Abstract: A marker and method for detection and monitoring of HIV latency and activation and an assay for detection of the marker. The assay sensitively detects HIV transcription and monitors HIV transcriptional activity by detecting the presence of short and long transcripts, quantifying both and determining the ratio of short to long transcripts. Short transcripts are abundant and a low ratio correlates with a latent-type transcriptional activity of HIV whereas the appearance of long transcripts signifies increased efficiency of transcriptional activity of HIV and the transition from latency to activation. The size difference between the TAR fragments appearing predominantly in latency and the full length transcripts appearing predominantly during the HIV activation is detected by RT-PCR assay that utilizes novel primers and probes. The results are expressed as a ratio of short to long transcripts.