We employed a newly developed genotyping technique with direct representational detection of LMP-1 gene sequences to study the molecular epidemiology of Epstein-Barr virus (EBV) infection in healthy individuals. Infections with up to five different EBV genotypes were found in two of nine individuals studied. These results support the hypothesis that multiple EBV infections of healthy individuals are common. The implications for the development of an EBV vaccine are discussed.Multiple Epstein-Barr virus (EBV) infections are common among immunocompromised individuals (21,29,31,39,41,43,44,46), but the origin of the multiple EBV strains remains a mystery. Multiple EBV strains could accumulate as superinfections in individuals who have lost previous protective immunity to EBV. Alternatively, they could represent the reactivation of latent EBV strains that were acquired prior to the onset of immunodeficiency. The reported prevalence of multiple EBV infections in healthy individuals ranges broadly between 0 and 100% (Table 1) (4,7,13,16,19,20,23,30,32,35,38,45; M. L. Lung and R. S. Chang, Letter, J. Infect. Dis. 162:994-995, 1990), but differences among these studies in the molecular detection and definition of an EBV strain confound the interpretation of their results.Molecular epidemiologic studies requiring EBV isolation by B-lymphocyte transformation (16,19,23,45; Lung and Chang, letter) suffer from selection bias toward transformation-competent EBV isolates (10,27,33). PCR amplification directly detects the EBV genome and avoids transformation selection bias, but the genetic definition of an EBV strain has been inconsistent across studies. Restriction fragment length polymorphisms detect either point mutations within restriction enzyme cleavage sites or variations of large repetitive regions within genome fragments (19,23,35; Lung and Chang, letter). Similarly, size variation in EBNA proteins ("EBNotype" or "EBNAprint") (16, 45) and size variation in specific gene PCR products (LMP-1, BZLF1, EBNA-6) (13, 35) reflect variations in repetitive and other genome sequences. However, many EBV genome sequences are susceptible to intrastrain homologous and nonhomologous recombination during productive replication and the number of repeat units present may vary in different isolates of the same EBV strain (12,38,(41)(42)(43). Studies examining the major sequence divergence between EBV types 1 and 2 have reported EBV coinfection rates ranging from 0 to 53% (4,13,20,34,35,45). However, EBV types 1 and 2 can both be further subdivided into different strains (1,24,41) and only three studies to date have utilized EBV gene nucleotide sequence variation to define EBV strains in healthy individuals (7,30,38).EBV genotyping assay. A consistent approach is needed for the definition and nomenclature of EBV genomes. It is impractical or even impossible to physically isolate (culture) and fully characterize the EBV genome(s) in clinical infections. A reasonable goal would be to identify an EBV genetic marker that represents the broad...