Development and Evaluation of a Novel Relatively Low-Cost Method to Derive HIV-1 Integration Sites and Proviral Sequences

In people taking antiretroviral therapy (ART) for HIV infection, the methods to characterize latent and active HIV reservoirs remain costly and labor-intensive. Our objective was to develop a relatively low-cost technique to amplify and sequence the proviruses that persist during ART along with the site in the human genome where each provirus is integrated. We developed a novel HIV-specific Multiple Displacement Amplification (<b>HIV-MDA</b>) assay that specifically amplifies HIV-1 proviruses and their associated integration site. Upon comparison of our HIV-MDA to an established commercial kit designed to amplify cellular DNA, we found that the HIV-MDA (1) typically yielded a greater number of HIV integration site (<b>HIV IS</b>) sequences per 150,000 cells analyzed; (2) improved rates of proviral DNA amplification; and (3) amplified HIV IS at a fraction of the cost (13.6 times less expensive). Thus, the HIV-MDA method appears to be a more sensitive and cost-effective approach to sequencing HIV IS and the associated proviruses compared to a commercial kit.