Infection with the Epstein-Barr virus (EBV) is often subclinical in the presence of a healthy immune response; thus, asymptomatic infection is largely uncharacterized. This study analyzed the nature of EBV infection in 20 asymptomatic immunocompetent hosts over time through the identification of EBV strain variants in the peripheral blood and oral cavity. A heteroduplex tracking assay specific for the EBV gene LMP1 precisely identified the presence of multiple EBV strains in each subject. The strains present in the peripheral blood and oral cavity were often completely discordant, indicating the existence of distinct infections, and the strains present and their relative abundance changed considerably between time points. The possible transmission of strains between the oral cavity and peripheral blood compartments could be tracked within subjects, suggesting that reactivation in the oral cavity and subsequent reinfection of B lymphocytes that reenter the periphery contribute to the maintenance of persistence. In addition, distinct virus strains persisted in the oral cavity over many time points, suggesting an important role for epithelial cells in the maintenance of persistence. Asymptomatic individuals without tonsillar tissue, which is believed to be an important source of virus for the oral cavity, also exhibited multiple strains and a cyclic pattern of transmission between compartments. This study revealed that the majority of patients with infectious mononucleosis were infected with multiple strains of EBV that were also compartmentalized, suggesting that primary infection involves the transmission of multiple strains. Both the primary and carrier states of infection with EBV are more complex than previously thought.Epstein-Barr virus (EBV) is a human herpesvirus that establishes a life-long persistent infection in more than 90% of the world's population. Primary infection with the virus is usually asymptomatic but can result in the self-limiting disease infectious mononucleosis. EBV is associated with numerous pathologies that develop in B lymphocytes and epithelial cells, including Burkitt's lymphoma, Hodgkin's disease, AIDS-associated and posttransplant lymphomas, nasopharyngeal carcinoma, hairy leukoplakia, and several others (21).EBV persists in memory B lymphocytes, which may expand in response to their cognate antigen and subsequently differentiate into plasma cells, in which viral reactivation and replication may occur (1, 2). The role of EBV replication in the maintenance of persistent infection is not well characterized. Viral proteins indicative of replication have been detected in lymphocytes in the tonsillar tissue, and replicating virus has been detected in sloughed oropharyngeal epithelial cells (1,14,17,23,29). The replication and subsequent release of virus into the oral cavity permit transmission of the virus to a new host and possibly reinfection of oropharyngeal epithelial cells and B lymphocytes. The virus detected in the oropharynx is thought to be released from epithelial cells or ly...