ArticleBMC evolutionary biology2011
The mode and tempo of hepatitis C virus evolution within and among hosts.
Article in BMC evolutionary biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 1 of them a synthesis that pooled it.
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Who cites it
84 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Coalescent inference for infectious disease: meta-analysis of hepatitis C.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Pooled it
- Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus.Journal of clinical microbiology · 2015Trial
- Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States.Nature communications · 2025Article
- Conserved recombination patterns across hepatitis B genotypes: a retrospective study.Virology journal · 2025Article
- Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.PLoS pathogens · 2025Article
- Review
- Contemporary Insights into Hepatitis C Virus: A Comprehensive Review.Microorganisms · 2024Review
- Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020.BMC infectious diseases · 2023Article
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Healthcare-Related HCV Genotype 4d Infections in Kayseri, Turkey.The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology · 2022Article
- Molecular Epidemiology and Baseline Resistance of Hepatitis C Virus to Direct Acting Antivirals in Croatia.Pathogens (Basel, Switzerland) · 2022Article
- Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus.PLoS genetics · 2022Article
- Uncovering Resistance to Hepatitis C Virus Infection: Scientific Contributions and Unanswered Questions in the Irish Anti-D Cohort.Pathogens (Basel, Switzerland) · 2022Review
- Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States.Journal of medical virology · 2022Article
- Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data.PLoS pathogens · 2021Article
- Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a.Viruses · 2021Article
- Time and Mode of Epidemic HCV-2 Subtypes Spreading in Europe: Phylodynamics in Italy and Albania.Diagnostics (Basel, Switzerland) · 2021Article
- Molecular detection and genomic characterization of diverse hepaciviruses in African rodents.Virus evolution · 2021Article
- Impact of virus subtype and hostRNA (New York, N.Y.) · 2020Article
- PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences.Molecular biology and evolution · 2020Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus' public health importance and a wealth of sequence data, basic aspects of HCV molecular evolution remain poorly understood. Here we investigate three sets of whole HCV genomes in order to directly compare the evolution of whole HCV genomes at different biological levels: within- and among-hosts. We use a powerful Bayesian inference framework that incorporates both among-lineage rate heterogeneity and phylogenetic uncertainty into estimates of evolutionary parameters.
resultsMost of the HCV genome evolves at ~0.001 substitutions/site/year, a rate typical of RNA viruses. The antigenically-important E1/E2 genome region evolves particularly quickly, with correspondingly high rates of positive selection, as inferred using two related measures. Crucially, in this region an exceptionally higher rate was observed for within-host evolution compared to among-host evolution. Conversely, higher rates of evolution were seen among-hosts for functionally relevant parts of the NS5A gene. There was also evidence for slightly higher evolutionary rate for HCV subtype 1a compared to subtype 1b.
conclusionsUsing new statistical methods and comparable whole genome datasets we have quantified, for the first time, the variation in HCV evolutionary dynamics at different scales of organisation. This confirms that differences in molecular evolution between biological scales are not restricted to HIV and may represent a common feature of chronic RNA viral infection. We conclude that the elevated rate observed in the E1/E2 region during within-host evolution more likely results from the reversion of host-specific adaptations (resulting in slower long-term among-host evolution) than from the preferential transmission of slowly-evolving lineages.
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