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 journalArticle

Abstract

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
Volume89
Issue number16
DOIs
StatePublished - 2015

Fingerprint

Human Herpesvirus 2
Genome
Human herpesvirus 1
Herpes Genitalis
Uganda
South Africa
Genetic Recombination
Cluster Analysis
Epidemiology
Nucleotides
DNA
Infection

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Newman, R. M., Lamers, S. L., Weiner, B., Ray, S. C., Colgrove, R. C., Diaz, F., ... Knipe, D. M. (2015). Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. Journal of Virology, 89(16), 8219-8232. DOI: 10.1128/JVI.01303-15

Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. / Newman, Ruchi M.; Lamers, Susanna L.; Weiner, Brian; Ray, Stuart C.; Colgrove, Robert C.; Diaz, Fernando; Jing, Lichen; Wang, Kening; Saif, Sakina; Young, Sarah; Henn, Matthew; Laeyendecker, Oliver; Tobian, Aaron A R; Cohen, Jeffrey I.; Koelle, David M.; Quinn, Thomas C.; Knipe, David M.

In: Journal of Virology, Vol. 89, No. 16, 2015, p. 8219-8232.

Research output: Contribution to journalArticle

Newman, RM, Lamers, SL, Weiner, B, Ray, SC, Colgrove, RC, Diaz, F, Jing, L, Wang, K, Saif, S, Young, S, Henn, M, Laeyendecker, O, Tobian, AAR, Cohen, JI, Koelle, DM, Quinn, TC & Knipe, DM 2015, 'Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2' Journal of Virology, vol 89, no. 16, pp. 8219-8232. DOI: 10.1128/JVI.01303-15
Newman RM, Lamers SL, Weiner B, Ray SC, Colgrove RC, Diaz F et al. Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2. Journal of Virology. 2015;89(16):8219-8232. Available from, DOI: 10.1128/JVI.01303-15

Newman, Ruchi M.; Lamers, Susanna L.; Weiner, Brian; Ray, Stuart C.; Colgrove, Robert C.; Diaz, Fernando; Jing, Lichen; Wang, Kening; Saif, Sakina; Young, Sarah; Henn, Matthew; Laeyendecker, Oliver; Tobian, Aaron A R; Cohen, Jeffrey I.; Koelle, David M.; Quinn, Thomas C.; Knipe, David M. / Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2.

In: Journal of Virology, Vol. 89, No. 16, 2015, p. 8219-8232.

Research output: Contribution to journalArticle

@article{466fdfaa9217409f855be73e9340c6b3,
title = "Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2",
abstract = "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.",
author = "Newman, {Ruchi M.} and Lamers, {Susanna L.} and Brian Weiner and Ray, {Stuart C.} and Colgrove, {Robert C.} and Fernando Diaz and Lichen Jing and Kening Wang and Sakina Saif and Sarah Young and Matthew Henn and Oliver Laeyendecker and Tobian, {Aaron A R} and Cohen, {Jeffrey I.} and Koelle, {David M.} and Quinn, {Thomas C.} and Knipe, {David M.}",
year = "2015",
doi = "10.1128/JVI.01303-15",
volume = "89",
pages = "8219--8232",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "16",

}

TY - JOUR

T1 - Genome sequencing and analysis of geographically diverse clinical isolates of herpes simplex virus 2

AU - Newman,Ruchi M.

AU - Lamers,Susanna L.

AU - Weiner,Brian

AU - Ray,Stuart C.

AU - Colgrove,Robert C.

AU - Diaz,Fernando

AU - Jing,Lichen

AU - Wang,Kening

AU - Saif,Sakina

AU - Young,Sarah

AU - Henn,Matthew

AU - Laeyendecker,Oliver

AU - Tobian,Aaron A R

AU - Cohen,Jeffrey I.

AU - Koelle,David M.

AU - Quinn,Thomas C.

AU - Knipe,David M.

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84938066521&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84938066521&partnerID=8YFLogxK

U2 - 10.1128/JVI.01303-15

DO - 10.1128/JVI.01303-15

M3 - Article

VL - 89

SP - 8219

EP - 8232

JO - Journal of Virology

T2 - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 16

ER -