A low cost duplex polymerase chain reaction to detect common HIV-1 CRF 01AE reverse transcriptase inhibitors resistance-associated mutations: 103N/181C and 151M/ 215Y

Abstract

Background: Two nucleoside plus one non-nucleoside-reverse transcriptase inhibitors (2 NRTIs+NNRTI) combination is prescribed worldwide as a first-line antiretroviral therapy. The cost-effective antiretroviral resistance testing can improve the clinical management of HIV-1 infection. Objective: To develop a prototype low cost and simple genotypic test to detect common NNRTI- and NRTIassociated RAMs in HIV-1 CRF01_AE in HIV-infected patients. Methods: The duplex 103N/181C and 151M/215Y/F amplification refractory mutation system (ARMS) were developed and tested with plasma samples from antiretroviral therapy (ART)-naive (group I, n=20) and ARTexperienced (>6 months) (group II, n=25) patients whose HIV-1 RNA >1,000 copies/ml in comparison to the standard HIV-1 RT sequencing analysis (ABI, USA). Results: An excellent concordance (94.3%) was found with the detection limit of duplex ARMS at HIV-1 RNA >1,000 copies/mL. No mutations were observed in the antiretroviral therapy (ART)-naive group (0/20), while 23 out of the 25 (92%) ART-experienced (>6 months) harbored drug-resistant mutant viruses (p <0.01). T215Y/F mutation was the most common genotypic resistance (80%). The NNRTI associated mutations (K103N, Y181C) was found in 6/9 (67%) of patients taking NNRTIs. The NRTI-multidrug resistance (MDR) Q151M was found in 4%. Conclusion: With the high sensitivity (96%) and specificity (98%), as well as lower cost, this duplex ARMS was valid for further cost-effective HIV drug resistance surveillance study in resource-limited setting. However, clinical uses need further validation in a larger scale study.