title: Sensitive detection of the K103N non-nucleoside reverse transcriptase inhibitor resistance mutation in treatment-naïve HIV-1 infected individuals by rolling circle amplification.
abstract: Primary or transmitted antiretroviral drug resistance mutations pose a significant obstacle for optimizing antiviral treatment. When present at low-levels, resistance mutations are less likely to be detected by standard genotyping assays. This study utilizes a novel rolling circle amplification (RCA) method using padlock probes to achieve the sensitive, specific and low-level detection of the NNRTI resistance K103N from 59 HIV+ treatment-naïve patients from Beijing, China. Using standard genotyping methods, primary drug resistance mutations to either protease or RT inhibitors were found in 25% (15/59) of patients attending hospital clinics in Beijing. Among these 15 patients with antiretroviral (ARV) resistance mutations, standard sequence-based genotyping revealed that most (10/15) had the 103N. Using a highly sensitive RCA assay, 5 more patients among the 59 treatment-naïve cohort were found to have the 103N, but at low-levels, leading to an overall rate of 103N at 25.4% (15/59) in this population. The high prevalence of the 103N suggests that baseline resistance testing should be performed before treatment in this population. Importantly, the new RCA technology allows large-scale, sensitive detection of drug resistance mutations, including detection of minority populations with minimal equipment requirement.
authors.affiliation: Center for Virus Research, Westmead Millennium Institute, University of Sydney, Sydney, NSW 2145, Australia. bin_wang@wmi.usyd.edu.au
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Dominic E
authors.initials: DE
authors.lastname: Dwyer
authors.forename: Choo Beng
authors.initials: CB
authors.lastname: Chew
authors.forename: Chenda
authors.initials: C
authors.lastname: Kol
authors.forename: Zhong Ping
authors.initials: ZP
authors.lastname: He
authors.forename: Hemal
authors.initials: H
authors.lastname: Joshi
authors.forename: Megan C
authors.initials: MC
authors.lastname: Steain
authors.forename: Anthony L
authors.initials: AL
authors.lastname: Cunningham
authors.forename: Nitin K
authors.initials: NK
authors.lastname: Saksena
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D002681:China; D024882:Drug Resistance, Viral; D015658:HIV Infections / Q000821:virology*; D054303:HIV Reverse Transcriptase / Q000235:genetics*; D015497:HIV-1 / Q000187:drug effects*; D006801:Humans; D020125:Mutation, Missense; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry / Q000235:genetics; D015995:Prevalence; D012680:Sensitivity and Specificity
chemical_list: D019380:Anti-HIV Agents; D015345:Oligonucleotide Probes; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase