Genomic sequences of a low passage herpes simplex virus 2 clinical isolate and its plaque-purified derivative strain

ABSTRACT Herpes simplex virus 1 (HSV-1) is a well-adapted human pathogen that can invade the peripheral nervous system and persist there as a lifelong latent infection. Despite their ubiquity, only one natural isolate of HSV-1 (strain 17) has been sequenced. Using Illumina high-throughput sequencing of viral DNA, we obtained the genome sequences of both a laboratory strain (F) and a low-passage clinical isolate (H129). These data demonstrated the extent of interstrain variation across the entire genome of HSV-1 in both coding and noncoding regions. We found many amino acid differences distributed across the proteome of the new strain F sequence and the previously known strain 17, demonstrating the spectrum of variability among wild-type HSV-1 proteins. The clinical isolate, strain H129, displays a unique anterograde spread phenotype for which the causal mutations were completely unknown. We have defined the sequence differences in H129 and propose a number of potentially causal genes, including the neurovirulence protein ICP34.5 (RL1). Further studies will be required to demonstrate which change(s) is sufficient to recapitulate the spread defect of strain H129. Unexpectedly, these data also revealed a frameshift mutation in the UL13 kinase in our strain F isolate, demonstrating how deep genome sequencing can reveal the full complement of background mutations in any given strain, particularly those passaged or plaque purified in a laboratory setting. These data increase our knowledge of sequence variation in large DNA viruses and demonstrate the potential of deep sequencing to yield insight into DNA genome evolution and the variation among different pathogen isolates.

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

Journal of Virology ◽

10.1128/jvi.01303-15 ◽

2015 ◽

Vol 89 (16) ◽

pp. 8219-8232 ◽

Cited By ~ 48

Author(s):

Ruchi M. Newman ◽

Susanna L. Lamers ◽

Brian Weiner ◽

Stuart C. Ray ◽

Robert C. Colgrove ◽

...

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Genital Herpes ◽

Causative Agent ◽

The United States ◽

Passage Number ◽

Low Passage ◽

Simplex Virus ◽

Herpes Simplex Virus 2 ◽

Hsv 1

ABSTRACTHerpes 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 low-passage-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.

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Identification of syncytial mutations in a clinical isolate of herpes simplex virus 2

Virology ◽

10.1016/j.virol.2004.07.027 ◽

2004 ◽

Vol 328 (2) ◽

pp. 244-253 ◽

Cited By ~ 15

Author(s):

Martin I. Muggeridge ◽

Michael L. Grantham ◽

F. Brent Johnson

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Clinical Isolate ◽

Simplex Virus ◽

Herpes Simplex Virus 2

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Genomic, Phylogenetic, and Recombinational Characterization of Herpes Simplex Virus 2 Strains

Journal of Virology ◽

10.1128/jvi.00416-15 ◽

2015 ◽

Vol 89 (12) ◽

pp. 6427-6434 ◽

Cited By ~ 34

Author(s):

Aaron W. Kolb ◽

Inna V. Larsen ◽

Jacqueline A. Cuellar ◽

Curtis R. Brandt

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Tandem Repeats ◽

Genomic Sequences ◽

Separate Species ◽

Intergenic Regions ◽

Genital Ulcers ◽

Microsatellite Mapping ◽

Simplex Virus ◽

Herpes Simplex Virus 2

ABSTRACTHerpes simplex virus 2 (HSV-2) is a major global pathogen, infecting 16% of people 15 to 49 years old worldwide and causing recurrent genital ulcers. Little is known about viral factors contributing to virulence, and there are currently only two genomic sequences available. In this study, we determined nearly complete genomic sequences of six additional HSV-2 isolates, using Illumina MiSeq. We report that HSV-2 has a genomic overall mean distance of 0.2355%, which is less than that of HSV-1. There were approximately 100 amino-acid-encoding and indels per genome. Microsatellite mapping found a bias toward intergenic regions in the nonconserved microsatellites and a genic bias in all detected tandem repeats. Extensive recombination between the HSV-2 strains was also strongly implied. This was the first study to analyze multiple HSV-2 sequences, and the data will be valuable in future evolutionary, virulence, and structure-function studies.IMPORTANCEHSV-2 is a significant worldwide pathogen, causing recurrent genital ulcers. Here we present six nearly complete HSV-2 genomic sequences, and, with the addition of two previously sequenced strains, for the first time genomic, phylogenetic, and recombination analysis was performed on multiple HSV-2 genomes. Our results show that microsatellite mapping found a bias toward intergenic regions in the nonconserved microsatellites and a genic bias in all detected tandem repeats and confirm that chimpanzee herpesvirus 1 (ChHV-1) is a separate species and that each of the HSV-2 strains is a genomic mosaic.

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