ASJC Scopus subject areas

  • Insect Science
  • Virology
  • Microbiology
  • Immunology


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