A tandem repeat sequence found in a heterogeneous fragment of UL of herpes simplex virus type 1.

We found a tandem repeat sequence in the region (designated BS7) in which restriction fragments BamHI D and SalI B overlap each other, near the centre of the unique long sequence (UL) of the herpes simplex virus type 1 (HSV-1) strain F genome. The SmaI physical map of BS7 was constructed, and the position of a heterogeneous SmaI subfragment from HSV-1 isolates and plaque-purified clones from a single strain was defined on the map. The maximum size difference in the SmaI subfragment was estimated to be 600 bp between these isolates and 100 bp between the clones. The 0.23 kb SmaI subfragment recloned from BS7 was sequenced, and was shown to contain a tandem repeat sequence consisting of 15 units of 12 bp, 5' TTGGGGCTGGGG 3'. These results suggest that the fragment length heterogeneity in the UL of HSV-1 isolates and clones is attributable to copy number variation of the tandem repeat sequence.