ArticleGenome research2007
Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 228 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
228 citing papers in PubMed, 407 citations in OpenAlex.
- The Value of Combined Radial Endobronchial Ultrasound-Guided Transbronchial Lung Biopsy and Metagenomic Next-Generation Sequencing for Peripheral Pulmonary Infectious Lesions.Canadian respiratory journal · 2020Trial
- Single Genome Analysis for the Detection of Linked Multiclass Drug Resistance Mutations in HIV-1-Infected Children After Failure of Protease Inhibitor-Based First-Line Therapy.Journal of acquired immune deficiency syndromes (1999) · 2015Trial
- Identification of the NS5B S282T resistant variant and two novel amino acid substitutions that affect replication capacity in hepatitis C virus-infected patients treated with mericitabine and danoprevir.Antimicrobial agents and chemotherapy · 2014Trial
- Comparison of genotypic and phenotypic HIV type 1 tropism assay: results from the screening samples of Cenicriviroc Study 202, a randomized phase II trial in treatment-naive subjects.AIDS research and human retroviruses · 2014Trial
- Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of hepatitis C virus genotype 1-infected patients.Journal of virology · 2013Trial
- Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters.Retrovirology · 2013Trial
- Trial
- Trial
- Trial
- Omics-Level Approaches to Studying Gammaherpesvirus Infection.Pathogens (Basel, Switzerland) · 2026Review
- A bibliometric analysis of HIV-1 drug-resistant minority variants from 1999 to 2024.AIDS research and therapy · 2025Article
- Article
- Epidemiological surveillance and phylogenetic diversity of Orthohantavirus hantanense using high-fidelity nanopore sequencing, Republic of Korea.PLoS neglected tropical diseases · 2025Article
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Isolation and characterization of genetic variants of Orthohantavirus hantanense from clinical cases of HFRS in Jiangxi Province, China.PLoS neglected tropical diseases · 2024Article
- Quantification of in vitro replication kinetics of Alagoas vesiculovirus isolates by digital droplet RT-PCR.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
- Role of Proviral HIV-1 DNA Genotyping for People Living with HIV (PLWH) Who Had Low-Level Viremia While Receiving Antiretroviral Therapy.Infection and drug resistance · 2023Article
- Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting.Viruses · 2022Article
- Multiple Molecular Dynamics Simulations and Energy Analysis Unravel the Dynamic Properties and Binding Mechanism of Mutants HIV-1 Protease with DRV and CA-p2.Microbiology spectrum · 2022Article
- Detection of Chimeric Cellular: HIV mRNAs Generated Through Aberrant Splicing in HIV-1 Latently Infected Resting CD4+ T Cells.Frontiers in cellular and infection microbiology · 2022Article
168 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
5 authors at 1 institution in 1 country.
Funding
Abstract
The detection of mutant spectra within a population of microorganisms is critical for the management of drug-resistant infections. We performed ultra-deep pyrosequencing to detect minor sequence variants in HIV-1 protease and reverse transcriptase (RT) genes from clinical plasma samples. We estimated empirical error rates from four HIV-1 plasmid clones and used them to develop a statistical approach to distinguish authentic minor variants from sequencing errors in eight clinical samples. Ultra-deep pyrosequencing detected an average of 58 variants per sample compared with an average of eight variants per sample detected by conventional direct-PCR dideoxynucleotide sequencing. In the clinical sample with the largest number of minor sequence variants, all 60 variants present in > or =3% of genomes and 20 of 35 variants present in <3% of genomes were confirmed by limiting dilution sequencing. With appropriate analysis, ultra-deep pyrosequencing is a promising method for characterizing genetic diversity and detecting minor yet clinically relevant variants in biological samples with complex genetic populations.
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.