Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection
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
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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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Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manabe YC, Pekosz A, Smith RL, McManus DD, Brooke CB. Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. J Virol. 2024 Jan 4:e0161823. doi: 10.1128/jvi.01618-23. Epub ahead of print. PMID: 38174928.
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This article is based on a previously available preprint in bioRxiv, https://doi.org/10.1101/2022.06.21.497047