Quantitative assessment of integrated and episomal HIV DNA

Antiretroviral combination therapy for HIV-1 infection can reduce plasma virus to undetectable levels for prolonged period of times. However, current treatments are unable to eradicate the infection, since HIV-1 can latently persist in resting CD4 super(+) T cells. The size of this latent reservoir has been measured in the peripheral blood of highly active antiretroviral therapy (HAART)-treated patients by elegant experimental protocols requiring the separation of resting CD4 super(+) T cells and the measurement of viral production in culture supernatants. This method, however, requires a great number of lymphocytes, is quite time consuming, and generates semi-quantitative results. With these limitations in mind, we developed a quantitative molecular biology assay that is able to monitor accurately the virological changes induced by various antiretroviral treatments. By using this method, we have shown that total HIV DNA is significantly reduced when interleukin 2 is added to antiretroviral therapy. Cell-associated HIV DNA is a mixture of integrated DNA, which is a marker of latency, and unintegrated DNA, which is commonly considered an indicator of active replication. Although the number of integrated copies of HIV DNA does not completely reflect the levels of replication-competent virus, nevertheless its quantification offers an important estimate of the latent HIV pool before and during treatment.