Analysis of genomic polymorphism among herpes simplex virus type 2 isolates from four areas of Japan and three other countries.

Genomic polymorphism of 307 epidemiologically unrelated strains of herpes simplex virus type 2 (HSV-2) from four areas of Japan and three other countries (Korea, Sweden and the U.S.A.) was analysed by using 16 variable markers selected from 97 restriction endonuclease (RE) sites with five REs. In addition to the 16 markers, 26 rare variable RE sites were found in 307 isolates. Five and four of 16 markers (RE sites) were found to differ in the frequency of isolates with the markers between isolates from Japan and Sweden and between those from Japan and the U.S.A., respectively, suggesting that they are genomically different from each other. In this manner, 307 HSV-2 isolates from four countries could be classified into 68 different genotypes (no. of isolates/no. of genotypes = 4.5). Some isolates from one country or more than two countries at times were classified into the same genotypes, which were referred to as predominant genotypes. The most predominant genotypes for isolates from Japan, Sweden and the U.S.A. were genotypes 30, 26 (32) and 3, respectively, indicating that they are different by the country. In genotypes 1 and 6, the frequency of isolates was found to be significantly different between Japan and Sweden and between Japan and the U.S.A., respectively. Nine out of 16 markers differed in the most genomically distant isolates, each of which was obtained in Sweden and Japan. In addition, high correlation coefficients (r) in the Japanese isolates were detected in different pairs of markers from those in the Swedish isolates, suggesting that isolates from these two countries are evolutionarily distant.