ArticlePLoS pathogens2020
Drivers of within-host genetic diversity in acute infections of viruses.
Article in PLoS pathogens, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 33 citations in OpenAlex.
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- Genomic evolution and minority variant dynamics of RSV during the first season of nirsevimab implementation in Italy (2024-5).Virus evolution · 2026Article
- Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.Nature communications · 2025Article
- Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle.Molecular biology and evolution · 2025Article
- The ageing virus hypothesis: Epigenetic ageing beyond the Tree of Life.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients.Virus evolution · 2025Article
- Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.bioRxiv : the preprint server for biology · 2024Article
- Reovirus infection induces transcriptome-wide unique A-to-I editing changes in the murine fibroblasts.Virus research · 2024Article
- Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes.Journal of virology · 2023Article
- Open questions in the social lives of viruses.Journal of evolutionary biology · 2023Review
- Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments.The Journal of clinical investigation · 2023Observational
- Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation.Virus evolution · 2023Article
- Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants.iScience · 2022Article
- A general approach to identify low-frequency variants within influenza samples collected during routine surveillance.Microbial genomics · 2022Article
- Thermal stress triggers productive viral infection of a key coral reef symbiont.The ISME journal · 2022Article
- Article
- Global genetic diversity and evolutionary patterns amongFrontiers in microbiology · 2022Article
- The evolution of cheating in viruses.Nature communications · 2021Review
- Review
- Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections.Virus evolution · 2021Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic diversity is the fuel of evolution and facilitates adaptation to novel environments. However, our understanding of what drives differences in the genetic diversity during the early stages of viral infection is somewhat limited. Here, we use ultra-deep sequencing to interrogate 43 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV. Hundreds to thousands of virus templates were sequenced per sample, allowing us to reveal dramatic differences in within-host genetic diversity among virus populations. We found that increased diversity was mostly driven by presence of multiple divergent genotypes in HIV and CMV samples, which we suggest reflect multiple transmitted/founder viruses. Conversely, we detected an abundance of low frequency hyper-edited genomes in RSV samples, presumably reflecting defective virus genomes (DVGs). We suggest that RSV is characterized by higher levels of cellular co-infection, which allow for complementation and hence elevated levels of DVGs.
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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.