Analysis of strain variation of R1 repeated structure in varicella-zoster virus DNA by polymerase chain reaction.

The tandem direct reiteration R1 in the varicella-zoster virus genome consists of two elements: units composed of 18 bp and those having 15 bp, both of whose numbers and types of combination patterns vary among strains. The variations of the R1 structure were examined in order to differentiate between the wild strains and a varicella vaccine (Oka) strain by the polymerase chain reaction using two primer sets. The results showed that the 31 wild strains were classified into nine patterns: the R1 structure consisted of a combination of 5 to 7 18-bp units and 8 to 12 15-bp units. The strain with a combination of 6 18-bp units and 10 15-bp units was found to be predominant in Japan, and the same pattern was found in the vaccine strain, so that differentiation between the vaccine strain and the wild strains in Japan merely by analysis of R1 in VZV genome is difficult.