Utility of a Relatively Affordable In-House HIV-1 Genotyping Assay for Drug Resistance Testing among Non B HIV-1 Infected Drug Naive Patients in Nigeria

Background: The introduction of antiretroviral (ARV) in resource-limited settings has increased life expectancy among non-B HIV-1 infected individuals. We used a validated In-house genotyping assay to characterize non-B HIV-1 and to determine drug resistance mutations among treatment-naive patients. Methods: Plasma samples from 105 HIV-1 infected drug-naive adult patients attending a tertiary hospital Jos, Nigeria were subjected to HIV-1 RNA extraction, reverse transcription amplification, and population-based sequencing of the partial pol gene on the ABI 3130xl genetic analyzer. Subtyping and phylogenetic analyses were performed by REGA Subtyping Tool v2.0 and MEGA v5.0 respectively. Drug resistance profiles were evaluated according to IAS-USA 2013 drug resistance mutations list. Result: One hundred samples (95.2%) were successfully genotyped. The distribution of the non-B HIV-1 subtypes were; CRF02_AG-48%, G-41.0%, CRF06_cpx-6.0%, and A-5.0%. Ten percent of the isolates had at least one major drug resistance mutation in the pol gene. The drug-class specific resistance prevalences were 6.0% for NRTIs; M41L-1.0%, K65KR-1.0%, M184IM-1.0%, M184V-2.0%, and T215ADNT-1%, 8.0% for NNRTIs; K103N-2%, 1.0% for K101E, E138A, G190A, P225HP, Y181I, Y188L, Y181C including protease inhibitors’ Q58E (1.0%). Conclusion: HIV-1 was heterogeneously distributed; CRF02_AG and G predominate and some known major mutations associated with NRTIs and NNRTIs were determined. The In-house assay is suitable for both characterization of non-B HIV-1 subtypes and detection of drug resistance at a significant lower cost than available commercial genotyping assays. This finding underscores the need to consider use of low-cost In-house genotyping assay as an alternative in resource-limited settings with non-B HIV-1 epidemic.