Background: In sub-Saharan Africa, 25.5 million people are living with HIV, representing 70% of the global total. The need for second-line antiretroviral therapy (ART) is projected to increase in the next decade in keeping with the expansion of treatment provision. Outcome data are required to inform policy.

Methods: We performed a systematic review and meta-analysis of studies reporting the virological outcomes of protease inhibitor (PI)-based second-line ART in sub-Saharan Africa. The primary outcome was virological suppression (HIV-1 RNA <400 copies/ml) after 48 and 96 weeks of treatment. The secondary outcome was the proportion of patients with PI resistance. Pooled aggregate data were analysed using a DerSimonian-Laird random effects model. PROSPERO registration: CRD42016048985.

Results: By intention-to-treat, virological suppression occurred in 69.3% (95% confidence interval 58.2, 79.3) at week 48 (4558 participants, 14 studies), and in 61.5% (47.2, 74.9) at week 96 (2145 participants, 8 studies). Pre-existing resistance to the nucleos(t)ide reverse transcriptase inhibitors (NRTIs) increased the likelihood of virological suppression. Major protease resistance mutations occurred in median 17% (IQR 0-25) of the virological failure population and increased with duration of second-line ART.

Conclusions: One third of patients receiving PI-based second-line ART with continued NRTI use in sub-Saharan Africa did not achieve virological suppression although among viraemic patients protease resistance was infrequent. There remain significant challenges in implementation of viral load monitoring. Optimising definitions and strategies for management of second-line ART failure is a research priority.