ArticleNucleic acids research2015
Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Evolution of Multiple Domains of the HIV-1 Envelope Glycoprotein during Coreceptor Switch with CCR5 Antagonist Therapy.Microbiology spectrum · 2022Trial
- HIV-1 variants are archived throughout infection and persist in the reservoir.PLoS pathogens · 2020Trial
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1AIDS research and human retroviruses · 2024Article
- Quasispecies Fitness Partition to Characterize the Molecular Status of a Viral Population. Negative Effect of Early Ribavirin Discontinuation in a Chronically Infected HEV Patient.International journal of molecular sciences · 2022Article
- QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads.Bioinformatics (Oxford, England) · 2022Article
- Article
- Assessment of a diverse panel of transmitted/founder HIV-1 infectious molecular clones in a luciferase based CD8 T-cell mediated viral inhibition assay.Frontiers in immunology · 2022Article
- Assessment of the Current Status of Potyviruses in Watermelon and Pumpkin Crops in Spain: Epidemiological Impact of Cultivated Plants and Mixed Infections.Plants (Basel, Switzerland) · 2021Article
- Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts.Frontiers in microbiology · 2021Article
- Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections.Frontiers in microbiology · 2021Review
- Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection.PLoS pathogens · 2020Article
- Better Viral Control despite Higher CD4Journal of virology · 2020Article
- From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics.The Journal of infectious diseases · 2020Review
- Article
- A Highly Unusual V1 Region of Env in an Elite Controller of HIV Infection.Journal of virology · 2019Article
- Next-generation sequencing of HIV-1 single genome amplicons.Biomolecular detection and quantification · 2019Article
- Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing.Plant molecular biology · 2019Article
- HIV transmission in discordant couples in Africa in the context of antiretroviral therapy availability.AIDS (London, England) · 2018Article
- Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics.Nucleic acids research · 2018Review
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.
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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.