Background: Despite combination antiretroviral therapy (ART), HIV-1 RNA can be detected in plasma and peripheral blood mononuclear cells (PBMCs), indicating proviral transcription and production of virions, i.e. an active reservoir of HIV. It is not known whether proviral copy number, HIV-1 transcription, and residual plasma viremia on ART are related.
Methods: We conducted a cross-sectional study of viremic patients off ART and of virologically suppressed (<50 cps/ml) patients on ART. PBMCs were tested for total cell-associated (CA) HIV-1 DNA and unspliced HIV-1 RNA using sensitive qPCR targeting 3' pol. Plasma was tested for residual viremia by single copy assay targeting the same pol region. Unpaired t-test was used to compare viremic and patients on ART. Correlations between plasma viremia and cellular nucleic acids were assessed with Pearson's coefficient. Results: 12 viremic patients and 23 patients on ART were studied. In patients on ART, median CA HIV-1 DNA was 310 copies/106 PBMCs (range: 45, 984) and median CA HIV-1 RNA was 59 copies/106 PBMCs (range: 1, 454), both were significantly lower than in viremic patients (median 565 [range: 48, 4680], p = 0.033; median 296 [range: 33, 19172], p = 0.030; for CA HIV-1 DNA and RNA, respectively). The 5-fold reduction in CA HIV-1 RNA on ART is small compared with the > 4 log10 difference in plasma viremia between these two groups (median 0.44 [range: 0.4, 26] vs. 10542 [range: 564, 474211] copies/mL on and off ART, respectively), indicating substantial persistence of HIV-1 transcription despite ART. A strong, positive correlation was detected between cell-associated HIV-1 DNA and unspliced RNA in both viremic (Pearson’s r = 0.974; p < 0.001) and patients on ART (r =0.779; p <0.001). In viremic patients, the levels of plasma HIV-1 RNA also show strong, positive correlations with cell-associated HIV-1 DNA and RNA (Pearson's r = 0.849 and 0.843, respectively; p < 0.001). By contrast, in patients on ART, residual plasma viremia was not correlated with cell-associated HIV-1 DNA (r = 0.06; p = 0.78) or RNA (r = -0.18; p = 0.39). Conclusions: This is the first study to show i) a strong, positive correlation between the number of HIV-infected cells and the level of cell-associated HIV-1 RNA in patients on ART, and ii) no correlation between cell-associated HIV-1 RNA and the levels of persistent viremia. These findings suggest that most of persistent HIV-1 transcription in patients on ART does not result in viremia.