New tools for quantifying HIV-1 reservoirs: plasma RNA single copy assays and beyond

Abstract

Quantification of plasma HIV-1 RNA below the limit of FDA-approved assays by a single copy quantitative PCR assays (SCA) has provided significant insights into HIV-1 persistence despite potent antiretroviral therapy as well as a means to assess the impact of therapeutic strategies, such as treatment intensification, on residual viremia. In this review, we discuss insights gained from plasma HIV-1 RNA SCA and highlight the need for additional assays to characterize better the cellular and tissue reservoirs of HIV-1. Accurate, reproducible, and sensitive assays to quantify HIV-1 reservoirs, before and after therapeutic interventions, are essential tools in the quest for a cure of HIV-1 infection.

Fig. 1

Decay dynamics of plasma HIV-1 RNA during ART. Upon initiation of ART, viremia decays in multiple overlapping phases, which reflects the turnover of cells infected prior to ART with different half-lives. The first phase of decay has a half-life of approximately 1.5 days and represents the turnover of free virus and productively infected T cells [8, 9, 10••]. The second phase of decay, with a half-life of approximately 28 days, represents the attrition of cells more resistant to HIV cytopathicity, such as partially activated T cells and cells of the monocyte-macrophage lineage [11, 12••]. The third phase of decay, which has a half-life of approximately 273 days, levels off to a stable set point that represents a fourth phase showing no evidence of further decay [2••]. Viremia persists at this stable set point for at least 7 years following the initiation of ART and reflects the remarkable stability of the long-lived cellular reservoirs that maintain residual viremia [16••]. Blue = above clinical limit of detection (LOD). Red = below clinical LOD (ie, detectable by SCA). Dotted lines = theoretical decay slopes