ArticlePloS one2010
Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 69 citations in OpenAlex.
- Article
- Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2023Article
- Next-Generation Sequencing for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations.Viruses · 2020Review
- Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences.PloS one · 2020Article
- Amino Acid Prevalence of HIV-1AIDS research and human retroviruses · 2019Article
- An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.Genome biology · 2019Article
- A novel framework for inferring parameters of transmission from viral sequence data.PLoS genetics · 2018Article
- Comparison of anJournal of clinical microbiology · 2018Article
- Detection of minority drug resistant mutations in Malawian HIV-1 subtype C-positive patients initiating and on first-line antiretroviral therapy.African journal of laboratory medicine · 2018Article
- No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men.Journal of virology · 2017Article
- On the effective depth of viral sequence data.Virus evolution · 2017Article
- HIV-1 Drug Resistance by Ultra-Deep Sequencing Following Short Course Zidovudine, Single-Dose Nevirapine, and Single-Dose Tenofovir with Emtricitabine for Prevention of Mother-to-Child Transmission.Journal of acquired immune deficiency syndromes (1999) · 2016Article
- Treatment failure and drug resistance in HIV-positive patients on tenofovir-based first-line antiretroviral therapy in western Kenya.Journal of the International AIDS Society · 2016Article
- Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain.AIDS research and human retroviruses · 2015Article
- Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq.Frontiers in microbiology · 2015Article
- Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2015Article
- Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.PloS one · 2015Article
- Frequency of Antiretroviral Resistance Mutations among Infants Exposed to Single-Dose Nevirapine and Short Course Maternal Antiretroviral Regimens: ACTG A5207.Journal of AIDS & clinical research · 2014Article
- HIV-1 drug resistance in the iPrEx preexposure prophylaxis trial.The Journal of infectious diseases · 2014Article
- Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing.Journal of clinical microbiology · 2014Article
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe HIV-1 nucleoside RT inhibitor (NRTI)-resistance mutation, K65R confers intermediate to high-level resistance to the NRTIs abacavir, didanosine, emtricitabine, lamivudine, and tenofovir; and low-level resistance to stavudine. Several lines of evidence suggest that K65R is more common in HIV-1 subtype C than subtype B viruses. METHODS AND
findingsWe performed ultra-deep pyrosequencing (UDPS) and clonal dideoxynucleotide sequencing of plasma virus samples to assess the prevalence of minority K65R variants in subtype B and C viruses from untreated individuals. Although UDPS of plasma samples from 18 subtype C and 27 subtype B viruses showed that a higher proportion of subtype C viruses contain K65R (1.04% vs. 0.25%; p<0.001), limiting dilution clonal sequencing failed to corroborate its presence in two of the samples in which K65R was present in >1.5% of UDPS reads. We therefore performed UDPS on clones and site-directed mutants containing subtype B- and C-specific patterns of silent mutations in the conserved KKK motif encompassing RT codons 64 to 66 and found that subtype-specific nucleotide differences were responsible for increased PCR-induced K65R mutation in subtype C viruses.
conclusionsThis study shows that the RT KKK nucleotide template in subtype C viruses can lead to the spurious detection of K65R by highly sensitive PCR-dependent sequencing techniques. However, the study is also consistent with the subtype C nucleotide template being inherently responsible for increased polymerization-induced K65R mutations in vivo.
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