Herpes simplex virus type 1 (HSV-1) and varicella-zoster virus (VZV) establish lifelong latent infections in human sensory ganglia, processes that have been investigated extensively but are still not fully elucidated. It is well established that during latency, infectious HSV-1 and VZV particles are not produced (40,41,56), but small subsets of their genes are expressed (11,12,13,21,25,27,31,35,44,52). These latent viruses, however, are subject to single or multiple rounds of reactivation and can result in recrudescent disease (7, 59). For HSV, gene expression in latency is extremely restricted in that only the latency-associated transcripts (LAT) accumulate to levels high enough to be detected by in situ hybridization (ISH) (4,11,13,44,49,50,52). Although there is no confirmation that LAT encodes a protein that regulates HSV latency and reactivation, it has been documented that the 5Ј portion of the LAT gene facilitates the efficient establishment and reactivation from latency in experimentally infected animals (3,10,16,23,38,48,54,55).The discovery and detection of LAT by ISH enabled an indirect estimate of the percentages of animal and human sensory ganglion neurons that are latently infected. ISH studies in our laboratory, for example, showed that LAT can be detected in 0.2 to 4.3% of the neurons in human trigeminal ganglia (TG) (11), a range similar to that reported for experimentally infected mice, rabbits, and guinea pigs (4,22,44). Because the in situ detection of LAT is merely a surrogate marker for HSV latency, it is possible that many more neurons are latently infected but their LAT expression or accumulation is too low to be detected by this technique. In accord with this possibility, a variety of tools have been used to better estimate the numbers of HSV-1 DNA-containing neurons in experimental animals, including in situ PCR (27,33,34,42,43), contextual analysis (45, 47), and laser-capture microdissection (LCM) (6). These studies revealed that, in mice and rats, neurons that are LAT positive by ISH represent but a fraction of those harboring HSV-1 DNA (6,33,42,45).In the past several years, using real-time DNA PCR assays, the latent HSV-1 DNA load in human TG was estimated to be hundreds to thousands of copies/g of total ganglion DNA (9, 39), suggesting that a higher proportion of cells might be latently infected than are identified by ISH. The actual percentages of neurons that harbor latent HSV-1 DNA and the ranges of viral genome copy numbers in individual neurons, however, were addressed more directly only recently by PCR of dissociated human TG cells (5).As complex as the analysis of HSV latency in human ganglia has been, studies of the cellular distribution of latent VZV DNA in human ganglia have been even more so, despite numerous attempts using ISH (12,21,25,27,31), in situ PCR (17, 27), immunohistochemical staining (8, 26, 32, 36), and PCR of dissociated ganglion cells (28, 30). There had long remained controversy, for example, as to which cells primarily harbor latent VZV. Our laboratory r...