title: Rapid Detection of Common HIV-1 Drug Resistance Mutations by Use of High-Resolution Melting Analysis and Unlabeled Probes.
abstract: HIV rapidly accumulates resistance mutations following exposure to subtherapeutic concentrations of antiretroviral drugs that reduces treatment efficacy. High-resolution melting analysis (HRMA) has been used to successfully identify single nucleotide polymorphisms (SNPs) and to genotype viral and bacterial species. Here, we tested the ability of HRMA incorporating short unlabeled probes to accurately assign drug susceptibilities at the 103, 181, and 184 codons of the HIV-1 reverse transcriptase gene. The analytical sensitivities of the HRMA assays were 5% of mixed species for K103N and Y181C and 20% for M184V. When applied to 153 HIV-1 patient specimens previously genotyped by Sanger population sequencing, HRMA correctly assigned drug sensitivity or resistance profiles to 80% of the samples at codon 103 (K103K/N) (Cohen's kappa coefficient [κ] > 0.6; P < 0.05), 90% at 181 (Y181Y/C) (κ > 0.74, P < 0.05), and 80% at 184 (M184M/V) (κ > 0.62; P < 0.05). The frequency of incorrect genotypes was very low (≤1 to 2%) for each assay, which in most cases was due to the higher sensitivity of the HRMA assay. Specimens for which drug resistance profiles could not be assigned (9 to 20%) often had polymorphisms in probe binding regions. Thus, HRMA is a rapid, inexpensive, and sensitive method for the determination of drug sensitivities caused by major HIV-1 drug resistance mutations and, after further development to minimize the melting effects of nontargeted polymorphisms, may be suitable for surveillance purposes.
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors: David
authors: D
authors: Sacks
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa.
authors: Johanna
authors: J
authors: Ledwaba
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors: Lynn
authors: L
authors: Morris
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa gillianh@nicd.ac.za.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors: Gillian M
authors: GM
authors: Hunt
mesh_terms: D003365:Costs and Cost Analysis; D024882:Drug Resistance, Viral; D060005:Genotyping Techniques / Q000191:economics / Q000379:methods*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000191:economics / Q000379:methods*; D020125:Mutation, Missense; D012680:Sensitivity and Specificity; D013997:Time Factors; D044366:Transition Temperature
keywords: HRMA; drug resistance; human immunodeficiency virus