Viral In-depth Characterization Through Immunocapture to Identify the Cellular Sources and Genetic Diversity of the HIV-1 Reservoirs

PROJECT SUMMARY Despite the remarkable success of antiretroviral therapy (ART) to control HIV-1 infection, viral reservoirs persist indefinitely under treatment. These remaining viral populations constitute the principal burden for an effective HIV-1 cure, as they lead to a rapid “rebound” in viremia when treatment fails or is discontinued. Viral reservoirs in ART treated individuals are constituted by latently infected long-lived immune cells. Additionally, the reservoir comprises populations that produce low levels of viremia even in presence of high levels of ART. The sources of this residual viremia might play a key role in the fast “viral rebound” often observed after therapy cessation. Different studies demonstrate that the reservoirs are rapidly established early after infection and distributed throughout the body in multiple anatomical sites. In addition to T-CD4+ cells, a growing number of studies suggest that other T-cells and myeloid cells such as macrophages and mast cells constitute potential active and/or inducible reservoirs too. This capacity to establish reservoirs in a wide variety of cellular targets and anatomical compartments is promoted by HIV-1 accessory and regulatory proteins and might lead to viral characteristics directly associated with the producer cell type. In this proposal, we aim to characterize viruses produced by different cell types and their corresponding integrated provirus using tissue “ex vivo” infections. Furthermore, we will study the sources and characteristics of the viral particles that comprise the residual viremia from various anatomical compartments using clinical samples from people living with HIV-1 under ART. We will use our newly developed pipeline that combines viral immuno-capture (v-IC) from multiple cell types, with proviral sequencing in the same cell types, long-read deep viral sequencing, and viral particle multi-omics. This new pipeline will be very relevant for HIV-1 cure studies to identify the sources of viremia during ART and to better analyze the viral reservoirs.