Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2

Ruchi M. Newman, Susanna L. Lamers, Brian Weiner, Stuart C. Ray, Robert C. Colgrove, Fernando Diaz, Lichen Jing, Kening Wang, Sakina Saif, Sarah Young, Matthew Henn, Oliver Laeyendecker, Aaron A.R. Tobian, Jeffrey I. Cohen, David M. Koelle, Thomas C. Quinn, David M. Knipe

Research output: Contribution to journalArticlepeer-review

42 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)8219-8232
Number of pages14
JournalJournal of virology
Issue number16
StatePublished - 2015

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology


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