ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2015
Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure.
Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it.
- RNA-seq research landscape in Africa: systematic review reveals disparities and opportunities.European journal of medical research · 2023Pooled it
- Size, Composition, and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc.Journal of virology · 2018Trial
- HIV-1 Drug Resistance in Children and Implications for Pediatric Treatment Strategies: A Systematic Review and Meta-analysis.Open forum infectious diseases · 2025Review
- Global, regional, and national prevalence of HIV-1 drug resistance in treatment-naive and treatment-experienced children and adolescents: a systematic review and meta-analysis.EClinicalMedicine · 2024Article
- Article
- Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance.Microbiology spectrum · 2022Article
- Next generation sequencing based in-house HIV genotyping method: validation report.AIDS research and therapy · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing.Viruses · 2020Article
- MiDRMViruses · 2019Article
- Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations.PLoS pathogens · 2019Article
- Measurement error and variant-calling in deep Illumina sequencing of HIV.Bioinformatics (Oxford, England) · 2019Article
- Transient and asymptomatic meningitis in human immunodeficiency virus-1 subtype C: a case study of genetic compartmentalization and biomarker dynamics.Journal of neurovirology · 2018Article
- Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay.AIDS research and therapy · 2018Article
- Article
- Metagenomic Analysis ofFrontiers in cellular and infection microbiology · 2018Article
- Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses.Frontiers in cellular and infection microbiology · 2018Article
- No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men.Journal of virology · 2017Article
- Dynamic of CSF and serum biomarkers in HIV-1 subtype C encephalitis with CNS genetic compartmentalization-case study.Journal of neurovirology · 2017Article
- Decreased emergence of HIV-1 drug resistance mutations in a cohort of Ugandan women initiating option B+ for PMTCT.PloS one · 2017Article
Corrections and comments
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10 authors.
Funding
Abstract
backgroundNext generation sequencing (NGS) allows the detection of minor variant HIV drug resistance mutations (DRMs). However data from new NGS platforms after Prevention-of-Mother-to-Child-Transmission (PMTCT) regimen failure are limited.
objectiveTo compare major and minor variant HIV DRMs with Illumina MiSeq and Life Technologies Ion Personal Genome Machine (PGM) in infants infected despite a PMTCT regimen. STUDY
designWe conducted a cross-sectional study of NGS for detecting DRMs in infants infected despite a zidovudine (AZT) and Nevirapine (NVP) regimen, before initiation of combination antiretroviral therapy. Sequencing was performed on PCR products from plasma samples on PGM and MiSeq platforms. Bioinformatic analyses were undertaken using a codon-aware version of the Smith-Waterman mapping algorithm and a mixture multinomial error filtering statistical model.
resultsOf 15 infants, tested at a median age of 3.4 months after birth, 2 (13%) had non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs (K103N and Y181C) by bulk sequencing, whereas PGM detected 4 (26%) and MiSeq 5 (30%). NGS enabled the detection of additional minor variant DRMs in the infant with K103N. Coverage and instrument quality scores were higher with MiSeq, increasing the confidence of minor variant calls.
conclusionsNGS followed by bioinformatic analyses detected multiple minor variant DRMs in HIV-1 RT among infants where PMTCT failed. The high coverage of MiSeq and high read quality improved the confidence of identified DRMs and may make this platform ideal for minor variant detection.
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