Table 1 A comparison of the strengths and weaknesses of cell culture and PCR-based assays for the quantification of the HIV-1 reservoir
From: Single-molecule techniques to quantify and genetically characterise persistent HIV
Assay name | PCR or cell culture based | Strengths of the assay | Weaknesses of the assay |
|---|---|---|---|
Quantification of HIV-1 RNA in plasma and CSF | PCR | Fast and high throughput | The low levels of viremia in participants on long-term ART could affect accuracy of this assay. Not a true representation of the intracellular reservoir |
Quantification of intracellular HIV-1 RNA and DNA | PCR | Fast and high throughput | Overestimates the size of the reservoir. Does not provide an indication of replication competency |
Single-genome sequencing | PCR | High throughput | Overestimates the size of the reservoir. Does not provide an indication of replication competency |
Full-length individual proviral sequencing | PCR | Relatively high throughput | Expensive technique. Slightly overestimates the size of the reservoir. Replication competency of genetically intact proviruses will require confirmation by in vitro assays |
Quantitative viral outgrowth assay | Cell culture | Quantifies replication-competent virus | Requires large numbers of resting memory T cells and is labour-intensive. Underestimates the size of the reservoir due to non-induced proviruses |
Tat/rev induced limiting dilution assay | Cell culture | Gives an indication of the size of the inducible reservoir | Requires sizeable numbers of cells and cannot be used for sorted T cell subsets. Overestimates the size of the reservoir |