Sensitive detection of the K103N non-nucleoside reverse transcriptase inhibitor resistance mutation in treatment-naïve HIV-1 infected individuals by rolling circle amplification

• Published in: Journal of virological methods 2009-10, Vol.161 (1), p.128-135
• Main Authors: Wang, Bin, Dwyer, Dominic E., Chew, Choo Beng, Kol, Chenda, He, Zhong Ping, Joshi, Hemal, Steain, Megan C., Cunningham, Anthony L., Saksena, Nitin K.
• Format: Article
• Language: English
• Subjects: 103N; Anti-HIV Agents - pharmacology; ARV treatment-naïve; Biological and medical sciences; China; Drug Resistance, Viral; Fundamental and applied biological sciences. Psychology; HIV drug resistance/resistance mutations; HIV Infections - virology; HIV Reverse Transcriptase - genetics; HIV-1; HIV-1 - drug effects; Human immunodeficiency virus 1; Humans; Microbiology; Mutation, Missense; Nucleic Acid Amplification Techniques - methods; Oligonucleotide Probes - chemistry; Oligonucleotide Probes - genetics; Prevalence; Rolling circle amplification (RCA); Sensitivity and Specificity; Techniques used in virology; Virology
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2009.06.004

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.