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Evolution and diversity in human herpes simplex virus genomes.

Publication ,  Journal Article
Szpara, ML; Gatherer, D; Ochoa, A; Greenbaum, B; Dolan, A; Bowden, RJ; Enquist, LW; Legendre, M; Davison, AJ
Published in: J Virol
January 2014

Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan. In this diverse collection of passaged strains, we found that one-fifth of the newly sequenced members share a gene deletion and one-third exhibit homopolymeric frameshift mutations (HFMs). Individual strains exhibit genotypic and potential phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphisms, although the protein sequence identity between strains exceeds 90% on average. In the first genome-scale analysis of positive selection in HSV-1, we found signs of selection in specific proteins and residues, including the fusion protein glycoprotein H. We also confirmed previous results suggesting that recombination has occurred with high frequency throughout the HSV-1 genome. Despite this, the HSV-1 strains analyzed clustered by geographic origin during whole-genome distance analysis. These data shed light on likely routes of HSV-1 adaptation to changing environments and will aid in the selection of vaccine antigens that are invariant worldwide.

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Published In

J Virol

DOI

EISSN

1098-5514

Publication Date

January 2014

Volume

88

Issue

2

Start / End Page

1209 / 1227

Location

United States

Related Subject Headings

  • Virology
  • Viral Proteins
  • Sequence Alignment
  • Republic of Korea
  • Phylogeny
  • Molecular Sequence Data
  • Kenya
  • Japan
  • Humans
  • Herpesvirus 1, Human
 

Citation

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Szpara, M. L., Gatherer, D., Ochoa, A., Greenbaum, B., Dolan, A., Bowden, R. J., … Davison, A. J. (2014). Evolution and diversity in human herpes simplex virus genomes. J Virol, 88(2), 1209–1227. https://doi.org/10.1128/JVI.01987-13
Szpara, Moriah L., Derek Gatherer, Alejandro Ochoa, Benjamin Greenbaum, Aidan Dolan, Rory J. Bowden, Lynn W. Enquist, Matthieu Legendre, and Andrew J. Davison. “Evolution and diversity in human herpes simplex virus genomes.J Virol 88, no. 2 (January 2014): 1209–27. https://doi.org/10.1128/JVI.01987-13.
Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ, et al. Evolution and diversity in human herpes simplex virus genomes. J Virol. 2014 Jan;88(2):1209–27.
Szpara, Moriah L., et al. “Evolution and diversity in human herpes simplex virus genomes.J Virol, vol. 88, no. 2, Jan. 2014, pp. 1209–27. Pubmed, doi:10.1128/JVI.01987-13.
Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ, Enquist LW, Legendre M, Davison AJ. Evolution and diversity in human herpes simplex virus genomes. J Virol. 2014 Jan;88(2):1209–1227.

Published In

J Virol

DOI

EISSN

1098-5514

Publication Date

January 2014

Volume

88

Issue

2

Start / End Page

1209 / 1227

Location

United States

Related Subject Headings

  • Virology
  • Viral Proteins
  • Sequence Alignment
  • Republic of Korea
  • Phylogeny
  • Molecular Sequence Data
  • Kenya
  • Japan
  • Humans
  • Herpesvirus 1, Human