We have compared dIII and RI restriction sites in the long and short unique regions of the human cytomegalovirus (HCMV) genome among 20 low passage clinical isolates and four high passage laboratory strains (AD169, Davis, Towne, UW-1). This was done by hybridizing digested DNA on Southern blots with a series of subgenomic cloned fragments of AD169. Fourteen dIII sites were conserved and three fragments (O, V, W) co-migrated among all strains. Nine dIII sites found in AD169 were absent in one or more other strains. Eight additional dIII sites were identified and three more hypothesized by the appearance of slightly smaller fragments. Sixteen RI sites were conserved and six fragments (c, Y, S, W, B, R) co-migrated among all strains. Twelve RI sites were absent or in altered locations and at least seven additional sites were identified in one or more strains. Although no two of these strains were identical throughout the genome, identical patterns of variation in a given region frequently occurred in multiple strains. Polymorphisms occurred throughout the entire genome, including the region specifying immediate early functions. All strains studied showed an identical fragment which hybridized to the transforming fragment of AD169. These restriction site polymorphisms may in the future serve as convenient markers for identification of functional variation among HCMV strains.


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