Detection of inducible replication-competent HIV-1C provirus despite long-term antiretroviral treatment in perinatally infected adolescents in Botswana.

While antiretroviral therapy (ART) effectively suppresses HIV replication, the latent reservoir remains the barrier to HIV eradication. It remains unknown whether long term ART impacts levels of inducible replication-competent provirus. To address this knowledge gap, we assessed the proviral reservoir in HIV-1 perinatally infected adolescents having received ART for over 13 years. We recruited 15 vertically infected adolescents living with HIV in Botswana. Historical viral load, CD4+ T cell count, and treatment data were retrieved from their outpatient medical records. Inducible replication-competent proviruses from cryopreserved peripheral blood mononuclear cells (PBMCs) were quantified using a TZM-bl cell-based assay (TZA). Total proviral DNA copies were quantified using droplet digital PCR (ddPCR). The mean age of study participants was 16 (STD 0.7) years and median CD4+ T cell count at enrollment was 784 (IQR 728.8-1288) cells/mm3. Median age at ART initiation was 8 (IQR 6-12) months. Fourteen (93%) participants had HIV-1 RNA <400 copies/mL at the time of enrollment in the study. A median of 19 (IQR 18-27) HIV-1 RNA measurements were available per participant. Six (40%) participants displayed viral suppression at all clinic visits since initiating ART, while the remaining 9 (60%) had one or more clinic visits with detectable HIV-1 RNA. The median inducible replication-competent provirus count was 7.4 infectious units per million cells (IUPM; IQR 6.7-19.2), and did not differ significantly by either complete or incomplete viral suppression (7.2 vs 7.4, p=0.86), or by age at ART initiation (7.4 if < 12 months, 11.2 if > 12 months, p=0.85). The median total HIV DNA count was 129.1 copies/million cells (IQR 18.9-212.3). Our data suggest that long-term ART initiated within the first year in perinatally infected infants did not eliminate proviral DNA or inducible replication-competent proviruses.