Variable Restriction Endonuclease Sites of Herpes Simplex Virus Type 1 Isolates from Encephalitic, Facial and Genital Lesions and Ganglia

Chaney, S. M. J.; Warren, K. G.; Subak‐Sharpe, J. H.

doi:10.1099/0022-1317-64-12-2717

Cited by 19 publications

(9 citation statements)

References 52 publications

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“…Since gains or losses of cleavage sites are more efficient markers than fragment length (Roizman, 1979;Chaney et al, 1983b;Sakaoka et al, 1985Sakaoka et al, , 1986, they were chosen for the comparative analysis of isolates. In addition, the cleavage sites have been shown not to vary in epidemiologically related isolates (Lonsdale et al, 1979(Lonsdale et al, , 1980Roizman & Tognon, 1983;Maitland et al, 1983;Sakaoka et al, 1984Sakaoka et al, , 1986b or in randomly cloned stocks of a single strain (Lonsdale et al, 1980;Davison & Wilkie, 1981;Roizman & Tognon, 1983).…”

Section: Discussionmentioning

confidence: 99%

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Genomic Comparison of Herpes Simplex Virus Type 1 Isolates from Japan, Sweden and Kenya

Sakaoka

Saitô

Sekine

et al. 1987

Journal of General Virology

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SUMMARYOne-hundred and seventy-two epidemiologically unrelated herpes simplex virus type 1 (HSV-I) strains isolated in Japan (104 strains) and Sweden (68 strains) were compared by analysis of their genome structures using four restriction endonucleases, BamHI, KpnI, SalI and HindlII. In addition, 32 Kenyan HSV-1 isolates previously compared to Japanese isolates were included for further comparison with the Swedish isolates. Remarkable and statistically significant differences were found between the HSV-1 isolates from the three countries. One-hundred and thirty cleavage sites were examined, and it was shown that isolates from two of the three countries were statistically distinguishable at 27 of these loci. Pairwise comparison between isolates from Japan and Sweden, Kenya and Sweden, and Japan and Kenya revealed variation in 18, 16 and 23 sites, respectively. By considering gains and losses of 19 sites, the total of 204 strains could be classified into 92 distinct cleavage patterns. Isolates from the three countries could be distinguished from each other by the pattern, except for one Swedish and two Kenyan isolates which shared a pattern. Twenty-one fragments that were present or absent only in individual isolates from one or other of the three countries could be detected. These results show that HSV-1 strains from geographically separate countries or anthropologically different races have distinct distributions of endonuclease recognition sites.

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Section: Discussionmentioning

confidence: 99%

“…Using a similar approach, Chaney et al (1983b) reported that HSV-1 strains from five different geographical locations could be significantly distinguished by the frequencies of RE sites. However, the number of isolates in this comparison was too small for definite conclusions to be drawn.…”

Section: Discussionmentioning

confidence: 99%

Genomic Comparison of Herpes Simplex Virus Type 1 Isolates from Japan, Sweden and Kenya

Sakaoka

Saitô

Sekine

et al. 1987

Journal of General Virology

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“…In order to compare the correlation coefficient (r) of every pair of RE sites. Pearson's product moment correlation coefficient was calculated with a 2 x 2 contingency table by using the same formula as that employed by Chaney et al (1983b). Nucleotide diversity.…”

Section: H Sakaoka and Othersmentioning

confidence: 99%

Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus

Sakaoka¹,

Kurita²,

Iida

et al. 1994

Journal of General Virology

159

110

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Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients (] r ] > 0.42; P < 0.01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolutionarily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (~), was estimated for HSV-1 genomes within (~x or ~y) and between (~xY) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0-0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (~xY) was highest between isolates from the three Asian countries and Kenya (0.0075 to 0.0081) and lowest among those from the three Asian countries (0.0032 to 0.0040). The mutation rate (k) for HSV-1 was estimated to be 3-5 x 10 S/site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.

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“…HSV-1 strains differ slightly in their DNA sequences, which are used as molecular markers of genomic polymorphism. The method generally used to differentiate HSV-1 strains is restriction fragment length polymorphism (RFLP) analysis of total HSV-1 DNA (4,7,26,36) or RFLP-PCR-based analysis (23,49,53). Determination of the nucleotide sequences of PCR-amplified DNA fragments encompassing reiterated regions (33) is another approach currently used to characterize the genomes of HSV-1 strains.…”

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Utilization of Microsatellite Polymorphism for Differentiating Herpes Simplex Virus Type 1 Strains

et al. 2009

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The herpes simplex virus type 1 (HSV-1) genome is a linear double-stranded DNA of 152 kpb. It is divided into long and short regions of unique sequences termed U L and U S , respectively, and these are flanked by regions of inverted internal and terminal repeats. Microsatellites are short tandem repeats of 1-to 6-nucleotide motifs; they are often highly variable and polymorphic within the genome, which raises the question of whether they may be used as molecular markers for the precise differentiation of HSV-1 strains. In this study, 79 different microsatellites (mono-, di-, and trinucleotide repeats) in the HSV-1 complete genome were identified by in silico analysis. Among those microsatellites, 45 were found to be distributed in intergenic or noncoding inverted repeat regions, while 34 were in open reading frames. Length polymorphism analysis of the PCR products was used to investigate a set of 12 distinct HSV-1 strains and allowed the identification of 23 polymorphic and 6 monomorphic microsatellites, including two polymorphic trinucleotide repeats (CGT and GGA) within the UL46 and US4 genes, respectively. A multiplex PCR method that amplified 10 polymorphic microsatellites was then developed for the rapid and accurate genetic characterization of HSV-1 strains. Each HSV-1 strain was characterized by its own microsatellite haplotype, which proved to be stable over time in cell culture. This relevant innovative tool was successfully applied both to confirm the close relationship between sequential HSV-1 isolates collected from patients with multiple recurrent infections and to investigate putative nosocomial infections.Herpes simplex virus type 1 (HSV-1) is a member of the subfamily Alphaherpesvirinae. The seroprevalence of HSV-1 infection increases progressively from childhood and is inversely proportional to an individual's socioeconomic background (35). Primary HSV-1 infections in children are typically asymptomatic but can give rise to herpetic gingivostomatitis. After primary infection of the orofacial region, HSV-1 is transported in a retrograde manner to the nuclei of the trigeminal sensory neurons through their axons, which innervate the infected area. HSV-1 then establishes a life-long latent infection in the nuclei of sensory neurons, where the genome lies in a nonreplicating chromatin-associated state. Recurrent HSV-1 lesions occur following the reactivation of latent HSV-1, axonal transport of the reactivated virus, and HSV-1 replication on the skin and mucous membranes. Recurrent infections typically give rise to herpes labialis or may be responsible for more severe clinical manifestations, including keratitis, meningoencephalitis, bronchopneumonitis (22), chronic or disseminated infections in immunosuppressed patients, or eczema herpeticum. Eczema herpeticum, or Kaposi-Juliusberg disease, is an uncommon herpes simplex virus superinfection that occurs in patients with atopic dermatitis. Additionally, HSV-1 accounts for about half of the new cases of genital herpes in developed countries (14).The HS...

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Variable Restriction Endonuclease Sites of Herpes Simplex Virus Type 1 Isolates from Encephalitic, Facial and Genital Lesions and Ganglia

Cited by 19 publications

References 52 publications

Genomic Comparison of Herpes Simplex Virus Type 1 Isolates from Japan, Sweden and Kenya

Genomic Comparison of Herpes Simplex Virus Type 1 Isolates from Japan, Sweden and Kenya

Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus

Utilization of Microsatellite Polymorphism for Differentiating Herpes Simplex Virus Type 1 Strains

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