ArticleJournal of virology2024
Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection.
Article in Journal of virology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 22 citations in OpenAlex.
- Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity.bioRxiv : the preprint server for biology · 2026Article
- Dose-dependent effects of recombinant spike protein-based vaccination on SARS-CoV-2 evolutionary dynamics and the emergence of variants in hamster models.The Journal of general virology · 2026Article
- SIMPLICITY is an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution.Communications biology · 2026Article
- Pathology and viral evolutionary dynamics in a hamster model of persistent SARS-CoV-2 infection.Communications biology · 2026Article
- SARS-CoV-2 intra-host evolution during acute infection in COVID-19 patients.Frontiers in microbiology · 2026Article
- Anellovirus constraint from 2 to 6 months postpartum followed by betatorquevirus and gammatorquevirus dominance in serum and milk.Journal of virology · 2025Article
- In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants.PLoS pathogens · 2025Article
- SARS-CoV-2 genomic evolution during a severe and long-lasting omicron infection under antiviral therapy.BMC infectious diseases · 2025Article
- Article
- Dispersal of influenza virus populations within the respiratory tract shapes their evolutionary potential.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections.Virus evolution · 2025Article
- Article
- Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons.bioRxiv : the preprint server for biology · 2024Article
- Review
- Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection.Virus evolution · 2024Article
- Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons.Virus evolution · 2024Article
- Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection.Cell reports. Medicine · 2023Article
- Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2.mSphere · 2023Article
- Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants.Nature communications · 2023Article
- Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants.bioRxiv : the preprint server for biology · 2022Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 1 country.
Funding
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.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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.