Genome differences among varicella-zoster virus isolates

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.

Prolonged varicella-zoster virus reinfection in an adult after unrelated cord blood transplantation

Most varicella-zoster virus (VZV) infections after cord blood transplantation (CBT) present as localized herpes zoster. Here, we report a case of VZV reinfection in an adult patient after CBT that appeared clinically to be varicella. A 50-year-old Japanese man underwent CBT for the management of acute lymphoblastic leukemia. Seventeen months later, he developed a small number of vesicles with umbilicated centers. A skin biopsy showed an intraepidermal blister containing degenerated balloon cells. Subsequently, the skin eruption developed over his entire body. The patient was treated with intravenous acyclovir for 5 days, followed by oral valacyclovir for 9 days. It took more than 3 weeks for most of the skin lesions to scab. Serum levels of anti-VZV IgG on days 3 and 33 after the onset of the skin eruption were negative and 260 mIU/ml, respectively. Serum anti-VZV IgM on days 3 and 33 was not detected. Our patient was diagnosed with VZV reinfection.

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.

Varicella zoster virus infection: clinical features, molecular pathogenesis of disease, and latency

Varicella zoster virus (VZV) is an exclusively human neurotropic alphaherpesvirus. Primary infection causes varicella (chickenpox), after which virus becomes latent in cranial nerve ganglia, dorsal root ganglia, and autonomic ganglia along the entire neuraxis. Years later, in association with a decline in cell-mediated immunity in elderly and immunocompromised individuals, VZV reactivates and causes a wide range of neurologic disease. This article discusses the clinical manifestations, treatment, and prevention of VZV infection and reactivation; pathogenesis of VZV infection; and current research focusing on VZV latency, reactivation, and animal models.

Vaccine Oka variants and sequence variability in vaccine-related skin lesions

As with most live attenuated viral vaccines, varicella vaccine comprises a mixture of variant strains. Knowledge about the pathogenic potential of individual strains in the varicella vaccine is limited. Vaccination against chickenpox causes a usually modified varicella-like rash in a small percentage of healthy children, and vaccine virus reactivates on rare occasions to cause herpes zoster (HZ). In several published studies, our respective laboratories have analyzed genomic variation among specimens from cases of postvaccination rash and HZ in vaccine recipients, focusing on polymorphisms between vaccine Oka strains and the parental Oka strain. In most respects, these studies were in close agreement, identifying the set of wild-type markers among vaccine adverse event isolates, each occurring at similar frequencies. The same 3 universally present vaccine markers, at positions 106262, 107252, and 108111, were also identified by both laboratories. One notable difference has been the observation of mostly clonal vaccine virus among isolates examined by one laboratory and mostly mixed viruses in isolates examined by the other. In addition to reviewing and comparing our combined observations, we propose possible explanations for our contrasting findings and propose future studies to reconcile them.

Molecular studies of Varicella zoster virus

VZV is a highly cell-associated member of the Herpesviridae family and one of the eight herpesviruses to infect humans. The virus is ubiquitous in most populations worldwide, primary infection with which causes varicella, more commonly known as chickenpox. Characteristic of members of the alphaherpesvirus sub-family, VZV is neurotropic and establishes latency in sensory neurones. Reactivation from latency, usually during periods of impaired cellular immunity, causes herpes zoster (shingles). Despite being one of the most genetically stable human herpesviruses, nucleotide alterations in the virus genome have been used to classify VZV strains from different geographical regions into distinct clades. Such studies have also provided evidence that, despite pre-existing immunity to VZV, subclinical reinfection and reactivation of reinfecting strains to cause zoster is also occurring. During both primary infection and reactivation, VZV infects several PBMC and skin cell lineages. Difficulties in studying the pathogenesis of VZV because of its high cell association and narrow host range have been overcome through the development of the VZV severe combined immunodeficient mouse model carrying human tissue implants. This model has provided a valuable tool for studying the importance of individual viral proteins during both the complex intracellular replication and assembly of new virions and for understanding the underlying mechanism of attenuation of the live varicella vaccine. In addition, a rat model has been developed and successfully used to uncover which viral proteins are important for both the establishment and maintenance of latent VZV infection.

Varicella seroprevalence and molecular epidemiology of varicella-zoster virus in Argentina, 2002

There is limited data on immunity against varicella-zoster virus (VZV) in adults in different parts of Argentina, and it is not known which VZV strains are circulating in Argentina. The objectives of this study were as follows: (i) to evaluate seroprevalence of varicella among adults, assessing the accuracy of clinical history and determining the sociodemographic factors associated with seropositivity; and (ii) to determine the VZV strains circulating in Argentina. A cross-sectional serological survey enrolling 2,807 women aged 15 to 49 years attending public health-care settings in four cities in Argentina (i.e., Buenos Aires, Salta, Mendoza, and Rosario) and one rural area was conducted from August to November 2002. Specimens for identification of VZV strains were obtained from vesicular lesions from 13 pediatric patients with varicella from different areas of the country. PCR amplification was used for genotyping. The overall seroprevalence of varicella antibodies was 98.5% (95% confidence interval, 98.0 to 98.9), ranging from 97.2% in central Buenos Aires to 99.3% in southern Buenos Aires and Salta. Varicella seroprevalence increased with age. Crowding and length of residence in the same place were associated with seropositivity. The positive predictive value of varicella history for immunity to varicella was 99.4%; however, the negative predictive value was 2.5%. The European genotype was identified in all viral specimens. In Argentina, seroprevalence in women more than 15 years old was high regardless of the area of residence. Negative or uncertain varicella history was not a good predictor of immunity. VZV genotype was stable in all areas of the country.

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 of varicella-zoster virus: evidence for geographical separation of strains

Heteroduplex mobility assay was used to identify variants of varicella-zoster virus (VZV) circulating in the United Kingdom and elsewhere. Forty variable positions were identified. Sixteen substitutions were non-synonymous, resulting in an amino acid change, the majority of which were clustered within surface expressed proteins. Phylogenetic analysis distinguished at least three major clades (strains A, B, C) supported by significant bootstrap values. Apart from the United Kingdom and Brazil where all three strains were found, genotypes appeared to be closely associated with the geographical region in which they were sampled. Allelic co-segregation of widely spaced single nucleotide polymorphisms (SNPs) confirmed the genetic stability of the VZV. Recombination rates were difficult to calculate because of the low intra genotypic variation. However, one haplotype originating from Brazil is most parsimoniously explained as a recombinant between A and C strains, which co-occur in the region. Two further UK strains appeared to be recombinants between groups B and C.

Analysis of numbers of repeated units in R2 region among varicella-zoster virus strains

BACKGROUND

A variable region, R2, on the varicella-zoster virus (VZV) genome contains a repeated 42-bp unit.

OBJECTIVE

The purpose of this study is the derivation of significance from tandem reiteration structure in the R2 region.

METHODS

Fifty-two specimens were collected from 52 patients with herpes zoster in Osaka and Tokyo, Japan. After treatment of the specimens to release viral DNA, the samples were amplified directly by polymerase chain reaction. In addition, 14 samples were collected from 7 of these zoster patients after valaciclovir or aciclovir therapy.

RESULTS

Analyses of the 52 specimens revealed that the number of repeats ranged from 4 to 13. Interestingly, the numbers of repeats among various VZV strains showed a normal distribution pattern, so that 6-9 repeats were found to be predominant in both Osaka (85%) and Tokyo (72%). The pre- and post-treatment strains taken from the same individuals showed the same numbers of repeats (7-9 in 6 cases and 11 in one).

CONCLUSION

Our results suggest that the 6-9 repetitions of the 42-bp unit, with presumed stability, may offer these virus strains an advantage in virulence to human skin.

New variant of varicella-zoster virus

In 1998, a varicella-zoster virus glycoprotein E (gE) mutant virus (VZV-MSP) was isolated from a child with chickenpox. VZV-MSP, representing a second VZV serotype, was considered a rarity. We isolated another VZV-MSP-like virus from an elderly man with herpes zoster. These gE mutant viruses may have arisen through independent mutation or may represent a distinct VZV subpopulation that emerged more than 50 years ago.

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.

Nucleotide sequence analysis of varicella-zoster virus glycoprotein E epitope coding regions

Varicella-zoster virus (VZV) glycoprotein E [gE] contains 623 amino acid residues. Fifty percent of the gE gene, codons 39 to 344 that encompasses two epitope coding regions e1 and c1, was sequenced and analyzed for variation among the 30 VZV isolates. A total of eleven isolates showed variance when compared with Dumas VZV strain sequence through base substitutions, with two isolates showing an amino acid change of tryptophan to arginine outside the coding regions of the epitopes e1 and c1 that are recognized by monoclonal antibodies 4F9 and c1, respectively. The results suggest that these epitopes were stable in the various VZV isolates. Thus, VZV glycoproteins with conserved epitopes are suitable candidates for both primary and booster vaccines.

Improved identification and differentiation of varicella-zoster virus (VZV) wild-type strains and an attenuated varicella vaccine strain using a VZV open reading frame 62-based PCR

A new method was developed to identify and differentiate varicella-zoster virus (VZV) wild-type strains from the attenuated varicella Oka vaccine strain. The PCR technique was used to amplify a VZV open reading frame (ORF) 62 region. A single specific amplicon of 268 bp was obtained from 71 VZV clinical isolates and several laboratory strains. Subsequent digestion of the VZV ORF 62 amplicons with SmaI enabled accurate strain differentiation (three SmaI sites were present in amplicons of vaccine strain VZV, compared with two enzyme cleavage sites for all other VZV strains tested). This method accurately differentiated the Oka vaccine strain from wild-type VZV strains circulating in countries representing all six populated continents. Moreover, the assay more reliably distinguished wild-type Japanese strains from the vaccine strain than did previously described methods.

Expression of neutralizing recombinant human antibodies against Varicella Zoster virus for use as a potential prophylactic

Chickenpox is a highly infectious disease that can be life-threatening to certain groups such as the newborn of nonimmune mothers and immunocompromised patients. At present, prophylactic treatment of individuals at risk involves the use of a polyclonal antibody preparation derived from the pooled sera of hyperimmune donors. While this product is effective, there are problems associated with maintaining supply, which depends on the availability of donors, and the variation of potency between batches. An effective human monoclonal preparation would be of value by providing a well-characterized and standardized preparation available on demand. In this study recombinant human anti-varicella zoster virus (VZV) monoclonals were generated from the mRNA of unstable anti-VZV secreting heterohybridoma cell lines, and characterized according to their molecular weight, isoelectric point, glycosylation, binding to C1q, and efficacy at neutralizing VZV in vitro. In one antibody (AEVZ 5.3) the VH region was grafted from the IgG1 parent antibody onto an IgG3 backbone to determine the effect of isotype on neutralization in vitro. Antibodies were expressed from NSO cells at concentrations of 3-24 microg/mL and contained the expected heavy and light chain fragments and N-linked glycan structures. Both AEVZ 5.1 and AVEZ 4 antibodies were IgG1 and recognized the viral coat protein glycoprotein E; both showed complement-independent and complement-enhanced neutralization. Changing the isotype of AEVZ 5.1 from IgG1 to IgG3 (AEVZ 5.3) further enhanced VZV neutralization in the presence of complement, but reduced its neutralization capacity in the absence of complement. Complement enhancement was consistent with our findings that the IgG3 form could bind more molecules of C1q. The results demonstrate the successful use of recombinant methods to generate stable, functional monoclonal antibodies. Modifications of the original antibodies were made with the aim of improving functionality. The resulting cell lines could be used for large-scale production of well-characterized antibodies for therapeutic use.

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.

Live attenuated varicella vaccine

Varicella-zoster virus (VZV) is a ubiquitous human pathogen that causes varicella, commonly called chicken pox; establishes latency; and reactivates as herpes zoster, referred to as shingles. A live attenuated varicella vaccine, derived from the Oka strain of VZV has clinical efficacy for the prevention of varicella. The vaccine induces persistent immunity to VZV in healthy children and adults. Immunization against VZV also has the potential to lower the risk of reactivation of latent virus. The varicella vaccine may eventually reduce or eliminate herpes zoster, which is a serious problem for elderly and immunocompromised individuals.

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.

Comparative analysis of the restriction endonuclease profiles of the Dumas and Singapore strains of varicella-zoster virus

The incidence of varicella in Singapore has been increasing since 1984. In 1991, 17,930 cases were reported in a population of about 3 million. A serological survey completed in 1990 demonstrated that only 43% of the cohort had antibodies to varicella-zoster virus (VZV), indicating inadequate herd immunity. To exclude novel VZV strains, representative VZV isolates from 9 chicken pox and 4 zoster patients were characterised by restriction endonuclease analysis. DNAs were extracted from viral isolates propagated in MRC5 human embryo lung cells and were digested separately with BglII, EcoRI, PstI, SalI, and XbaI enzymes. The cleavage profiles of these VZV strains derived from both chicken pox and zoster lesions revealed no distinct differences. This observation implies that the current upsurge of chicken pox most likely stems from closely related VZV genotypes infecting a susceptible population with insufficient herd immunity. Comparison of the restriction fragments of the Singapore and the Dumas strains revealed polymorphisms of the SalI-D, SalI-E, and XbaI-I fragment lengths, which correlated with variable regions I, II, and III of the VZV genome, thereby representing geographically distinct genotypic variants of VZV.

Detection of varicella-zoster virus DNA by polymerase chain reaction in the cerebrospinal fluid of patients suffering from neurological complications associated with chicken pox or herpes zoster

The polymerase chain reaction (PCR) was used to detect varicella-zoster virus (VZV) DNA in the cerebrospinal fluid of patients with VZV infection associated with neurological symptoms. Positive results were obtained in three of five children with post-chicken pox cerebellitis and in seven of seven herpes zoster patients with neurological symptoms. The PCR thus provides a useful tool for the early diagnosis of VZV-associated neurological disease.

Comparison of biotinylated DNA and RNA probes for rapid detection of varicella-zoster virus genome by in situ hybridization

We describe a general method for the production of nonisotopic DNA and RNA probes for the detection of the varicella-zoster virus (VZV) genome by in situ hybridization. VZV DNA was extracted from purified viral nucleocapsids, cleaved with restriction enzyme (RE) BamHI, and cloned into plasmid pBR322 by the standard vector insert procedure. We cloned over 85% of the VZV genome and obtained 18 recombinants. Plasmids containing the B, F, G, H, and J fragments of VZV DNA were labeled by the nick translation method with biotin-11-dUTP as the dTTP analog. Additionally, the B fragment was cleaved with RE AvaI, subcloned into the plasmid pGEM-4 transcription vector, and subsequently linearized with REs PstI and EcoRI. RNA was transcribed with T7 or SP6 polymerase, with a substitution of allylamine-UTP as the UTP analog, and labeled with epsilon-caproylamidobiotin-N-hydroxysuccinimide ester. The DNA and RNA probes were used under full-stringency conditions for in situ hybridization with alkaline phosphatase as the detector and 5-bromo-4-chloro-3-indolyl phosphate-Nitro Blue Tetrazolium as the substrate. When tested under comparable conditions, the RNA probe was slightly more sensitive than was the DNA probe: both probes showed homology only with VZV-infected cells and clinical tissues and not with the other herpesviruses. Probes prepared from variable regions of the genome (fragments F and J) performed as well as did those from conserved regions (fragments B. G. and H). Biotinylated probes have distinct advantages over isotopic probes and retain their full potency for more than 2 years when stored properly.

Differentiation of oka varicella vaccine strain from wild varicella-zoster virus strains isolated from vaccinees and household contact

The Oka varicella vaccine strain can be differentiated from wild-type strains by its unique restriction endonuclease fingerprinting (REFP: HpaI-K and EcoRI-P) pattern of the gpV-coding region of the varicella-zoster virus (VZV) genome. VZV-DNAs from patients with complicated clinical courses related to vaccination were examined to determine whether they were vaccine-derived or wild-type. A virus was isolated from a one year-old boy with acute lymphocytic leukemia (ALL) who developed typical varicella 28 days after vaccination (case A). Another virus was isolated from a four-year-old boy without clinical symptoms following household contact with varicella patients at the age of two months, and he developed zoster 14 months after vaccination (case B). Also, two strains (OK1 and OK2) were isolated from household contacts (mother and sister) with a vaccine with ALL in Oklahoma who developed varicella 18 days after vaccination (case C). In case C, BgII-REFP did not determine conclusively whether the two strains (OK1 and OK2) were vaccine-derived or wild-type because the patterns obtained were different from both the Oka varicella vaccine strain and American wild-type strains [Gelb et al., Journal of Infectious Diseases, 155:633-640, 1987]. All VZV strains examined in the present study were identified as wild-type by our method using HpaI-K and EcoRI-P fragments as marker fragments. Thus it is becoming evident that REFP using HpaI and EcoRI endonucleases is a convenient and reliable means of distinguishing between the Oka vaccine virus strain and wild-type viruses isolated from individuals developing vesicular rashes shortly and long after varicella vaccination.

Organization and function of the ORIs sequence in the genome of EHV-1 DI particles

Equine herpesvirus type 1 (EHV-1) cultures enriched for defective interfering particles (DIP) mediate oncogenic transformation and persistent infection in permissive hamster embryo fibroblasts. We have recently demonstrated that an origin of replication (ORI) is located within the central portion (map units 0.828 and 0.948) of the inverted repeat sequence (IRs) of the short region of the standard EHV-1 genome. In the generation of the genome of EHV-1 DI particles, sequences from this internal portion of the IRs recombine with sequences at the long region terminus at nucleotides 3244-3251. In this paper we report that the ORIs sequence is precisely conserved in the DIP genome, that direct repeat sequences near the ORIs sequence which may enhance DNA replication are mutated in the DIP genome, and that the ORI sequence of DIP DNA is functional in DNA replication assays.

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

The Oka vaccine strains of varicella-zoster virus (VZV) have a significantly different BgII DNA restriction pattern from that of American wild-type isolates of VZV. This difference consists primarily of an additional BgII site, which lies within the BamHI "D" fragment. In conjunction with a study of the efficacy of an experimental Merck/Oka VZV vaccine, the area of the genome from which the most marked restriction pattern alteration arises was studied more closely to determine if there are other significant differences between the Oka strains and American wild-type strains. BamHI "D" fragments from the DNA of the Oka parent strain (the progenitor of the vaccine strain), the RIT/Oka vaccine strain (a derivative of the Oka parent strain), the Merck/Oka vaccine strain, and the EF strain (an American wild type), were submitted to extensive endonuclease digestion studies to ascertain if additional unique restriction sites are present in the Oka parent or vaccine strains. The extra BgII restriction site characteristic of the Merck/Oka vaccine strain is also present in the DNA of the parent virus as well as its derivatives and was therefore not produced by the "attenuation" process. No other novel sites were found in the Oka parent or Oka-derived strains in this section of the genome. The Merck/Oka vaccine strain of VZV, despite its Japanese origin, is therefore quite similar to circulating American varicella-zoster virus strains. Varicella-zoster virus DNA, at least in the area of the BamHI D fragment, also appears to be remarkably stable from strain to strain.

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

We located a region of interstrain size variability in a short segment in an area at the right-hand end of the long unique sequence of the varicella-zoster viral genome. Varicella-zoster virus strains isolated in a district of Japan were classified into three groups on the basis of the size of this segment. Sequence comparison of the variable segment among strains from different groups revealed that the tandem direct repeat, R5, in the segment was variable among strains. R5, which was first discovered in a European strain (Dumas), contained a direct duplication of 88-base-pair (bp) elements separated by a 24-bp element (A.J. Davison and J.E. Scott, J. Gen. Virol. 67:1759-1816, 1986). We found that one 88-bp element and one 24-bp element constitute a repeating unit whose copy number varied from one to three among strains. The simplest R5 we detected was similar to that of Dumas, but there were a few base mismatches between these two R5 structures.

Variation of R1 repeated sequence present in open reading frame 11 of varicella-zoster virus strains

We molecularly cloned the tandem direct reiteration (R1) present in open reading frame (ORF) 11 from three independent strains of varicella-zoster virus. Comparison of the R1 sequences among varicella-zoster virus strains revealed that, although the portion of R1 near the 5' terminus of ORF 11 was conserved among strains, the 3'-terminal portion varied remarkably. This variation was due to the different arrangement of two elements (A and B) and a segment produced by fusion of A and B and to a single-base change in the A element. Since the difference in the size of R1 among strains was a multiple of 3 base pairs, the variation in R1 caused no frame shift in ORF 11.

Recombination in tissue culture between varicella-zoster virus strains

Several clinical varicella-zoster virus isolates obtained during testing of a live varicella vaccine had DNA restriction fragment patterns resembling neither vaccine nor wild-type virus [Gelb et al., J Infect. Dis. 155, 633-640, 1987]. One explanation for these isolates was recombination in vivo. To determine if such recombination is likely, two strains of varicella-zoster virus, distinguishable by restriction endonuclease fragment size differences (wild-type strain EF and the OKA vaccine strain), were grown together in tissue culture. After three passages, the mixed infection virus was plaque-purified. DNA from about 13% of the plaque-purified isolates had one or more BglI fragments found in neither parental virus. Hybridization studies showed that isolates containing one of the new BglI fragments were recombinants of the two parental strains. The BglI restriction fragment pattern of these recombinants resembled those of the unusual varicella isolates from individuals either vaccinated with the live attenuated OKA varicella vaccine and later exposed to natural varicella, or simultaneously exposed to both a recent recipient of the vaccine and natural varicella.

Genome variation among varicella-zoster virus isolates derived from different individuals and from the same individuals

We have used 12 restriction enzymes to analyse the DNA of 24 clinical isolates of VZV derived from 12 patients in order to compare isolates derived from different individuals and derived serially from the same individual. As reported previously, only a small proportion of the isolates differed with respect to the presence or absence of restriction sites. However, we found that the size of DNA fragments generated from all the isolates derived from different patients varied in any of four regions, one of which was first recognized in this study. In one case, where multiple isolates recovered from the same individual were analysed, each was distinguished from the others not only by differences in the variable regions but also by the presence or absence of a restriction site in a nonvariable region. This suggests that multiple strains of VZV can be present in the same human host.

Rapid method for the identification and screening of herpesviruses by DNA fingerprinting combined with blot hybridization

Rapid characterization of herpesvirus isolates exemplified by equine herpesviruses is described. Total DNAs were isolated from virus infected small scale cell cultures. The DNA fragments obtained after restriction enzyme digestion were separated on agarose gels, transferred and immobilized on filter membranes. A radioactively labelled probe derived from the purified DNA of an EHV-1 reference strain was used for hybridization in order to detect the restriction fragments of different EHV-1 field isolates. This method allows the typing of many isolates within a short period of time.

Putative glycoprotein gene of varicella-zoster virus with variable copy numbers of a 42-base-pair repeat sequence has homology to herpes simplex virus glycoprotein C

A strain variation of varicella-zoster virus that maps to the UL region of the genome was found to be due to different copy numbers of a high GC 42-base-pair repeat. DNA sequence analysis of this variable region showed the sequence to be 5-GCGGGATCGGGCTTTCGGG(A/T)AGCGGCCGAGGTGGGCGCGACG-3. Strains Scott and Webster both contain 7 and 32/42 copies of the repeat, whereas strain Oka has exactly 4 copies less. Microheterogeneity exists within the repeated sequences, depending on the strain and the repeat number. Sequencing of the entire EcoRI P fragment (which contains the repeated sequences) and part of the adjacent EcoRI M and EcoRI Q fragments from strain Scott showed that the repeats are part of a large open reading frame that could code for a polypeptide core with a molecular weight of 66,000. Several potential TATA boxes exist upstream and two polyadenylation signals are found downstream of the open reading frame. The predicted protein bears several characteristics of a glycoprotein. The region is transcriptionally active in varicella-zoster virus-infected cells, specifying at least three RNA species of 1.7, 1.95, and 2.5 kilobases, which are transcribed from the same DNA strand. Part of the predicted protein has a high degree of homology to the herpes simplex virus type 1 glycoprotein gC.

Errant processing and structural alterations of genomes present in a varicella-zoster virus vaccine

Five minority populations of aberrant, varicella-zoster virus (VZV)-derived genomes were identified among the encapsidated DNAs obtained from the nuclear and cytoplasmic fractions of an in vitro infection initiated with a lyophilized sample of the BIKEN VZV vaccine (strain Oka). These were (i) VZV genomes, present within nuclear but not cytoplasmic viral capsids, which had been cleaved at a specific site within the short segment and which were, therefore, 3.15 megadaltons (approximately 4% of the VZV genome length) short of full length; (ii) highly deleted, repetitive VZV genomes which contained the errant cleavage site but not the usual VZV genome terminal sequences; (iii) VZV genomes into which multiples of 1 through 5 defective genome repeat units had been inserted into a homologous site; (iv) VZV genomes with additions of 0.1 or 0.18 megadaltons of DNA at both the terminal and internal ends of the short segment; and (v) VZV DNA which had lost the HindIII restriction site at map position 0.11.

Fine mapping and sequencing of a variable segment in the inverted repeat region of varicella-zoster virus DNA

A strain variation in the internal and terminal repeats which bind the short unique sequence of varicella-zoster virus (VZV) DNA was found to be due to an insertion or deletion of DNA sequences at a single site. DNA sequence analysis showed that the nucleotide sequence CCGCCGATGGGGAGGGGGCGCGGTACC is tandemly duplicated a variable number of times in different VZV strains and is responsible for the observed variation in mobilities of restriction fragments from this region of VZV DNA. The variable region sequence shares some homology with tandemly repeated regions in the a and c sequences of herpes simplex virus type 1 and probably exists in a noncoding region of the VZV genome.

Biochemical techniques for the genetic and phenotypic analysis of viruses: 'molecular epidemiology'

New technologies now enable virologists to study small genetic and antigenic differences between field isolates of animal viruses at a higher level of discrimination than has been possible using conventional serological techniques. The most important of the laboratory techniques revolve around the use of monoclonal antibodies, peptide mapping, fingerprinting of whole RNA virus genomes, RNA:RNA hybridization, ‘electropherotyping’ of virus RNA or polypeptides, restriction enzyme analysis of virus DNA genomes, cloning of genes and rapid sequencing of viral DNAs and RNAs, in the latter case using primer extension techniques (reviewed by Palese & Roizman, 1980). From a practical point of view, genetic and phenotypic heterogeneity among viruses may be of considerable importance in attempts to control certain virus diseases by chemo- or immunoprophylaxis.

Silver staining of DNA restriction fragments for the rapid identification of adenovirus isolates: application during nosocomial outbreaks

The ultrasensitive photochemical silver stain for nucleic acids, described by Beidler et al. (1982), has been applied to the detection of adenovirus restriction fragments as a relatively rapid technique for the identification of virus isolates. In this study, restriction enzyme cleavage analysis was used to characterize adenovirus isolates from what appeared to be two nosocomial outbreaks. The first outbreak was thus shown to include two clusters of patients, and involved two serotypes Ad7c and Ad40. The second outbreak was unrelated and involved Ad35. Although restriction analysis does not replace serum neutralization as a routine method for typing adenoviruses, it is a much more rapid means of discriminating between different patient isolates, providing a current rather than retrospective analysis of a nosocomial outbreak. During the first outbreak, restriction analysis identified two distinct adenovirus serotypes from one patient--Ad7c from a nasopharyngeal aspirate and Ad41 from a stool specimen. Restriction analysis is also valuable for the sub-typing of virus isolates. In this study, the Ad40 and Ad41 isolates were shown to be variants of the respective prototype strains.

Physical maps of varicella-zoster virus DNA derived with 11 restriction enzymes

Varicella-zoster virus DNA was digested with 11 restriction endonucleases, and the resulting fragments were separated on agarose gels. Terminal fragments were identified by lambda exonuclease digestion. Physical maps were then constructed using a combination of double restriction enzyme digestion and hybridization to cloned BamHI fragments to place the remaining fragments in order.

DNA mapping of paired varicella-zoster virus isolates from patients with shingles

Varicella-zoster virus (VZV) was isolated from two separate sites in each of three patients with shingles (herpes zoster). The DNAs of the six VZV isolates were compared by high-resolution restriction endonuclease analysis with HindIII, KpnI, and HpaI. DNA cleavage patterns for each pair of VZV isolates were indistinguishable. These studies suggest that clinical shingles is the manifestation of a single VZV strain that becomes reactivated and causes both a viraemia and a dermatomal exanthem.