Homogeneity and diversity of genome polymorphism in a set of herpes simplex virus type 1 strains classified as the same genotypic group.

Restriction fragment length polymorphism (RFLP) of 327 strains of herpes simplex virus type 1 (HSV-1) isolated in Japan were analyzed using six restriction endonucleases (REs) recognizing 6 base pairs (BamHI, HindIII, KpnI, PvuII, SalI, XhoI). The presence of strains with the same RFLP profile became evident. Fifteen strains of each of the two predominant sets with the same RFLP profile were further analyzed using two different methods, that is analyses of RFLP using 3 restriction endonucleases recognizing 4 base pairs (4-bp REs) (HaeIII, HhaI, MboI) and analyses of the variation of 3 reiterated sequences (reiterations I, IV, VII). Most of the epidemiologically unrelated strains could be differentiated by variation of the reiterations. RFLPs differentiating the strains were detected with the 4-bp REs, and epidemiologically related strains shared a specific RFLP, thereby confirming the relationship. These results verified the utility of the two methods for use in molecular epidemiological studies. Homogeneity of RFLP among the strains suggested derivation from a common ancestor (making up a genotypic group) while diversity in strains of the same genotypic group was indicative of a separate replication.