Reiterated sequences of herpes simplex virus type 1 (HSV-1) genome can serve as physical markers for the differentiation of HSV-1 strains.

The stability of regions containing tandemly reiterated sequences in the S component of the herpes simplex virus type 1 (HSV-1) genome was determined, by comparing restriction fragments of the regions among sets of HSV-1 isolates derived from a single source. The 6 reiterations examined were grouped into three. Reiteration VII (within protein coding regions of genes US10 and US11) and reiteration IV (within introns of genes US1 and US12) were stable between the isolates (group 1). Regions containing one of four other reiterations were detected as a set of ladder-like fragments. Reiteration II (between "a" sequence and IE 175 gene) and reiteration VI (within an intergenic region on the 3' side of the 3' co-terminal family of genes US10, US11, and US12) (group 3) were more unstable than reiteration I (within "a" sequence) and reiteration III (between "a" sequence and IE175 gene) (group 2). The mode of fluctuation of the reiterations observed within a set of HSV-1 strains isolated from an individual was similar to that observed between HSV-1 single-plaque clones separated in cultured cells. These reiterations, except for group 3, can serve as sensitive and convenient markers for differentiating HSV-1 strains.