Latency-associated transcripts have been detected in human cytomegalovirus (CMV)-infected granulocyte-macrophage progenitors and have been shown to be encoded from both DNA strands in the ie1/ie2 region of the viral genome. One class includes differentially spliced transcripts that extends exon 1 by initiating at two novel start sites 292 and 356 nucleotides in the ie1/ie2 promoter/enhancer region, upstream of the start site used during productive infection. The other class includes an unspliced transcript antisense to ie1 exons 2,3, and 4. These transcripts are specific to latently infected cells and are not detected during productive infection of human fibroblast cells. Several open reading frames are found within these cytomegalovirus latency-specific transcripts (CLTs), including one 94 codons long that begins in the extended exon 1 region and is predicted to remain open through the exon1/2 and exon 2/3 splice junctions. Expression of latent transcripts was detected in bone marrow-derived hematopoietic samples from CMV-seropositive healthy donors but not from seronegative donors.