title: Genomic sequences of a low passage herpes simplex virus 2 clinical isolate and its plaque-purified derivative strain.
abstract: Herpes simplex virus 2 is an important human pathogen as the causative agent of genital herpes, neonatal herpes, and increased risk of HIV acquisition and transmission. Nevertheless, the only genomic sequence that has been completed is the attenuated HSV-2 HG52 laboratory strain. In this study we defined the genomic sequence of the HSV-2 SD90e low passage clinical isolate and a plaque-purified derivative, SD90-3P. We found minimal sequence differences between SD90e and SD90-3P. However, in comparisons with the HSV-2 HG52 reference genome sequence, the SD90e genome ORFs contained numerous point mutations, 13 insertions/deletions (indels), and 9 short compensatory frameshifts. The indels were true sequence differences, but the compensatory frameshifts were likely sequence errors in the original HG52 sequence. Because HG52 virus is less virulent than other HSV-2 strains and may not be representative of wildtype HSV-2 strains, we propose that the HSV-2 SD90e genome serve as the new HSV-2 reference genome.
authors: Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States.
authors: Robert
authors: R
authors: Colgrove
authors: Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States.
authors: Fernando
authors: F
authors: Diaz
authors: Broad Institute, Cambridge, MA, United States.
authors: Ruchi
authors: R
authors: Newman
authors: Broad Institute, Cambridge, MA, United States.
authors: Sakina
authors: S
authors: Saif
authors: Broad Institute, Cambridge, MA, United States.
authors: Terry
authors: T
authors: Shea
authors: Broad Institute, Cambridge, MA, United States.
authors: Sarah
authors: S
authors: Young
authors: Broad Institute, Cambridge, MA, United States.
authors: Matt
authors: M
authors: Henn
authors: Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States. Electronic address: david_knipe@hms.harvard.edu.
authors: David M
authors: DM
authors: Knipe
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D016679:Genome, Viral; D023281:Genomics; D006558:Herpes Genitalis / Q000821:virology*; D018258:Herpesvirus 2, Human / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012692:Serial Passage; D010948:Viral Plaque Assay
keywords: DNA virus genome; Genital herpes; Herpes simplex virus 2; Sexually transmitted disease