Although combined antiretroviral therapy (ART) can reduce the plasma HIV-1 viral load below the detection limit of available commercial assays (<20 copies/ml), with the use of more sensitive tests, it is possible to detect residual HIV-1 RNA in the plasma of almost all patients on ART. A number of nucleic acid-based detection methods can be used to detect low levels of HIV-1 RNA or DNA, including PCR (standard, quantitative competitive, real time, in situ), branched DNA signal amplification (bDNA), strand displacement amplification (SDA), transcription-mediated amplification (TMA), and nucleic acid sequence-based amplification (NASBA).

HIV-positive adults with known, detectable viral load (>40 copies/ml) or undetectable viral load were recruited from two clinic-based cohorts in San Francisco (the PLUS study and the SCOPE cohort). The study was approved by the local Institutional Review Board of the University of California, San Francisco (UCSF). All participants gave informed consent.