Genomic characterization of two predominant genotypes of herpes simplex virus type 1

Umene, Kenichi; Yoshida, Masami

doi:10.1007/bf01379078

Cited by 29 publications

(59 citation statements)

References 36 publications

(45 reference statements)

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“…(a) Structure of the HSV-I genome arranged in prototype orientation. Sall fragments at the ends of the L and S components of HSV-I strain GN28 are shown (Umene, 1993 ;Umene & Yoshida, 1993). The nomenclature of the Sail fragments is from Locker & Frenkel (1979).…”

Section: Draimentioning

confidence: 99%

Replication of Herpes Simplex Virus Type 1 DNA is Inhibited in a Temperature-sensitive Mutant of BHK-21 Cells Lacking RCC1 (Regulator of Chromosome Condensation) and Virus DNA Remains Linear

Umene

Nishimoto

1996

Journal of General Virology

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Section: Draimentioning

confidence: 99%

Replication of Herpes Simplex Virus Type 1 DNA is Inhibited in a Temperature-sensitive Mutant of BHK-21 Cells Lacking RCC1 (Regulator of Chromosome Condensation) and Virus DNA Remains Linear

Umene

Nishimoto

1996

Journal of General Virology

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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 (12-15). 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). However, these approaches have limitations.…”

mentioning

confidence: 99%

Evolution and Diversity in Human Herpes Simplex Virus Genomes

Szpara

Gatherer

Ochoa

et al. 2014

J Virol

193

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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“…To date, three research groups, including our own, have advanced the development of a strategy for practical VZV genotyping (14, 33, 34, 44; (1,4,7,9,32,43,46). Nevertheless, careful genotypic analysis could lead to the identification of virulence factors and hence to an improved understanding of VZV biology (35).…”

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Global Identification of Three Major Genotypes of Varicella-Zoster Virus: Longitudinal Clustering and Strategies for Genotyping

Loparev

González

DeLeon-Carnes

et al. 2004

J Virol

135

252

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By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E-and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples.Varicella-zoster virus (VZV) is a human herpesvirus that commonly causes chicken pox (varicella), usually in young children. Following primary infection a lifelong latent infection is established, and the virus often reactivates in adulthood or senescence to cause shingles (zoster). The VZV genome consists of 125 kb of linear, double-stranded DNA comprising one long and one short unique region, each flanked by inverted repeats (10), and five internal repeat regions (R1 to R5) have been identified. The VZV genome contains at least 71 open reading frames (ORFs), and the functions of many of the proteins they encode have been characterized (10).During the past 2 decades, several groups attempted to evaluate VZV phylogeny. Early efforts in VZV typing used DNA restriction fragment length polymorphism (RFLP) analysis (13,37,38), an approach that confirmed the identity of the VZV strain that causes varicella on primary infection and later reactivates to cause zoster. Relatively consistent restriction enzyme digestion profiles for different VZV strains were observed, providing the first evidence that VZV has a highly conserved genome. Intrastrain variation in restriction enzyme fragment profiles among wild-type VZV isolates was observed (22,36,37). However, the most prominent differences were linked to variation in the number and composi...

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Genomic characterization of two predominant genotypes of herpes simplex virus type 1

Cited by 29 publications

References 36 publications

Replication of Herpes Simplex Virus Type 1 DNA is Inhibited in a Temperature-sensitive Mutant of BHK-21 Cells Lacking RCC1 (Regulator of Chromosome Condensation) and Virus DNA Remains Linear

Replication of Herpes Simplex Virus Type 1 DNA is Inhibited in a Temperature-sensitive Mutant of BHK-21 Cells Lacking RCC1 (Regulator of Chromosome Condensation) and Virus DNA Remains Linear

Evolution and Diversity in Human Herpes Simplex Virus Genomes

Global Identification of Three Major Genotypes of Varicella-Zoster Virus: Longitudinal Clustering and Strategies for Genotyping

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