ArticlePloS one2011
Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Absence of neurocognitive disadvantage associated with paediatric HIV subtype A infection in children on antiretroviral therapy.Journal of the International AIDS Society · 2017Trial
- Longitudinal Clinical and Molecular Characterization of a Single Pediatric Case of Vertically Acquired HIV-1 Subtype C with Baseline Resistance to Protease Inhibitors.Microorganisms · 2026Article
- Prevalence, associated factors and geospatial patterns of HIV drug resistance in South Africa among the virally unsuppressed adults: updated results from the 2017 national HIV household survey.BMC public health · 2026Article
- Improper use of TDF/FTC PrEP leading to acute HIV infection with low-level viremia and transient K70KR mutation: diagnostic challenges and drug resistance dynamics.Virology journal · 2025Article
- HIV-1 prevalence, drug resistance, and associated factors in the urban Ethiopian population.Scientific reports · 2025Article
- Impact of Chitosan Nanoparticles-Coated Dendritic Cell-Based Vaccine as Cancer Immunotherapy.Vaccines · 2025Article
- Resistance to Dolutegravir in Treatment-experienced Patients in South Africa: A Retrospective Cohort Study.Journal of acquired immune deficiency syndromes (1999) · 2025Article
- Higher Genotyping Performance of the Applied Biosystems TaqPath Seq HIV-1 Genotyping Kit Against ViroSeq HIV-1 Genotyping Kit in HIVInfection and drug resistance · 2025Article
- Article
- Immunological and molecular assessment of HIV-1 mutations for antiretroviral drug resistance in Saudi Arabia.PloS one · 2024Article
- Review
- HIV-1 Disease Progression and Drug Resistance Mutations among Children on First-Line Antiretroviral Therapy in Ethiopia.Biomedicines · 2023Article
- Resistance is common in paediatric patients failing ART in South Africa.The Journal of antimicrobial chemotherapy · 2023Article
- Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine.PNAS nexus · 2023Article
- Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings.AIDS research and therapy · 2023Article
- Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries.PLOS global public health · 2023Review
- A Partially Multiplexed HIV Drug Resistance (HIVDR) Assay for Monitoring HIVDR Mutations of the Protease, Reverse-Transcriptase (PRRT), and Integrase (INT).Microbiology spectrum · 2022Article
- Dolutegravir Resistance in Malawi's National HIV Treatment Program.Open forum infectious diseases · 2022Article
- Pretreatment Human Immunodeficiency Virus (HIV) Drug Resistance Among Treatment-Naive Infants Newly Diagnosed With HIV in 2016 in Namibia: Results of a Nationally Representative Study.Open forum infectious diseases · 2022Article
- Past and current status of adolescents living with HIV in South Africa, 2005-2017.BMC research notes · 2022Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledCommercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR) and reverse transcriptase (RT) regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96). Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P<0.001) and TRUGENE® and ViroSeq® assays. When the optimized in-house assay was applied to genotype samples collected for HIVDR surveys (N = 230), all 72 (100%) plasma and 69 (95.8%) of the matched dried blood spots (DBS) in the Vietnam transmitted HIVDR survey were genotyped and nucleotide sequence concordance was 98.8%; Testing of treatment-experienced patient plasmas with viral load (VL) ≥ and <3 log10 copies/ml from the Nigeria and Malawi surveys yielded 100% (N = 46) and 78.6% (N = 14) genotyping rates, respectively. Furthermore, all 18 matched DBS stored at room temperature from the Nigeria survey were genotyped. Phylogenetic analysis of the 236 sequences revealed that 43.6% were CRF01_AE, 25.9% subtype C, 13.1% CRF02_AG, 5.1% subtype G, 4.2% subtype B, 2.5% subtype A, 2.1% each subtype F and unclassifiable, 0.4% each CRF06_CPX, CRF07_BC and CRF09_CPX.
conclusionsThe optimized in-house assay is broadly sensitive in genotyping HIV-1 group M viral strains and more sensitive than the original in-house, TRUGENE® and ViroSeq® in detecting mixed viral populations. The broad sensitivity and substantial reagent cost saving make this assay more accessible for RLS where HIVDR surveillance is recommended to minimize the development and transmission of HIVDR.
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