Figure 2.

(A) HIV gag DNA PCR in sorted subsets from 19 HIV-infected individuals. Gels were exposed to a Phosphoscreen detector (Molecular Dynamics) and scanned on a PhosphorImager. The controls, labeled HIV-1 copies, represent the indicated cell numbers of ACH-2 cells, containing a single copy of HIV-1 per cell, that were diluted in a constant number of uninfected CEM cells (14). The patient samples are arranged in the same order in Table 1. (B) Estimate of HIV gag copy numbers in each sorted cell subset and quantification of the band intensities (see A). The estimated gag copy numbers were corrected by cell numbers, as measured with the FACSvantage counters at the end of each sort. (C) Correlation between cell number equivalents used for PCR and intensity of HLA-DQα PCR bands. Band intensities of cellular DQα PCRs correlated well with cell number equivalents determined by the FACS counter at the end of each sort. A good correlation was obtained with samples derived from sorted DN subsets of HIV-positive patients (similar results were obtained with sorted CD4 subsets). This result rules out variable efficiencies of DNA isolation and PCR amplification and indicates that the chosen range of cell number equivalents (<20,000 DN cells) allows quantitative assessment of cellular DNAs, such as HLA DQα. It also shows that HIV gag copy number can be calculated as a function of cell number (see B). (D) The correlation between plasma viral load and CD4 cellular viral load indicates that there is a variable viral load in CD4 cells in HAART-treated patients who have no detectable plasma viral load. (E) The correlation between plasma viral load and DN cellular viral load indicates that there is a variable viral load in DN T cells in HAART-treated patients who have no detectable plasma viral load. Undetectable plasma viral loads were assigned a value of 400 RNA copies per ml, i.e., the limit of detection of the clinical test used.