Genetic Analysis of HIV-1 Integrase Sequences from Treatment-Naïve Individuals in Yaoundé, Cameroon

Abstract

Aims: The present study analyzed HIV-1 integrase sequence in HIV treatment naïve individuals. Study design: A cross sectional study was employed. Place and Duration of Study: University Teaching Hospital (CHU) Yaoundé, Cameroon, between June 2024 and December 2024. Methodology: We included 130 treatment-naïve HIV-1–positive adults in Yaoundé. HIV-1 integrase sequences were obtained for 53/130 (40.8%). Resistance-associated mutations (RAMs) were interpreted using the Stanford HIVdb algorithm (v9.0, accessed December 2024) and classified according to the IAS–USA HIV Drug Resistance Mutations List (2025 update). Subtypes were assigned using the REGA v3.0 Subtyping Tool (accessed December 2024) and confirmed by phylogenetic analysis. Results: A major INSTI RAM (P145S) was detected in 1/53 (1.9% [95% CI 0.3%–9.9%]), conferring high-level elvitegravir resistance with preserved raltegravir and dolutegravir susceptibility. Accessory/polymorphic RAMs occurred in 44/53 (83.0% [70.8%–90.8%]). The predominant subtype was CRF02_AG: 29/53 (54.7% [41.5%–67.3%]), followed by A: 15/53 (28.3% [18.0%–41.6%]), G: 4/53 (7.5% [3.0%–17.9%]), C: 2/53 (3.8% [1.0%–12.8%]), F2: 2/53 (3.8% [1.0%–12.8%]), and CRF09_cpx: 1/53 (1.9% [0.3%–9.9%]). Conclusion: Major INSTI resistance is rare in ART-naïve individuals in Yaoundé, while accessory polymorphisms are frequent. These data support ongoing molecular surveillance to protect the effectiveness of DTG-based first-line regimens in Cameroon and other high-diversity, resource-limited settings.