ArticleRetrovirology2014
Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants.
Article in Retrovirology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Article
- Navigating the Fitness Landscape: Host Density, Epistasis, and Clonal Interference Drive Divergent Evolutionary Pathways in Phage Qβ.International journal of molecular sciences · 2025Article
- A bibliometric analysis of HIV-1 drug-resistant minority variants from 1999 to 2024.AIDS research and therapy · 2025Article
- Modelling HIV-1 control and remission.NPJ systems biology and applications · 2024Review
- Correlated Allele Frequency Changes Reveal Clonal Structure and Selection in Temporal Genetic Data.Molecular biology and evolution · 2024Article
- Article
- Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster.Nature ecology & evolution · 2022Article
- PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences.Molecular biology and evolution · 2020Article
- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway.Frontiers in microbiology · 2020Article
- Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1.Molecular biology and evolution · 2019Article
- Genomic characterization of hepatitis C virus transmitted founder variants with deep sequencing.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2019Article
- Towards multiscale modeling of the CD8Wiley interdisciplinary reviews. Systems biology and medicine · 2019Review
- Dynamics of virus and immune response in multi-epitope network.Journal of mathematical biology · 2018Article
- Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.PLoS computational biology · 2018Article
- Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms.Journal of the International AIDS Society · 2018Article
- Kinetics of HIV-Specific CTL Responses Plays a Minimal Role in Determining HIV Escape Dynamics.Frontiers in immunology · 2018Article
- How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response.Journal of virology · 2017Article
- Global properties of nested network model with application to multi-epitope HIV/CTL dynamics.Journal of mathematical biology · 2017Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFollowing transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible because next generation sequencing delivers relatively short reads.
resultsWe here provide a proof of principle that whole HIV-1 genomes can be reliably reconstructed from short reads, and use this to study the selection of immune escape mutations at the level of whole genome haplotypes. Using realistically simulated HIV-1 populations, we demonstrate that reconstruction of complete genome haplotypes is feasible with high fidelity. We do not reconstruct all genetically distinct genomes, but each reconstructed haplotype represents one or more of the quasispecies in the HIV-1 population. We then reconstruct 30 whole genome haplotypes from published short sequence reads sampled longitudinally from a single HIV-1 infected patient. We confirm the reliability of the reconstruction by validating our predicted haplotype genes with single genome amplification sequences, and by comparing haplotype frequencies with observed epitope escape frequencies.
conclusionsPhylogenetic analysis shows that the HIV-1 population undergoes selection driven evolution, with successive replacement of the viral population by novel dominant strains. We demonstrate that immune escape mutants evolve in a dependent manner with various mutations hitchhiking along with others. As a consequence of this clonal interference, selection coefficients have to be estimated for complete haplotypes and not for individual immune escapes.
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