Intact proviral DNA assay analysis of large cohorts of people with HIV provides a benchmark for the frequency and composition of persistent proviral DNA
Francesco R. Simonetti, Jennifer A. White, Camille Tumiotto, Kristen D. Ritter, Mian Cai, Rajesh T. Gandhi, Steven G. Deeks, Bonnie J. Howell, Luis J. Montaner, Joel N. Blankson, Albine Martin, Gregory M. Laird, Robert F. Siliciano, John W. Mellors, Janet D. Siliciano
Abstract
Significance Despite clinically effective antiretroviral therapy (ART), replication-competent HIV-1 persists as latent proviral DNA capable of rekindling viral replication when ART is stopped. To cure the infection, therapies are being developed to eliminate latent HIV-1. Accurate assays for intact or rebound-competent HIV-1 are important to this effort. We previously developed the intact proviral DNA assay (IPDA) as a more accurate and scalable assay for intact HIV-1 proviruses. Here we present IPDA analysis in a diverse cohort of 400 ART-treated individuals. We confirm that intact proviruses, although vastly outnumbered by defective proviruses, are present at significantly higher frequencies than previously detected by viral outgrowth assays. We also show that IPDA amplicon signal issues, observed in 6.3% of samples, result from sequence polymorphisms.