ArticlePloS one2010
Development of a low bias method for characterizing viral populations using next generation sequencing technology.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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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.
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Who cites it
34 citing papers in PubMed.
- Article
- VirGenA: a reference-based assembler for variable viral genomes.Briefings in bioinformatics · 2019Article
- A decade of RNA virus metagenomics is (not) enough.Virus research · 2018Review
- Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing.Frontiers in microbiology · 2018Article
- Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.Virus evolution · 2018Article
- Separation and assembly of deep sequencing data into discrete sub-population genomes.Nucleic acids research · 2017Article
- Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.Viruses · 2017Article
- Effects of host restriction factors and the HTLV-1 subtype on susceptibility to HTLV-1-associated myelopathy/tropical spastic paraparesis.Retrovirology · 2017Article
- An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.BMC genomics · 2016Article
- A Pan-HIV Strategy for Complete Genome Sequencing.Journal of clinical microbiology · 2016Article
- Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.Viruses · 2016Article
- Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.Algorithms for molecular biology : AMB · 2016Article
- Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.Bioinformatics (Oxford, England) · 2015Article
- Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.BMC bioinformatics · 2015Article
- Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq.Frontiers in microbiology · 2015Article
- Deep sequencing: becoming a critical tool in clinical virology.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2014Review
- Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use?Current infectious disease reports · 2014Article
- Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.Antimicrobial agents and chemotherapy · 2014Article
- Article
- V-Phaser 2: variant inference for viral populations.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundWith an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and an additional 4.1 million people becoming infected each year, it is important to understand how this virus mutates and develops resistance in order to design successful therapies. METHODOLOGY/PRINCIPAL
findingsWe report a novel experimental method for amplifying full-length HIV genomes without the use of sequence-specific primers for high throughput DNA sequencing, followed by assembly of full length viral genome sequences from the resulting large dataset. Illumina was chosen for sequencing due to its ability to provide greater coverage of the HIV genome compared to prior methods, allowing for more comprehensive characterization of the heterogeneity present in the HIV samples analyzed. Our novel amplification method in combination with Illumina sequencing was used to analyze two HIV populations: a homogenous HIV population based on the canonical NL4-3 strain and a heterogeneous viral population obtained from a HIV patient's infected T cells. In addition, the resulting sequence was analyzed using a new computational approach to obtain a consensus sequence and several metrics of diversity. SIGNIFICANCE: This study demonstrates how a lower bias amplification method in combination with next generation DNA sequencing provides in-depth, complete coverage of the HIV genome, enabling a stronger characterization of the quasispecies present in a clinically relevant HIV population as well as future study of how HIV mutates in response to a selective pressure.
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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.