Numerous length polymorphisms at short tandem repeats in human cytomegalovirus

We show the presence of numerous short tandem repeats in the human cytomega lovirus (HCMV) genome and assess their usefulness as molecular markers. The genome is shown to contain at least 24 microsatellite regions that exhibit length polymorphisms. Insertion-deletion polymorphisms at these short tand em repeats are common (80% of repeats examined are polymorphic among two la boratory strains and 10 clinical isolates). This is the first report of wid espread microsatellite length polymorphism in a viral genome. Some regions are highly polymorphic: one was revealed by DNA sequencing to contain lengt h variants at five closely linked sites, which combined resulted in 10 vari ants for this region among the 12 strains and isolates examined. This study not only provides a new molecular marker system for this virus but also ex tends our understanding of microsatellite polymorphism in two important way s. First, variable-length repeats in HCMV can be considerably shorter than polymorphic repeats previously found in other organisms. Second, highly var iable microsatellite repeats are not confined to prokaryotes and eukaryotes , as previously assumed. This variation provides a useful marker system for distinguishing viral isolates, and similar markers are also likely to be f ound in other large-genome DNA viruses.