In many studies of HIV replication, it is useful to quantify the number of HIV proviruses in
cells against a background of unintegrated forms of the HIV DNA. A popular method for
doing so involves quantitative PCR using one primer complementary to the HIV long
terminal repeat (LTR), and a second primer complementary to a cellular Alu repeat, so that
PCR product only forms from templates where a provirus is integrated in the human genome
near an Alu repeat. However, several recent studies have identified conditions that alter …