Abstract Background In the era of rapid dolutegravir rollout, concerns about neural tube defects have complicated the health systems response among women of childbearing potential. This qualitative study, which was nested within the DolPHIN-2 clinical trial, examined the current and future health system opportunities and challenges associated with the transition to dolutegravir-based regimen as first line antiretroviral therapy among women of childbearing potential in South Africa and Uganda. Method Semi-structured in-depth interviews with members of antiretroviral therapy guideline development groups and affiliates were conducted. Thirty-one participants were purposively selected for the study, including senior officials from the Ministry of Health and National Drug Regulatory Authority in Uganda and South Africa as well as health-sector development partners, activists, researchers and health workers. A thematic approach was used to analyse the data. Findings Despite differences in health system contexts, several common challenges and opportunities were identified with the transition among women of childbearing potential in South Africa and Uganda. In both contexts national stakeholders identified challenges with ensuring gender equity in roll out due to the potential teratogenicity of dolutegravir, paucity of data on dolutegravir use in pregnancy, potential stock out of effective contraceptives, poorly integrated contraception services, and limited pharmacovigilance in pregnancy. Participants identified opportunities that could be harnessed to accelerate the transition, including high stakeholder interest and commitment to transition, national approval and licensure of a generic tenofovir/lamivudine/dolutegravir regimen, availability of a network of antiretroviral therapy providers, and strong desire among women for newer and more tolerable regimens. Conclusion The transition to dolutegravir-based regimens has the potential to strengthen health systems in low- and middle-income countries to engender equitable access to optimised antiretroviral regimen among women. There is the need for a multi-sectoral effort to harness the opportunities of the health systems to addresses the bottlenecks to the transition and initiate extensive community engagement alongside individual and institutional capacity strengthening. Improvements in pregnancy pharmacovigilance and counselling and family planning services are critical to ensuring a successful transition among women of childbearing potential.
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