Mutations in the thymidine kinase gene (tk) of herpes simplex virus type 1 (HSV-1) explain most cases of virus resistance to acyclovir (ACV) treatment. Mucocutaneous lesions of patients with ACV resistance contain mixed populations of tk mutant and wild-type virus. However, it is unknown whether human ganglia also contain mixed populations since the replication of HSV tk mutants in animal neurons is impaired. Here we report the detection of mutated HSV tk sequences in human ganglia. Trigeminal and dorsal root ganglia were obtained at autopsy from an immunocompromised woman with chronic mucocutaneous infection with ACV-resistant HSV-1. The HSV-1 tk open reading frames from ganglia were amplified by PCR, cloned, and sequenced. tk mutations were detected in a seven-G homopolymer region in 11 of 12 ganglia tested, with clonal frequencies ranging from 4.2 to 76% HSV-1 tk mutants per ganglion. In 8 of 11 ganglia, the mutations were heterogeneous, varying from a deletion of one G to an insertion of one to three G residues, with the two-G insertion being the most common. Each ganglion had its own pattern of mutant populations. When individual neurons from one ganglion were analyzed by laser capture microdissection and PCR, 6 of 14 HSV-1-positive neurons were coinfected with HSV tk mutants and wild-type virus, 4 of 14 were infected with wild-type virus alone, and 4 of 14 were infected with tk mutant virus alone. These data suggest that diverse tk mutants arise independently under drug selection and establish latency in human sensory ganglia alone or together with wild-type virus.The deoxyguanosine homolog acyclovir (ACV) is the most common drug used to treat herpes simplex virus (HSV) infections. After being taken up into cells, ACV is sequentially converted into ACV monophosphate, ACV diphosphate, and finally its active form, ACV triphosphate. The first step of the sequential phosphorylations requires HSV-encoded thymidine kinase (TK); however, cellular enzymes perform the additional phosphorylations. ACV triphosphate is more efficiently incorporated into replicating DNA by HSV DNA polymerase than by the cellular DNA polymerase (8). These characteristics of ACV result in its selectivity for virus-infected cells and its extremely low toxicity to uninfected cells. However, if HSV loses its TK function (including an alteration in substrate specificity or the loss of TK activity) or its DNA polymerase has altered substrate affinity, the virus becomes ACV resistant (Acv r ). While viral TK function is crucial for ACV activity, TK is not essential for HSV to replicate in dividing cells (22) such as human epithelial cells, presumably due to the abundance of nucleotides in these cells. Thus, a TK Ϫ HSV mutant that is resistant to ACV therapy can still replicate in epithelial cells and cause lesions. In contrast, TK activity is important for virus replication in resting cells or neurons (22,38). Though Acv r HSV infection rarely has clinical significance in immunocompetent individuals (7,15,24,27,37), severe disease can occur in...