Herpes simplex virus 2 (HSV-2), the principal causative agent of recurrent genital herpes, is a highly prevalent viral infection worldwide. Limited information is available on the amount of genomic DNA variation between HSV-2 strains because only two genomes have been determined, the HG52 laboratory strain and the newly sequenced SD90e low-passage-number clinical isolate strain, each from a different geographical area. In this study, we report the nearly complete genome sequences of 34 HSV-2 lowpassage-number and laboratory strains, 14 of which were collected in Uganda, 1 in South Africa, 11 in the United States, and 8 in Japan. Our analyses of these genomes demonstrated remarkable sequence conservation, regardless of geographic origin, with the maximum nucleotide divergence between strains being 0.4% across the genome. In contrast, prior studies indicated that HSV-1 genomes exhibit more sequence diversity, as well as geographical clustering. Additionally, unlike HSV-1, little viral recombination between HSV-2 strains could be substantiated. These results are interpreted in light of HSV-2 evolution, epidemiology, and pathogenesis. Finally, the newly generated sequences more closely resemble the low-passage-number SD90e than HG52, supporting the use of the former as the new reference genome of HSV-2.
IMPORTANCEHerpes simplex virus 2 (HSV-2) is a causative agent of genital and neonatal herpes. Therefore, knowledge of its DNA genome and genetic variability is central to preventing and treating genital herpes. However, only two full-length HSV-2 genomes have been reported. In this study, we sequenced 34 additional HSV-2 low-passage-number and laboratory viral genomes and initiated analysis of the genetic diversity of HSV-2 strains from around the world. The analysis of these genomes will facilitate research aimed at vaccine development, diagnosis, and the evaluation of clinical manifestations and transmission of HSV-2. This information will also contribute to our understanding of HSV evolution.
Herpes simplex virus 1 (HSV-1) and herpes simplex virus 2 (HSV-2) are two closely related human species of herpesviruses in the genus Simplexvirus of the family Herpesviridae (1). HSV-1 is mostly associated with orofacial infections, while HSV-2 is generally associated with genital herpes. Both viruses cause significant human disease, so knowledge of the structure of their DNA genomes and the extent of their genetic variation is very important. A high overall GC content and the presence of highly reiterated repeat regions in both noncoding and coding portions of the genome complicate sequence determination (2).The HSV linear double-stranded DNA genomes consist of two covalent linked components, the long (L) and short (S) components, which invert relative to each other by intramolecular recombination (1). The L component consists of unique sequences (U L ) bounded by inverted repeats (R L and R L =), and the S component consists of unique sequences (U S ) bounded by inverted repeats (R S and R S =) (3). The termini con...