Strain variation of R5 direct repeats in the right-hand portion of the long unique segment of varicella-zoster virus DNA

Hondo, Ryo; Yogo, Yoshiaki

doi:10.1128/jvi.62.8.2916-2921.1988

Cited by 39 publications

(8 citation statements)

References 19 publications

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“…Our findings for the R5 and PS variable regions were similar to those presented in previous reports (4,5). Analysis of the PS variable region seemed especially useful for identifying the vaccine strain, which belonged to the minor group, PS negative.…”

Section: Discussionsupporting

confidence: 93%

“…The distribution of the R5 copy number (Fig. 2C) was generally in agreement with that given in a previous report (4). Twenty-three of 30 strains were identical to Oka-Va in their R5 copy numbers; Oka-Va had two copies (Fig.…”

Section: R2 Variable Regionsupporting

confidence: 90%

“…Five repeat elements, R1 to R5, have been mapped on the VZV genome, and the copy numbers of these repeat elements vary among strains (2,4). Use of R1 and R3 is thought to be inappropriate for discriminating VZV strains by PCR because of their instabilities (8,10).…”

mentioning

confidence: 99%

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Identification of varicella-zoster virus strains by PCR analysis of three repeat elements and a PstI-site-less region

et al. 1995

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We established a method of identifying varicella-zoster virus (VZV) strains, especially those of the Oka vaccine, in patients with clinical VZV infections. The DNAs of 30 clinically isolated strains and 4 laboratory strains including the Oka vaccine strain and its parent VZV strain, were analyzed by PCR with four sets of primers for the four variable regions, R2, R4, R5, and a region without a PstI site (PS). R4 was unstable in four laboratory VZV strains and was excluded from the study. The other regions were stable in several passages in cell culture. The number of copies in R2 and R5 were distributed from 2 to 13 and from 1 to 3, respectively, in the strains analyzed. The vaccine strain had seven copies in R2 and two copies in R5, and it was PS negative. Among 30 clinical isolates, 3, 23, and 11 strains had the same characteristics as the vaccine strain in R2, R5, and PS, respectively. Therefore, by this method, 97.2% of the isolates were distinguished from the Oka vaccine strain. This strategy will be useful in diagnosing VZV infections induced by the vaccine strain.

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Section: Discussionsupporting

confidence: 93%

Section: R2 Variable Regionsupporting

confidence: 90%

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Identification of varicella-zoster virus strains by PCR analysis of three repeat elements and a PstI-site-less region

et al. 1995

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“…The tandem repeat regions were difficult to sequence as they were often longer than the read length. Even when tandem repeats were short enough to be covered within a single read, they were observed to vary in length among strains, and sometimes within strains, as reported previously for EHV-1 (Nugent et al, 2006) and other alphaherpesviruses (Depledge et al, 2014;Hondo & Yogo, 1988). They also tended to be G+C-rich and thus seemed to be under-represented in the sequence libraries, making it inadvisable to estimate their lengths from coverage density data.…”

Section: Dna Sequencing Of Ehv-1 Strainsmentioning

confidence: 58%

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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“…The VZV genome has an additional R5 direct repeat sequence located within the 1400-bp noncoding region between ORFs 60 and 61 (Davison and Scott, 1986;Hondo and Yogo, 1988). The VZV R5 consists of an 88-bp element and an adjacent 24-bp element which together constitute a repeat unit whose copy number varies from one to three in various VZV strains.…”

Section: Repetitive Dnamentioning

confidence: 99%

The DNA Sequence of the Simian Varicella Virus Genome

et al. 2001

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In nonhuman primates, simian varicella virus (SVV) causes a natural disease which is clinically similar to human varicella-zoster virus (VZV) infections. The SVV and VZV genomes are similar in size and structure and share extensive DNA homology. This report presents the complete DNA sequence of the SVV genome. SVV DNA is 124,138 bp in size, 746 bp shorter than VZV DNA, and 40.4% G + C. The viral genome includes a 104,104-bp unique long component bracketed by 8-bp inverted repeat sequences and a short component composed of a 4904-bp unique short region bracketed by 7557-bp inverted repeat sequences. A total of 69 distinct SVV open reading frames (ORFs) were identified, including three that are duplicated within the inverted repeats of the short component. Each of the SVV ORFs shares extensive homology to a corresponding VZV gene. The only major difference between SVV and VZV DNA occurs at the leftward terminus. SVV lacks a VZV ORF 2 homolog. In addition, SVV encodes an 882-bp ORF A that is absent in VZV, but has homology to the SVV and VZV ORF 4. The results of this study confirm the relatedness of SVV and VZV and provide further support for simian varicella as a model to investigate VZV pathogenesis and latency.

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Strain variation of R5 direct repeats in the right-hand portion of the long unique segment of varicella-zoster virus DNA

Cited by 39 publications

References 19 publications

Identification of varicella-zoster virus strains by PCR analysis of three repeat elements and a PstI-site-less region

Identification of varicella-zoster virus strains by PCR analysis of three repeat elements and a PstI-site-less region

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

The DNA Sequence of the Simian Varicella Virus Genome

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