The Alphabet Soup of HIV Reservoir Markers

Abstract

Purpose of review Despite the success of antiretroviral therapy in suppressing HIV, life-long therapy is required to avoid HIV reactivation from long-lived viral reservoirs. Currently, there is intense interest in searching for therapeutic interventions that can purge the viral reservoir to achieve complete remission in HIV patients off antiretroviral therapy. The evaluation of such interventions relies on our ability to accurately and precisely measure the true size of the viral reservoir. In this review, we assess the most commonly used HIV reservoir assays, as a clear understanding of the strengths and weaknesses of each is vital for the accurate interpretation of results and for the development of improved assays. Recent findings The quantification of intracellular or plasma HIV RNA or DNA levels remains the most commonly used tests for the characterization of the viral reservoir. While cost-effective and high-throughput, these assays are not able to differentiate between replication-competent or defective fractions, or quantify the number of infected cells. Viral outgrowth assays provide a lower bound for the fraction of cells that can produce infectious virus, but these assays are laborious, expensive and substantially underestimate the potential reservoir of replication-competent provirus. Newer assays are now available that seek to overcome some of these problems, including full-length proviral sequencing, inducible HIV RNA assays, ultrasensitive p24 assays and murine adoptive transfer techniques. Summary The development and evaluation of strategies for HIV remission relies upon our ability to accurately and precisely quantify the size of the remaining viral reservoir. At this time, all current HIV reservoir assays have drawbacks such that combinations of assays are generally needed to gain a more comprehensive view of the viral reservoir. The development of novel, rapid, high-throughput assays that can sensitively quantify the levels of the replication-competent HIV reservoir is still needed.

Effect of Short-Term Antiretroviral Therapy Interruption on Levels of Integrated HIV DNA

“…While quantifying intact full-length proviral numbers and the viral outgrowth assay are the gold standards for measuring the HIV reservoir, these assays are costly, laborand time-intensive, dependent on large sample volumes, and challenging to implement for large-scale clinical studies (14)(15)(16). In HIV nonsuppressed individuals, it is difficult to interpret total HIV DNA levels given the presence of unintegrated forms of HIV DNA (8).…”

Cell-associated HIV-1 RNA predicts viral rebound and disease progression after discontinuation of temporary early ART

“…Recent efforts toward a cure for HIV-1 resulted in a renewed interest in the development of viral markers, which should allow the precise measurement of HIV-1 reservoirs and aid in monitoring the efficacy of novel therapies aimed at eliminating or reducing these reservoirs (18). In particular, because every potential curative intervention will ultimately necessitate an analytical treatment interruption (ATI) to assess its efficacy, it is very important to be able to identify individuals with small viral reservoirs, in whom ATI can be performed with the lowest risk of quick viral rebound, because the latter could result in HIV-1 reservoir replenishment, selection of drug resistance, disease progression, and elevated risk of HIV-1 transmission (19,20).…”

Prevalence and correlates of persistent intracellular HIV transcription in individuals on efavirenz versus atazanavir-based regimens: A prospective cohort study

“…The shift of the HIV research agenda towards strategies for the quantification and eradication of the viral reservoir has renewed interest in biomarkers beyond CD4 + cell counts and plasma viral load. [ 16 ] Cell-associated viral RNA(CA-RNA) in PBMCs has been linked to decreasing CD4+ T cell counts in untreated HIV patients,[ 17 ] and suggested as a predictor of treatment failure in patients on HAART. [ 18 ] Chronic immune activation and dysfunction seem to correlate with cell associated measures of viral persistence but further research is needed to disentangle the interactions between them.…”