Comparative Sequence Analysis of the Long Repeat Regions and Adjoining Parts of the Long Unique Regions in the Genomes of Herpes Simplex Viruses Types 1 and 2

We report the determination of the DNA sequence of the long repeat (R l ) region and adjacent parts of the long unique (U l ) region in the genome of herpes simplex virus type 2 (HSV-2) strain HG52. The DNA sequences and genetic content of the extremities of HSV-2 U l were found to be closely similar to those determined previously for HSV-1. The 5658 bp sequenced at the left end of HSV-2 U l contained coding regions for genes UL1 to UL4 plus part of UL5. The 4355 bp sequenced at the right end of U l contained coding regions for part of gene UL53, and the whole of genes UL54 to UL56. Comparison of the HSV-1 and HSV-2 UL56 sequences led to a correction in the published HSV-1 UL56 reading frame. The HSV-2 R l region, including one copy of the a sequence, was determined to be 9263 bp, with a base composition of 75.4% G+C and with many repetitive sequence elements. In HSV-2 R l , sequences were identified corresponding to HSV-1 genes encoding the immediate early IE110 (ICP0) transcriptional regulator and the ICP34.5 neurovirulence factor; the former HSV-2 gene was proposed to contain two introns, and the latter one intron. Downstream of the HSV-2 immediate early gene, the R l sequence encoding the latency-associated transcripts (LATs) was found to be dissimilar to that in HSV-1; the probable LAT promoter regions, however, showed similarities to HSV-1. Properties of the LAT sequences in both HSV-1 and HSV-2 were consistent with LATs being generated as an intron excised from a longer transcript.