Quantification and localization of integrated HIV-1 in memory and naïve CD4+ T cells from adolescents and young adults with perinatally-acquired HIV-1

HIV-1 establishes latency in resting memory CD4+ T cells, creating a long-lived reservoir that poses a barrier to HIV-1 cure. This reservoir is thought to form by initial infection of antigen-activated CD4+ T-cells that then transition into quiescent memory CD4+ T cells. However, naïve CD4+ T cells have been shown to harbor integrated HIV-1 in adults with non-perinatally acquired HIV-1, and more recently in young children. Given that perinatal HIV-1 transmission is established in an immune environment dominated by naïve CD4+ T cells, we hypothesized that naïve CD4+ T cells may be a substantial reservoir in young adults with longstanding perinatal infection. To investigate this, we studied a cohort of 10 adolescents and young adults (AYA) living with well-controlled, perinatally-acquired HIV-1. We quantified and characterized intact and defective HIV-1 proviruses and their location in sorted naïve and memory CD4+ T cells using an intact proviral DNA assay, near full-length single genome sequencing, and integration site profiling. We found that a median of 93.5% of HIV-1 proviruses resided in memory CD4+ T cells in AYA with perinatal HIV-1, with a few participants also having intact proviruses in naïve CD4+ T cells, but at substantially lower frequencies. HIV-1 integration site analysis, using the unbiased ligation-mediated PCR method, showed that 78.0% of proviruses were located within active transcription units in introns and 46.9% of integration sites were clonal, with detection in multiple cells. Overall, similar to adults with non-perinatally acquired HIV-1, integration sites were enriched in regions with epigenetic marks for active enhancers and transcription. Therapies to attain HIV-1 ART-free remission and cure for this population will need to consider reservoirs in non-canonical T cells subsets, as well as substantial HIV-1 infected cells arising from cellular proliferation.