Low Inducibility of Latent Human Immunodeficiency Virus Type 1 Proviruses as a Major Barrier to Cure

Abstract

The latent reservoir for human immunodeficiency virus type 1 (HIV-1) in resting CD4+ T cells is a major barrier to cure. The dimensions of the reservoir problem can be defined with 2 assays. A definitive minimal estimate of the frequency of latently infected cells is provided by the quantitative viral outgrowth assay (QVOA), which detects cells that can be induced by T-cell activation to release infectious virus. In contrast, the intact proviral DNA assay (IPDA) detects all genetically intact proviruses and provides a more accurate upper limit on reservoir size than standard single-amplicon polymerase chain reaction assays which mainly detect defective proviruses. The frequency of cells capable of initiating viral rebound on interruption of antiretroviral therapy lies between the values produced by the QVOA and the IPDA. We argue here that the 1-2-log difference between QVOA and IPDA values in part reflects that the fact that many replication-competent proviruses are not readily induced by T-cell activation. Findings of earlier studies suggest that latently infected cells can be activated to proliferate in vivo without expressing viral genes. The proliferating cells nevertheless retain the ability to produce virus on subsequent stimulation. The low inducibility of latent proviruses is a major problem for the shock-and-kill strategy for curing HIV-1 infection, which uses latency-reversing agents to induce viral gene expression and render infected cells susceptible to immune clearance. The latency-reversing agents developed to date are much less effective at reversing latency than T-cell activation. Taken together, these results indicate that HIV-1 eradication will require the discovery of much more effective ways to induce viral gene expression.

Keywords: HIV-1; IPDA; QVOA; latent reservoir.

Figure 1.

The size of the latent reservoir is bounded by the values from 2 reservoir assays, the quantitative viral outgrowth assay (QVOA) and the intact proviral DNA assay (IPDA). A, Summary of the landscape of proviruses persisting on patients receiving antiretroviral therapy. Infected cell frequencies are expressed as infected cells per 10⁶ CD4⁺ T cells. The Venn diagram shows median values from a large-scale (N = 400) analysis using the IPDA [70]. Each of these values varies over 2–3 logs in different individuals. Total infected cells were determined as the sum of intact, 3’ defective, and 5’ defective proviruses determined by IPDA, computed on a per-individual basis, and corrected for the approximately 4% of proviruses with very large deletions missed by IPDA. QVOA values are based on previous studies [3, 6, 7, 9, 62]. The frequency of infected cells expressing viral RNA after T-cell activation, as detected by various induction assays [73–76], is also shown. B, Factors associated with overestimation and underestimation of reservoir size by IPDA and QVOA. The reservoir here is defined as the set of infected cells with the potential to give rise to viral rebound on ART interuption. The actual frequency of cells constituting the reservoir lies between the values determined by these assays (dashed line).