A Genome-Wide Comparative Evolutionary Analysis of Herpes Simplex Virus Type 1 and Varicella Zoster Virus

Norberg, Peter; Tyler, Shaun; Severini, Alberto; Whitley, R. J.; Liljeqvist, Jan‐Åke; Bergström, Tomas

doi:10.1371/journal.pone.0022527

Cited by 66 publications

(98 citation statements)

References 44 publications

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“…High‐throughput genome sequencing has provided evidence of recombination between strains in other herpesviruses, namely HSV‐2, VZV, Marek's disease virus, HSV‐1, pseudorabies virus, human cytomegalovirus and infectious laryngotracheitis virus (Hughes & Rivailler, 2007; Kolb, Larsen, Cuellar, & Brandt, 2015; Lee et al., 2013; Norberg et al., 2011, 2015; Sijmons et al., 2015; Szpara et al., 2014; Szpara, Tafuri, et al., 2011; Zell et al., 2012). In the present study, network analysis suggested that recombination has also occurred between EHV‐1 strains.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Bryant

Wilkie

Russell

et al. 2018

Transbound Emerg Dis

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SummaryEquine herpesvirus 1 (EHV‐1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV‐1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term “neuropathic strain,” even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV‐1 diversity in the field, 78 EHV‐1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV‐1 clades, between EHV‐1 and equine herpesvirus 4, and between EHV‐1 and equine herpesvirus 8.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Bryant

Wilkie

Russell

et al. 2018

Transbound Emerg Dis

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“…The origin of the divergence in these strains is not immediately obvious. Furthermore, the average divergence for all ORFs was greater for HG52 ILMN than for (30). The analysis involved 37 nucleotide sequences.…”

Section: U S 4 and U S 11)mentioning

confidence: 99%

“…Taken together, the low level of sequence diversity, low rate of recombination, and relative lack of geographic clustering of HSV-2 strains are in contrast to what has been reported for geographically diverse HSV-1 strains. Several studies report that HSV-1 genomes display high levels of DNA diversity, as well as extensive recombination (6,30,31). Furthermore, analysis of genetic distances among HSV-1 strains isolated from Asia, Africa, North America, and Europe shows strong sequence clustering of strains based on geographic location.…”

Section: Figmentioning

confidence: 99%

Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2

Newman

Lamers²,

Weiner

et al. 2015

J Virol

100

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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. IMPORTANCEHerpes simplex virus 2 (HSV-2) is a causative agent of genital and neonatal herpes. Therefore, knowledge of its DNA genome and genetic variability is central to preventing and treating genital herpes. However, only two full-length HSV-2 genomes have been reported. In this study, we sequenced 34 additional HSV-2 low-passage-number and laboratory viral genomes and initiated analysis of the genetic diversity of HSV-2 strains from around the world. The analysis of these genomes will facilitate research aimed at vaccine development, diagnosis, and the evaluation of clinical manifestations and transmission of HSV-2. This information will also contribute to our understanding of HSV evolution. Herpes simplex virus 1 (HSV-1) and herpes simplex virus 2 (HSV-2) are two closely related human species of herpesviruses in the genus Simplexvirus of the family Herpesviridae (1). HSV-1 is mostly associated with orofacial infections, while HSV-2 is generally associated with genital herpes. Both viruses cause significant human disease, so knowledge of the structure of their DNA genomes and the extent of their genetic variation is very important. A high overall GC content and the presence of highly reiterated repeat regions in both noncoding and coding portions of the genome complicate sequence determination (2).The HSV linear double-stranded DNA genomes consist of two covalent linked components, the long (L) and short (S) components, which invert relative to each other by intramolecular recombination (1). The L component consists of unique sequences (U L ) bounded by inverted repeats (R L and R L =), and the S component consists of unique sequences (U S ) bounded by inverted repeats (R S and R S =) (3). The termini con...

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“…In contrast to both HSV-1 and HSV-2, the related human alphaherpesvirus, varicella-zoster virus (VZV), has relatively low interstrain diversity (12)(13)(14)(15). Decades of research comparing RFLP bands, polypeptide size, and PCR-based sequence analysis have revealed that HSV-1 strains vary between individuals, over sequential isolates from the same individual, and by geographic region (10,(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28).…”

mentioning

confidence: 99%

Evolution and Diversity in Human Herpes Simplex Virus Genomes

Szpara

Gatherer

Ochoa

et al. 2014

J Virol

197

280

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gHerpes 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. Herpes simplex virus 1 (HSV-1; species Human herpesvirus 1, genus Simplexvirus, subfamily Alphaherpesvirinae, family Herpesviridae, order Herpesvirales) is among the most successful human pathogens in terms of its global distribution, longevity in the host, and mild symptoms among the great majority of those exposed (1-4). HSV-1 is a large, enveloped DNA virus that infects lytically at epithelial surfaces and establishes a lifelong, latent infection in sensory neurons. HSV-1 infection produces a wide range of symptoms, ranging from few or none in many seropositive individuals to periodic lesions on epithelial surfaces in a significant proportion of people and to lethal encephalitis as an extreme manifestation in a few. There is no vaccine at present (5, 6). Studies in animal models have characterized the ways in which genetic variation between viral strains can influence the symptoms of pathology, including lesion severity and rates of reactivation from latency. The most recent phase III vaccine trial for HSV failed to provide protection from infection (7, 8), and one contributing factor to this failure may well be variation among HSV isolates found in the field.Based on early restriction fragment length polymorphism (RFLP) analyses, HSV-1 has been described as more diverse than HSV-2 (9-11). In contrast to both HSV-1 and HSV-2, the related human alphaherpesvirus, varicella-zoster virus (VZV), has relatively low interstrain diversity (12-15). Decades of research comparing RFLP bands, polypeptide size, and PCR-based sequence analysis have revealed that HSV-1 strains vary between individuals, over sequential isolates from the s...

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A Genome-Wide Comparative Evolutionary Analysis of Herpes Simplex Virus Type 1 and Varicella Zoster Virus

Cited by 66 publications

References 44 publications

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2

Evolution and Diversity in Human Herpes Simplex Virus Genomes

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