Restriction fragment differences between the genomes of the Oka varicella vaccine virus and American wild-type varicella-zoster virus

Meningitis without Rash after Reactivation of Varicella Vaccine Strain in a 12-Year-Old Immunocompetent Boy

Acute neurologic complications from Varicella-Zoster-Virus reactivation occur in both immunocompromised and immunocompetent patients. In this report, we describe a case of a previously healthy immunocompetent boy who had received two doses of varicella vaccine at 1 and 4 years. At the age of 12 he developed acute aseptic meningitis caused by vaccine-type varicella-zoster-virus without concomitant skin eruptions. VZV-vaccine strain DNA was detected in the cerebrospinal fluid. The patient made a full recovery after receiving intravenous acyclovir therapy. This disease course documents another case of a VZV vaccine-associated meningitis without development of a rash, i.e., a form of VZV infection manifesting as "zoster sine herpete".

Varicella-Zoster Virus-Genetics, Molecular Evolution and Recombination

This chapter first details the structure, organization and coding content of the VZV genome to provide a foundation on which the molecular evolution of the virus can be projected. We subsequently describe the evolution of molecular profiling approaches from restriction fragment length polymorphisms to single nucleotide polymorphism profiling to modern day high-throughput sequencing approaches. We describe how the application of these methodologies led to our current model of VZV phylogeograpy including the number and structure of geographic clades and the role of recombination in reshaping these.

Nationwide distribution of varicella-zoster virus clades in China

Background

In 2010, a universal nomenclature for varicella-zoster virus (VZV) clades was established, which is very useful in the monitoring of viral evolution, recombination, spread and genetic diversity. Currently, information about VZV clades has been disclosed worldwide, however, there are limited data regarding the characterization of circulating VZV clades in China, even where varicella remains widely epidemic.

Methods

From 2008 to 2012, clinical samples with varicella or zoster were collected in General Hospital in eight provinces and analyzed by PCR, restriction endonuclease digestion and sequencing. The viral clades were determined by analysis of five single nucleotide polymorphisms (SNPs) within the 447-bp fragment of open reading frame (ORF) 22, and the restriction fragment length polymorphisms (RFLPs) of ORF 38 (PstI), ORF 54 (BglI) and ORF 62 (SmaI) were evaluated to understand genetic diversity of VZV and determinate varicella vaccine adverse event (VVAE).

Results

Seventy-seven varicella and 11 zoster samples were identified as being positive for VZV. The five SNPs profile showed that the majority of VZV strains belonged to clade 2, but clade 5 and clade 4 strains were also found in Guangdong. The RFLPs analysis of the DNA fragments of ORF 38, 54 and 62 showed that 85 of these samples were characterized as PstI + BglI + SamI-, and the remaining three VZV strains from varicella patients were characterized as PstI-BglI + SamI+ which is the genetic profile of VVAEs.

Conclusions

The study suggested that the predominant clade 2 VZVs had been continually circulating since at least the 1950s in China. Nearly all VZV strains except VVAEs possessed the genetic profile of PstI + BglI + Sam-. However, the other clades were also found to be co-circulating with clade 2, especially in the border regions. These results highlighted the need for the constant and broad use of virologic surveillance to provide an important genetic baseline for varicella control and vaccination programs in China.

VZV molecular epidemiology

The molecular epidemiology of varicella zoster virus (VZV) has led to an understanding of virus evolution, spread, and pathogenesis. The availability of over 20 full length genomes has confirmed the existence of at least five virus clades and generated estimates of VZV evolution, with evidence of recombination both past and ongoing. Genotyping by restriction enzyme analysis (REA) and single nucleotide polymorphisms (SNP) has proven that the virus causing varicella is identical to that which later reactivates as zoster in an individual. Moreover, these methods have shown that reinfection, which is mostly asymptomatic, may also occur and the second virus may establish latency and reactivate. VZV is the only human herpesvirus that is spread by the respiratory route. Genotyping methods, together with epidemiological data and modeling, have provided insights into global differences in the transmission patterns of this ubiquitous virus.

Divergence and genotyping of human alpha-herpesviruses: an overview

Herpesviruses are large DNA viruses that are highly disseminated among animals. Of the eight herpesviruses identified in humans, three are classified into the alpha-herpesvirus subfamily: herpes simplex virus types 1 (HSV-1) and 2 (HSV-2), which are typically associated with mucocutaneous lesions, and varicella-zoster virus (VZV), which is the cause of chicken pox and herpes zoster. All three viruses establish lifelong infections and may also induce more severe symptoms, such as neurological manifestations and fatal neonatal infections. Despite thorough investigation of the genetic variability among circulating strains of each virus in recent decades, little is known about possible associations between the genetic setups of the viruses and clinical manifestations in human hosts. This review focuses mainly on evolutionary studies of and genotyping strategies for these three human alpha-herpesviruses, emphasizing the ambiguities induced by a high frequency of circulating recombinant strains. It also aims to shed light on the challenges of establishing a uniform genotyping strategy for all three viruses.

A real-time PCR assay to identify and discriminate among wild-type and vaccine strains of varicella-zoster virus and herpes simplex virus in clinical specimens, and comparison with the clinical diagnoses

A real-time PCR assay was developed to identify varicella-zoster virus (VZV) and herpes simplex virus (HSV) DNA in clinical specimens from subjects with suspected herpes zoster (HZ; shingles). Three sets of primers and probes were used in separate PCR reactions to detect and discriminate among wild-type VZV (VZV-WT), Oka vaccine strain VZV (VZV-Oka), and HSV DNA, and the reaction for each virus DNA was multiplexed with primers and probe specific for the human beta-globin gene to assess specimen adequacy. Discrimination of all VZV-WT strains, including Japanese isolates and the Oka parent strain, from VZV-Oka was based upon a single nucleotide polymorphism at position 106262 in ORF 62, resulting in preferential amplification by the homologous primer pair. The assay was highly sensitive and specific for the target virus DNA, and no cross-reactions were detected with any other infectious agent. With the PCR assay as the gold standard, the sensitivity of virus culture was 53% for VZV and 77% for HSV. There was 92% agreement between the clinical diagnosis of HZ by the Clinical Evaluation Committee and the PCR assay results.

Complete-genome phylogenetic approach to varicella-zoster virus evolution: genetic divergence and evidence for recombination

Recent studies of varicella-zoster virus (VZV) DNA sequence variation, involving large numbers of globally distributed clinical isolates, suggest that this virus has diverged into at least three distinct genotypes designated European (E), Japanese (J), and mosaic (M). In the present study, we determined and analyzed the complete genomic sequences of two M VZV strains and compared them to the sequences of three E strains and two J strains retrieved from GenBank (including the Oka vaccine preparation, V-Oka). Except for a few polymorphic tandem repeat regions, the whole genome, representing approximately 125,000 nucleotides, is highly conserved, presenting a genetic similarity between the E and J genotypes of approximately 99.85%. These analyses revealed that VZV strains distinctly segregate into at least four genotypes (E, J, M1, and M2) in phylogenetic trees supported by high bootstrap values. Separate analyses of informative sites revealed that the tree topology was dependent on the region of the VZV genome used to determine the phylogeny; collectively, these results indicate the observed strain variation is likely to have resulted, at least in part, from interstrain recombination. Recombination analyses suggest that strains belonging to the M1 and M2 genotypes are mosaic recombinant strains that originated from ancestral isolates belonging to the E and J genotypes through recombination on multiple occasions. Furthermore, evidence of more recent recombination events between M1 and M2 strains is present in six segments of the VZV genome. As such, interstrain recombination in dually infected cells seems to figure prominently in the evolutionary history of VZV, a feature it has in common with other herpesviruses. In addition, we report here six novel genomic targets located in open reading frames 51 to 58 suitable for genotyping of clinical VZV isolates.

New mosaic subgenotype of varicella-zoster virus in the USA: VZV detection and genotyping by oligonucleotide-microarray

A rapid and sensitive microarray-based method was used to distinguish the three major circulating genotypes of varicella-zoster virus (VZV). The method analyzes five variable positions located in a 447-nucleotide variable region 1 of open reading frame 22 (ORF 22r1); these single nucleotide polymorphisms (SNP) display in stably occurring patterns specific to each of the VZV genotypes established in previously published studies. Pairs of short oligonucleotide probes (oligoprobes) with sequences corresponding to all of the observed SNP were used to detect specific sequences. Fluorescently labeled ssRNA samples for hybridization with a chip were prepared by in vitro T7 polymerase driven transcription of the amplicons of ORF 22r1, followed by chemical labeling with Cy5 into RNA sample. Ratios between fluorescent hybridization signals from each pair of oligoprobes were used to assess the sequence at each SNP. We evaluated six reference VZV strains and 130 VZV clinical specimens to validate the method. The microarray method accurately identified strains isolated in the US in 2001-2002, representing all major genotypes as determined using more extensive sequence analysis, correctly assigning strains to genotypes E (81.5%), J (3%) and M (15.5%). In addition, a new M variant (M3) was identified.

Global identification of three major genotypes of varicella-zoster virus: longitudinal clustering and strategies for genotyping

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.

Genetic variation in clinical varicella-zoster virus isolates collected in Ireland between 2002 and 2003

Analysis of genetic variation in 16 varicella-zoster virus (VZV) isolates selected at random and circulating in the Irish population between March 2002 and February 2003 was carried out. A 919 bp fragment of the glycoprotein E gene (open reading frame 68) encompassing codon 150, at which a non-synonymous mutation defines the escape mutant VZV-MSP, and including two other epitope regions e1 and c1, was sequenced. No new single nucleotide polymorphisms (SNPs) were detected, indicating stability of these epitopes in clinical isolates of VZV. However, when four informative polymorphic markers consisting of defined regions from genes 1, 21, 50, and 54 were sequenced 14 variable nucleotide positions were identified. Phylogenetic analysis showed the presence of three highly supported clades A, B, and C circulating in the Irish population. Approximately one third (6/16; 37.5%) of the Irish VZV isolates in this study belonged to genotype C, 4/16 (25%) to genotype A, and 4/16 (25%) to genotype B. A smaller number 2/16 (12.5%) belonged to genotype J1. This indicates remarkable heterogeneity in the Irish population given the small sample size. No evidence was found to suggest any of the 16 isolates was a recombinant. These findings have implications for the model of geographic isolation of VZV clades to certain regions as the circulating Irish VZV population appears to comprise approximately equal numbers of each of the main genotypes. This data is inconsistent with a model of strict geographical separation of VZV genotypes and suggests that VZV diversity is more pronounced in certain areas than had been thought previously.

Phylogenetic analysis of varicella-zoster virus: evidence of intercontinental spread of genotypes and recombination

A heteroduplex mobility assay was used to identify variants of varicella-zoster virus circulating in the United Kingdom and elsewhere. Within the United Kingdom, 58 segregating sites were found out of the 23,266 examined (0.25%), and nucleotide diversity was estimated to be 0.00063. These are an order of magnitude smaller than comparable estimates from herpes simplex virus type 1. Sixteen substitutions were nonsynonymous, the majority of which were clustered within surface-expressed proteins. Extensive genetic correlation between widely spaced sites indicated that recombination has been rare. Phylogenetic analysis of varicella-zoster viruses from four continents distinguished at least three major genetic clades. Most geographical regions contained only one of these three strains, apart from the United Kingdom and Brazil, where two or more strains were found. There was minimal genetic differentiation (one or fewer substitutions in 1,895 bases surveyed) between the samples collected from Africa (Guinea Bissau, Zambia) and the Indian subcontinent (Bangladesh, South India), suggesting recent rapid spread and/or low mutation rates. The geographic pattern of strain distribution would favor a major influence of the former. The genetic uniformity of most virus populations makes recombination difficult to detect. However, at least one probable recombinant between two of the major strains was found among the samples originating from Brazil, where mixtures of genotypes co-occur.

Methods for subtyping and molecular comparison of human viral genomes

The development over the past two decades of molecular methods for manipulation of RNA and DNA has afforded molecular virologists the ability to study viral genomes in detail that has heretofore not been possible. There are many molecular techniques now available for typing and subtyping of viruses. The available methods include restriction fragment length polymorphism analysis, Southern blot analysis, oligonucleotide fingerprint analysis, reverse hybridization, DNA enzyme immunoassay, RNase protection analysis, single-strand conformation polymorphism analysis, heteroduplex mobility assay, nucleotide sequencing, and genome segment length polymorphism analysis. The methods have certain advantages and disadvantages which should be considered in their application to specific viruses or for specific purposes. These techniques are likely to become more widely used in the future for epidemiologic studies and for investigations into the pathophysiology of virus infections.

Molecular epidemiology of varicella-zoster virus in East London, England, between 1971 and 1995

The molecular epidemiology of varicella-zoster virus in London, England, between 1971 and 1995 was examined by using two informative polymorphic markers, variable repeat region R5 and a BglI restriction site in gene 54. Viruses from 105 cases of chickenpox and 144 of zoster were typed. Two alleles of R5, A and B, were found at prevalences of 89 and 6%, respectively. No difference in allele frequency between the zoster and chickenpox cases was found, and no change in the frequencies of these alleles was observed to occur over time. By contrast, a BglI restriction site (BglI+) was found with increasing frequency over time among cases of varicella (P < 0.005) and, to a lesser extent, cases of zoster. The BglI+ polymorphism was strongly associated (P < 0.0005) with zoster in subjects who had immigrated to the United Kingdom from countries with low adult immunity to varicella (LAIV). Sixty-three percent of the subjects with zoster who had emigrated from countries with LAIV carried the BglI+ virus, in contrast to 10% of adults who had grown up in countries with high adult immunity to varicella. The significance of these data, in view of the changing epidemiology of chickenpox, is discussed.

Application of long PCR method of identification of variations in nucleotide sequences among varicella-zoster virus isolates

Restriction fragment length polymorphism (RFLP) analysis of whole viral DNA of varicella-zoster virus (VZV) requires the time-consuming and laborious preparation of a large amount of purified viral DNA. RFLP analysis of small DNA fragments amplified by PCR was developed as an alternative method. However, its use has been limited because of the small number of variations in VZV. To overcome these drawbacks and to identify variations in VZV, we developed an RFLP analysis method combined with the long PCR method which has recently been developed for the amplification of DNA fragments between 5 and 35 kb in length. We amplified three DNA regions ranging from 6.8 to 11.4 kb and demonstrated that RFLP analyses of these regions allowed for the classification of 40 VZV isolates in Japan into 17 groups. One-fourth of the isolates contained a nucleotide difference of C versus T, which abolished the StyI site at position 76530; this alteration was linked to the reported PstI site polymorphism at position 69349 (nucleotide positions are based on those of strain Dumas). Nucleotide sequence variation in the examined regions among VZV isolates in Japan was estimated at roughly less than 0.05%, confirming the previously proposed idea that VZV is genetically stable and not highly diversified. Our method will be useful for studies of the molecular epidemiology of VZV.

Typing of varicella zoster virus by amplification of DNA polymorphisms

The polymerase chain reaction was used to amplify five variable regions of varicella zoster virus DNA from 20 samples of vesicle fluid. Two of the regions, R1 and R5, were found to be polymorphic, with the former having three alleles (A, B and C) and the latter, two (A and B). The R1 and R5 polymorphisms were stable up to passage five in tissue culture. The sensitivity of the PCR (down to six copies) enabled detection of virus from vesicle fluid dried on glass slides and overall the method was five times more sensitive than conventional tissue culture. The method described is simple, sensitive and informative and provides a means by which questions about the epidemiology and clinical biology of VZV infection may begin to be addressed.

Infection of human fetal dorsal root neurons with wild type varicella virus and the Oka strain varicella vaccine

The relative ability of a varicella-zoster virus (VZV) clinical isolate and a live attenuated VZV vaccine strain (Oka) to infect human neurons was determined in vitro. VZV infection of neurons prepared in culture from dorsal root ganglia of fetuses was assessed using an infectious center assay. Cultures were infected with 50-5,000 pfu of either VZV and assayed at either 24 or 48 hours post-VZV infection. Cultures infected with the clinical VZV isolate had seven-fold more infected neurons than cultures infected with the vaccine strain VZV.

Restriction fragment length polymorphism of polymerase chain reaction products from vaccine and wild-type varicella-zoster virus isolates

The nucleotide changes that result in two restriction endonuclease polymorphisms that differentiate wild-type varicella-zoster virus (VZV) from the vaccine strain were determined. Oligonucleotide primers that flank these sites were used to amplify the intervening sequences with the polymerase chain reaction to identify VZV DNA in clinical isolates. Restriction enzyme digestion of the amplification products distinguished vaccine and wild-type genomes from one another. This study confirms the feasibility of amplifying VZV sequences so that they may be detected in clinical specimens and provides a molecular epidemiological approach to strain identification of VZV in vesicular lesions.