ArticleAntimicrobial agents and chemotherapy2015
HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument.
Article in Antimicrobial agents and chemotherapy, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART.The Journal of antimicrobial chemotherapy · 2019Trial
- Article
- Identification of a Clade-Specific HLA-C*03:02 CTL Epitope GY9 Derived from the HIV-1 p17 Matrix Protein.International journal of molecular sciences · 2024Article
- Optimization of genetic distance threshold for inferring the CRF01_AE molecular network based on next-generation sequencing.Frontiers in cellular and infection microbiology · 2024Article
- Article
- 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
- Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance.Microbiology spectrum · 2022Article
- Low-frequency HIV-1 drug resistance mutations in antiretroviral naïve individuals in Botswana.Medicine · 2022Article
- Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience.International journal of molecular sciences · 2022Article
- Genetic Diversity and Acquired Drug Resistance Mutations Detected by Deep Sequencing in Virologic Failures among Antiretroviral Treatment Experienced Human Immunodeficiency Virus-1 Patients in a Pastoralist Region of Ethiopia.Infection and drug resistance · 2021Article
- Laboratory Optimization Tweaks for Sanger Sequencing in a Resource-Limited Setting.Journal of biomolecular techniques : JBT · 2020Article
- Are We Ready for NGS HIV Drug Resistance Testing? The Second "Winnipeg Consensus" Symposium.Viruses · 2020Article
- Article
- A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing.Scientific reports · 2020Article
- Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods.Scientific reports · 2019Article
- Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing.The Journal of molecular diagnostics : JMD · 2019Article
- Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2019Article
- A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance.Scientific reports · 2019Article
- Measurement error and variant-calling in deep Illumina sequencing of HIV.Bioinformatics (Oxford, England) · 2019Article
- Diagnosis of Human Immunodeficiency Virus Infection.Clinical microbiology reviews · 2019Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Limited access to HIV drug resistance testing in low- and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol to address this issue must be established to minimize negative therapeutic outcomes for HIV-1-infected individuals in such settings. This is an observational study to ascertain the potential of newer genomic sequencing platforms, such as the Illumina MiSeq instrument, to provide accurate HIV drug resistance genotypes for hundreds of samples simultaneously. Plasma samples were collected from Canadian patients during routine drug resistance testing (n = 759) and from a Ugandan study cohort (n = 349). Amplicons spanning HIV reverse transcriptase codons 90 to 234 were sequenced with both MiSeq sequencing and conventional Sanger sequencing methods. Sequences were evaluated for nucleotide concordance between methods, using coverage and mixture parameters for quality control. Consensus sequences were also analyzed for disparities in the identification of drug resistance mutations. Sanger and MiSeq sequencing was successful for 881 samples (80%) and 892 samples (81%), respectively, with 832 samples having results from both methods. Most failures were for samples with viral loads of <3.0 log10 HIV RNA copies/ml. Overall, 99.3% nucleotide concordance between methods was observed. MiSeq sequencing achieved 97.4% sensitivity and 99.3% specificity in detecting resistance mutations identified by Sanger sequencing. Findings suggest that the Illumina MiSeq platform can yield high-quality data with a high-multiplex "wide" sequencing approach. This strategy can be used for multiple HIV subtypes, demonstrating the potential for widespread individual testing and annual population surveillance in resource-limited settings.
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