Background: The development of Pretreatment Drug Resistance (PDR) is becoming an obstacle to the success of antiretroviral therapy (ART). Besides, data from developing settings including Ethiopia is still limited. Therefore, this study was aimed to assess HIV-1 genetic diversity and pretreatment drug resistance mutations among ART-naive newly diagnosed asymptomatic HIV-1 infected individuals in Addis Ababa, Ethiopia.

Method: Institutional based cross-sectional study was conducted from June to December 2018 in Addis Ababa, Ethiopia among ART naïve newly diagnosed asymptomatic individuals. Partial HIV-1 pol region covering the complete protease and partial reverse transcriptase regions of 51 samples were amplified and sequenced using in-house assay. Drug resistance mutations were examined using calibrated population resistance (CPR) tool version 6.0 from the Stanford HIV drug resistance database and the International Antiviral Society-USA (IAS-USA) 2019 mutation lists.

Result: According to both algorithms used, 9.8% (5/51) of analyzed samples had at least one PDR Mutation. PDR mutations to Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) were the most frequently detected mutation (7.8% and 9.8%, according to the CPR tool and IAS-USA algorithm, respectively). The most frequently observed NNRTIs associated mutations by both algorithms were K103N (2%), Y188L (2%), K101E (2%), and V106A (2%) while E138A (2%) was observed according to IAS-USA only. Y115F and M184V (mutations that confer resistance to NRTIs) were detected according to both criteria’s in a single study participant (2%) who had NNRTIs associated mutation (Y188L). Similarly, PDR mutation to protease inhibitors was found to be low (G73S; 2%) seen by the CPR tool only. In addition, a high rate of polymorphism both at PR and RT regions were detected. Phylogenetic analysis showed that all 51/51 (100%) of the study participants were infected with subtype C virus.

Conclusion: This study showed an increased level of PDR and persistence HIV-1C clade homogeneity after 15 years of the rollout of ART and 3 decades of HIV-1C circulation in Ethiopia, respectively. Therefore, routine genotypic drug resistance testing is warranted for successful ART program and the overall prevention of HIV transmission in the country and to support the global efforts in achieving the third 90 of the UN target.

Keywords: HIV-1; Drug resistance; Genetic diversity