Nucleotide sequences of the joint between the L and S segments of herpes simplex virus types 1 and 2

The a sequence of herpes simplex virus (HSV) is present as a direct repeat at the genomic termini and also in inverted orientation at the joint between the L and S segments. DNA sequences have been determined for the joint regions of the genomes of HSV-1 and HSV-2, and relative to these sequences the genomic termini are in both cases located close to a short direct repeat of 17 to 21 base pairs (bp) at the b-a and a-c junctions. The HSV-1 joint region contains three separate tandem direct reiterations of short sequences, (12, 16 and 17 bp in strain 17) and we conclude that size heterogeneity in the a and c sequences is due to variable copy numbers of these repeated units. It is likely that a considerable part of the HSV-1 joint region does not code for polypeptide.