Quantitation of HIV DNA integration: Effects of differential integration site distributions on Alu-PCR assays

► Alu-PCR is a popular method for quantifying integrated proviruses. ► The Alu-PCR method is potentially sensitive to the distributions of HIV integration sites in cells. ► Samples with considerably altered HIV integration site distributions were designed to test the accuracy of Alu-PCR. ► Altered integration site distributions exerted negligible effects on Alu-PCR quantitation of integrated proviruses.