Towards an HIV-1 cure: measuring the latent reservoir

Abstract

The latent reservoir (LR) of HIV-1 in resting memory CD4(+) T cells serves as a major barrier to curing HIV-1 infection. While many PCR- and culture-based assays have been used to measure the size of the LR, correlation between results of different assays is poor and recent studies indicate that no available assay provides an accurate measurement of reservoir size. The discrepancies between assays are a hurdle to clinical trials that aim to measure the efficacy of HIV-1 eradication strategies. Here we describe the advantages and disadvantages of various approaches to measuring the LR.

Keywords: HIV-1; assays; cure; latency.

Figure 1. Profile of different types of HIV-1 proviruses in resting CD4+ T cells

The major types of proviruses are shown, including those that pose a barrier to an HIV-1 cure and those that do not. Following a single round of T cell activation, some proviruses are induced to produce virions, which can go on to infect other cells (induced, replication-competent proviruses). Proviruses that are not induced to produce replication-competent virions following a single round of T cell activation are termed noninduced proviruses. Many of these noninduced proviruses are defective and contain large internal deletions, G→A hypermutations or other inactivating defects. However, some noninduced proviruses have fully intact genomes and, upon subsequent rounds of cellular activation, can produce virions. These proviruses are termed intact, noninduced proviruses (INPs). Culture-based assays detect only induced replication-competent proviruses, while PCR-based assays detect all types of proviruses. Only induced replication-competent proviruses and INPs pose a barrier to an HIV-1 cure.

Figure 2. Venn diagram comparison of proviral populations measured by different methods for assessing the latent reservoir

Typical or estimated results from different PCR- and culture-based assays are shown relative to a prediction of the true latent reservoir size. The frequency of infected cells detected with different assays is represented by the area of each circle. PCR-based assays overestimate the LR since most of the templates amplified represent defective viruses [18]. Additionally, some proviruses are likely deleted in primer binding sites for the PCR so PCR-based assays likely underestimate the total number of infected cells. The VOA underestimates the LR size because not every replication-competent virus is induced by a single round of T cell activation [19]. Assays involving T cell activation with a viral RNA readout give intermediate values but suffer from both of the problems mentioned above; some of the viral RNA detected is derived from defective proviruses and not all of the replication-competent proviruses are induced by a single round of activation [37,39,40]. There is a need for assays that measure only those proviruses that pose a threat to an HIV-1 cure.