The WIPE assay for selection and elimination of HIV-1 provirus in vitro using latency-reversing agents

Persistence of HIV-1 latent reservoir cells during antiretroviral therapy (ART) is a major obstacle for curing HIV-1. Latency-reversing agents (LRAs) are under intensive development to reactivate and eradicate latently infected cells; however, there are a few useful models for evaluating LRA activity in vitro. Here, we established a chronically HIV-1-infected culture system harboring thousands of different HIV-1-infected cell clones with a wide distribution of HIV-1 provirus similar to that observed in vivo. A combination of an LRA and an anti-HIV-1 drug successfully inhibited viral re-emergence after drug discontinuation, demonstrating “experimental cure” in the in vitro model. We demonstrated that the epigenetic environment of the integrated provirus plays a role in determining drug susceptibility. Our widely distributed intact provirus elimination (WIPE) assay will be useful for optimizing therapeutics against HIV-1 latency and provides mechanistic insights into the selection of heterogeneous HIV-1-infected clones during drug treatment.