Assessment of HIV-1 DNA copies per cell by real-time polymerase chain reaction

Measurements of HIV-1 DNA and plasma RNA levels represent unique entities, thus clinically and molecularly, data obtained from each can be used independently in assessing therapy or experiments. Plasma HIV-1 RNA levels are used to make clinical decisions regarding treatment strategies, but viral DNA can still be detectable when plasma RNA levels are undetectable. At the molecular level, accurate assessment of HIV-1 DNA copies/cell could increase the ability to target specific tissues for further analysis such as identification of site-specific integration of HIV in cellular DNA. Using real-time polymerase chain reaction (PCR), HIV-1 copies/cell were determined in peripheral blood mononuclear cells (PBMC), bone marrow (BM), and tissue. Duplicate specimens were analyzed for plasma HIV-1 RNA levels and for viral DNA copies/cell from 24 HIV-1 infected individuals. DNA from an additional 58 PBMC and 34 other tissue specimens were also assayed with the results reported as a log of HIV-1 DNA copies/cell. The log viral DNA copies/cell of the 24 matched specimens ranged from -2.699 to 0.278 with no correlation to the plasma HIV-1 RNA levels (range 52 to 2 X 105 copies/mL). Similar range in log HIV-1 DNA copies/cell was found in the other specimens. Real-time PCR assay for viral DNA copies/cell provides a rapid assessment of HIV-1 copies/cell in specimens independent of plasma HIV-1 RNA levels. From selected cases with relatively high HIV-1 DNA copies/cell, inverse PCR successfully identified viral integration. This type of assay could facilitate further studies when relatively high viral copies/cell are needed for screening.