ArticleNucleic acids research2014
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
74 citing papers in PubMed, 160 citations in OpenAlex.
- Trial
- Direct estimation of genotype fitness from time series.bioRxiv : the preprint server for biology · 2026Article
- Virus variant quantification with Orthanq.BMC bioinformatics · 2026Article
- Substantial deceleration of adaptation of HIV-1 within 1500 generations in an experimental evolution: a genomic perspective.Virus evolution · 2026Article
- Population sequencing for phylogenetic diversity and transmission analyses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Addressing data management and analysis challenges in viral genomics: The Swiss HIV cohort study viral next generation sequencing database.PLOS digital health · 2025Article
- Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development.Cell host & microbe · 2025Article
- Algorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2025Review
- VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.NAR genomics and bioinformatics · 2024Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen.PLoS pathogens · 2024Article
- The molecular epidemiology of a dengue virus outbreak in Taiwan: population wide versus infrapopulation mutation analysis.PLoS neglected tropical diseases · 2024Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study.Brain communications · 2024Article
- Absence of Proviral Human Immunodeficiency Virus (HIV) Type 1 Evolution in Early-Treated Individuals With HIV Switching to Dolutegravir Monotherapy During 48 Weeks.The Journal of infectious diseases · 2023Article
- Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018.The Journal of antimicrobial chemotherapy · 2023Article
- Capturing variation in metagenomic assembly graphs with MetaCortex.Bioinformatics (Oxford, England) · 2023Article
- AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.Bioinformatics (Oxford, England) · 2023Article
- HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization.Bioinformatics (Oxford, England) · 2022Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.
Indexed as
Identifiers
What OpenQuestion holds
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.