Dolutegravir (DTG) use in combination with tenofovir and lamivudine (TLD) is scaling up in Africa. However, HIV drug resistance (HIVDR) data to DTG remain scarce in Zimbabwe. We assessed the prevalence and genetic mechanisms of DTG resistance in people living with HIV initiating on TLD. A prospective cohort study was conducted between October 2021 and April 2023 among antiretroviral therapy (ART) naïve adults (≥18 years) attending care at an HIV clinic in Zimbabwe. Pre-treatment drug resistance (PDR) was assessed prior to TLD initiation and viral load (VL) outcome and acquired drug resistance (ADR) to TLD were described after 24 weeks follow-up. In total, 172 participants were enrolled in the study. The median (IQR) age and log₁₀ VL were 39 (29–48) years and 5.41 (4.80–5.74) copies/mL, respectively. At baseline, no PDR to DTG was found. However, as previously reported, PDR to non-nucleotide reverse transcriptase inhibitor (NNRTI) was high (15%) whilst PDR to NRTI was low (4%). After a median duration of 27 (25–30) weeks on TLD, virological suppression (VL < 1000 copies/mL) was 98% and among the 2 participants with VL ≥ 1000 copies/mL, no ADR was found. HIVDR to DTG is rare among ART naïve individuals. DTG is more likely to address the problems of HIVDR in Africa.

The HIV-1 epidemic continues to challenge global public health, especially in sub-Saharan Africa. The rise in drug-resistant viruses, particularly pan-resistant strains, threatens treatment effectiveness, hindering progress toward UNAIDS viral suppression goals. This is critical in low-to-middle income countries (LMICs) like Zimbabwe, where treatment options and access to drug resistance testing are limited. This cross-sectional study analyzed 102 genotypes from patients with HIV-1 RNA ≥ 1000 copies/mL after at least 6 months on a dolutegravir (DTG)-based ART. HIV-1 genotyping and drug resistance interpretation were performed using the Stanford HIV Drug Resistance Database. Overall, 62% of genotypes harbored at least one drug resistance mutation, with 27% showing integrase strand transfer inhibitor (INSTI)-associated mutations. High-level resistance to DTG and cabotegravir was found in 14% and 23% of integrase sequences, respectively, primarily driven by G118R and E138K/T mutations. Pan-resistance was observed in 18% of complete genotypes, with one case of four class resistance. These results highlight the emergence of INSTI resistance in LMICs. The study underscores the urgent need for enhanced HIV drug resistance testing, continuous surveillance, and strategic optimization of ART regimens in resource-constrained settings to ensure effective HIV management.

Background: HIV drug resistance (HIVDR) testing remains essential for optimizing antiretroviral therapy (ART), yet access remains constrained by high cost, low throughput, and limited availability of Sanger sequencing in resource-limited settings (RLS). Recent improvements in Oxford Nanopore Technologies (ONT) sequencing offer a potential alternative, especially following the expansion of genomic surveillance infrastructure established during the COVID-19 pandemic. Methods: A cross-sectional laboratory validation study was conducted comparing ONT MinION sequencing with Sanger sequencing for HIV-1 protease/reverse transcriptase (PR/RT) and integrase (IN) genotyping. Sixty-four stored amplicons from patients with virological failure on second-line protease inhibitor (PI)- or integrase strand transfer inhibitor (INSTI)-based regimens were sequenced on the MinION Mk1C (R10.4.1). ONT-derived consensus sequences were generated using a custom pipeline and compared to Sanger reference sequences to assess nucleotide identity and drug resistance mutation (DRM) concordance using the Stanford HIVdb v9.8. We also evaluated the cost and scalability of ONT to determine its feasibility for broader implementation. Results: ONT MinION sequencing produced high-quality consensus sequences with a median pairwise identity of 99.4% (IQR: 99.2–99.7). After resolving initial discrepancies through chromatogram review and high-depth Nanopore data, high concordance for major DRMs was observed across PR, RT, and IN coding regions. Using a 48-sample multiplexing configuration, the estimated reagent and consumable cost for ONT sequencing was approximately US$23.47 per sample. Published Sanger-based HIV drug resistance assays report per-sample costs in the range of approximately US$43 to US$100, although costs vary depending on laboratory workflow and testing volume. Moreover, ONT provided a substantially shorter turnaround time (~ 5 h from library prep to sequence data), offering a more efficient and cost-effective workflow overall. Conclusions: ONT MinION sequencing provides an accurate, rapid, and cost-effective alternative to Sanger sequencing for HIVDR genotyping in RLS. Its scalability, ability to detect minority variants, and compatibility with infrastructure setup up in response to the COVID-19 pandemic, make it a viable platform for both national HIVDR surveillance and decentralized clinical testing. Integrating ONT workflows into routine HIVDR monitoring could expand diagnostic access and enable more timely ART optimization in high-burden settings.