Characterization of human cytomegalovirus strains by analysis of short tandem repeat polymorphisms

Human cytomegalovirus (HCMV) strains display genetic polymorphisms, and the se polymorphisms can be analyzed to study viral transmission and pathogenes is. Recently, short tandem repeat (STR) length polymorphisms have been iden tified in the HCMV genome. We assessed the utility of STRs in characterizin g HCMV strains and found that a multiplexed PCR assay using primers based u pon these STRs accurately maps HCMV strains. Using primers for 10 microsate llite regions, the STR profiles of 44 wild-type and 2 laboratory strains of HCMV were characterized. The results of STR analysis were compared with th ose for strain characterization using nucleotide sequencing and restriction fragment length polymorphism analysis. In each instance, STR analysis accu rately and specifically identified strains that were indistinguishable or d istinct by conventional molecular analysis. Analysis of short tandem repeat s also detected polymorphisms that supported simultaneous excretion of two HCMV strains. These results indicate that STR analysis allows rapid, precis e molecular characterization of HCMV strains.