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

Autor:	Farjo M; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA., Koelle K; Department of Biology, Emory University, Atlanta, Georgia, USA., Martin MA; Department of Biology, Emory University, Atlanta, Georgia, USA.; Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA., Gibson LL; Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA., Walden KKO; High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA., Rendon G; High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA., Fields CJ; High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA., Alnaji FG; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA., Gallagher N; Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA., Luo CH; Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA., Mostafa HH; Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA., Manabe YC; Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA., Pekosz A; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA., Smith RL; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.; Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA., McManus DD; Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA., Brooke CB; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Jazyk:	angličtina
Zdroj:	Journal of virology [J Virol] 2024 Jan 23; Vol. 98 (1), pp. e0161823. Date of Electronic Publication: 2024 Jan 04.
DOI:	10.1128/jvi.01618-23
Abstrakt:	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.IMPORTANCEWe 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. Competing Interests: The authors declare no conflict of interest.
Databáze:	MEDLINE
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