PCR-based detection is unable to consistently distinguish HIV 1LTR circles.

Quantitative PCR methods are routinely used to measure multiple HIV cDNA forms, including linear cDNA, early and late reverse transcripts, 2LTR circles, and integrated provirus. PCR-based methods for the detection of 1LTR circles have been proposed, but are complicated by the inherent homology of the LTR sequence present in all cDNA forms. Amplicons with variable lengths of homology showed that it is difficult to discriminate 1LTR circles faithfully from other cDNA forms. Addition of formamide, DMSO, or glycerol did not eliminate amplification of spurious products. Thus, detection of 1LTR circles by PCR is not reliable.