Evolution and diversity in human herpes simplex virus genomes

Moriah Louise Szpara, Derek Gatherer, Alejandro Ochoa, Benjamin Greenbaum, Aidan Dolan, Rory J. Bowden, Lynn W. Enquist, Matthieu Legendre, Andrew J. Davison

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

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. Wealso 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.

Original languageEnglish (US)
Pages (from-to)1209-1227
Number of pages19
JournalJournal of virology
Volume88
Issue number2
DOIs
StatePublished - Jan 1 2014

Fingerprint

Human herpesvirus 1
herpes simplex
Human Herpesvirus 1
Simplexvirus
Genome
viruses
genome
frameshift mutation
Frameshift Mutation
Japan
Vaccines
vaccines
Republic of Korea
Proteins
gene deletion
Sequence Deletion
Viral Genome
Kenya
Gene Deletion
South Korea

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

Cite this

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. Journal of virology, 88(2), 1209-1227. https://doi.org/10.1128/JVI.01987-13
Szpara, Moriah Louise ; Gatherer, Derek ; Ochoa, Alejandro ; Greenbaum, Benjamin ; Dolan, Aidan ; Bowden, Rory J. ; Enquist, Lynn W. ; Legendre, Matthieu ; Davison, Andrew J. / Evolution and diversity in human herpes simplex virus genomes. In: Journal of virology. 2014 ; Vol. 88, No. 2. pp. 1209-1227.
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Szpara, ML, Gatherer, D, Ochoa, A, Greenbaum, B, Dolan, A, Bowden, RJ, Enquist, LW, Legendre, M & Davison, AJ 2014, 'Evolution and diversity in human herpes simplex virus genomes', Journal of virology, vol. 88, no. 2, pp. 1209-1227. https://doi.org/10.1128/JVI.01987-13

Evolution and diversity in human herpes simplex virus genomes. / Szpara, Moriah Louise; Gatherer, Derek; Ochoa, Alejandro; Greenbaum, Benjamin; Dolan, Aidan; Bowden, Rory J.; Enquist, Lynn W.; Legendre, Matthieu; Davison, Andrew J.

In: Journal of virology, Vol. 88, No. 2, 01.01.2014, p. 1209-1227.

Research output: Contribution to journalArticle

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Szpara ML, Gatherer D, Ochoa A, Greenbaum B, Dolan A, Bowden RJ et al. Evolution and diversity in human herpes simplex virus genomes. Journal of virology. 2014 Jan 1;88(2):1209-1227. https://doi.org/10.1128/JVI.01987-13