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. Author manuscript; available in PMC: 2021 Jul 13.
Published in final edited form as: Lancet HIV. 2020 Aug 10;7(9):e652–e660. doi: 10.1016/S2352-3018(20)30117-X

Table.

Approaches to Monitoring the HIV Reservoir

Assay Description Advantages Disadvantages
PCR-based assays to measure cell-associated proviral DNA54 Variety of quantitative PCR assays that can be used to measure both integrated55 and unintegrated56 HIV using a variety of platforms (real-time PCR, digital droplet PCR57 etc) Rapid. Can be applied to a variety of cell types and tissue.58 Requires small volume of sample. Measures both replication competent, infectious viruses as well as defective, mutated viruses. Since defective viruses account for the majority of proviral DNA,59 it has very low signal to noise ratio and may miss clinically significant reductions in the replication competent reservoir.
Single copy assay60 Quantitative polymerase chain reaction to measure residual HIV plasma RNA in patients on antiretroviral therapy. Has been used as an indirect measure of HIV persistence in several clinical trials of antiretroviral intensification.61–63 Requires less sample volume that culture-based assays. Most patients on antiretroviral therapy have only 1–3 copies HIV RNA/mL of plasma. Thus, this assay has poor dynamic range.
Quantitative viral outgrowth assay (qVOA)30 Culture-based assay where patient CD4 T cells (or other cells types) are plated in limiting dilution, stimulated to produce virus which is amplified by donor CD4 T cells or a transformed CD4+ T cell line expressing CCR5. Considered the gold-standard for measuring the minimal size of the replication competent latent viral reservoir. Can detect viral outgrowth from a single cell and is highly specific for infectious virus. Time and labor-intensive, also requires large volume sample. May underestimate the size of the reservoir as some cells may not be stimulated to produce virus on single-round stimulation.64
Intact proviral detection assay (IDPA)65 Droplet digital PCR using discriminatory probes for common deleted or hypermutated proviruses to distinguish from intact proviruses Rapid. Requires fewer cells/sample volume than culture-based assays. Considered both sensitive and specific for replication competent viruses as it New assay that has not yet been validated in clinical trials.