SQuHIVLa: A novel assay for Specific Quantification of inducible HIV-1 reservoir by LAMP

Abstract

Strategies toward HIV-1 cure aim to clear, inactivate, reduce or immunologically control the virus from a pool of latently infected cells such that combination antiretroviral therapy (cART) can be safely interrupted. In order to assess the impact of any putative curative interventions on the size and inducibility of the latent HIV-1 reservoir, robust and scalable assays are needed to precisely quantify the frequency of infected cells containing inducible replication competent HIV-1. Here, we present Specific Quantification of Inducible HIV-1 by LAMP (SQuHIVLa), a novel assay that leverages the high sensitivity and specificity of RT-LAMP, performed in a single reaction, to detect and quantify cells expressing Tat/Rev msRNA upon activation. Our LAMP primer/probe design exclusively detects subtype-specific HIV-1 Tat/Rev msRNA and exhibits high sensitivity, specificity, and reproducibility. Using SQuHIVLa we quantified the inducible viral reservoir in CD4+ T cells from a diverse group of people living with HIV-1 subtypes B and C on cART. SQuHIVLa presents a high throughput, scalable and specific HIV-1 reservoir quantification tool that is amenable to resource limited settings.