Analysis of strain variation of R1 repeated structure in varicella-zoster virus DNA by polymerase chain reaction

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.

Molecular studies of the Oka varicella vaccine

Varicella zoster virus (VZV) is one of eight members of the Herpesviridae family for which humans are the primary host; it causes two distinct diseases, varicella (chickenpox) and zoster (shingles). Varicella results from primary infection, during which the virus establishes latency in sensory neurons, a characteristic of all members of the Alphaherpesvirinae subfamily. Zoster is caused by reactivation of latent virus, which typically occurs when cellular immunity is impaired. VZV is the first human herpesvirus for which a vaccine has been licensed. The vaccine preparation, v-Oka, is a live-attenuated virus stock produced by the classic method of tissue culture passage in animal and human cell lines. Over 90 million doses of the vaccine have been administered in countries worldwide, including the USA, where varicella morbidity and mortality has declined dramatically. Over the last decade, several laboratories have been committed to investigating the mechanism by which the Oka vaccine is attenuated. Mutations have accumulated across the genome of the vaccine during the attenuation process; however, studies of the contribution of these changes to vaccine attenuation have been hampered by the lack of a suitable animal model of VZV disease and by the heterogeneity that exists among the viral population within the vaccine preparation. Notwithstanding, a wealth of data has been generated using various laboratory methodologies. Studies of the vaccine virus in human xenografts implanted in severe combined immunodeficiency-hu mice, have enabled analyses of the replication dynamics of the vaccine in dorsal root ganglia, T lymphocytes and skin. In vitro assays have been used to investigate the effect of vaccine mutations on viral gene expression and sequence analysis of vaccine rash viruses has permitted investigations into spread of the vaccine virus in a human host. We present here a review of what has been learned thus far about the molecular and phenotypic characteristics of the Oka vaccine.

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.

Laboratory diagnosis and characteristics of breakthrough varicella in children

The atypical features of varicella in vaccinated persons (breakthrough varicella [BTV]) present diagnostic challenges. We examined varicella-zoster virus (VZV) polymerase chain reaction (PCR) and immunoglobulin (Ig) M and IgG serologic test results for confirming BTV cases. Among 33 vaccinated children with varicella-like rash, we identified wild-type VZV in 58% overall and in 76% of those with adequate tissue specimens; no vaccine-type virus was found. Of the 12 subjects with PCR-confirmed BTV and acute-phase serum samples, 9 had detectable IgM, and all had highly elevated acute-phase IgG titers. Six subjects with negative PCR results had lower IgG titers and negative IgM results. Although PCR is the preferred method for laboratory confirmation of BTV, a positive serum varicella IgM test result should also be considered to be diagnostic in a suspected BTV case; however, a negative IgM test result cannot be used to rule out the diagnosis. The value of highly elevated IgG titers needs further evaluation. Larger studies are needed to confirm these results.

Analysis of repeat units in the R2 region among different Oka varicella-zoster virus vaccine strains and wild-type strains in Germany

OBJECTIVE

The present study compared the number of R2 repeat units in six different Oka strains and in 54 varicella-zoster virus (VZV) wild-type strains isolated from patients with varicella or zoster in Germany.

METHODS

The R2 genomic region was characterized by polymerase chain reaction and sequencing methods.

RESULTS

Five VZV Oka vaccine strains showed a number of seven 42-bp units and, in one, eight repeats were found. In 11 VZV wild-type strains isolated from patients with varicella, the copy number ranged between four and eight, and in 43 strains from zoster a similar range between four and nine copies was observed. About 80% of all strains showed between five and seven repeated units. More than one third of strains revealed seven repeats like Oka.

CONCLUSIONS

The size of the R2 repeat region can also be different in single Oka vaccine strains. In German VZV wild-type strains, the R2 fragment seems to be not as variable as in Japanese wild-type strains.

Genomic cartography of varicella-zoster virus: a complete genome-based analysis of strain variability with implications for attenuation and phenotypic differences

In order to gain a better perspective on the true variability of varicella-zoster virus (VZV) and to catalogue the location and number of differences, 11 new complete genome sequences were compared with those previously in the public domain (18 complete genomes in total). Three of the newly sequenced genomes were derived from a single strain in order to assess variations that can occur during serial passage in cell culture. The analysis revealed that while VZV is relatively stable genetically it does posses a certain degree of variability. The reiteration regions, origins of replication and intergenic homopolymer regions were all found to be variable between strains as well as within a given strain. In addition, the terminal viral sequences were found to vary within and between strains specifically at the 3' end of the genome. Analysis of single nucleotide polymorphisms (SNPs) identified a total of 557 variable sites, 451 of which were found in coding regions and resulted in 187 different in amino acid substitutions. A comparison of the SNPs present in the two gE mutant strains, VZV-MSP and VZV-BC, suggested that the missense mutation in gE was primarily responsible for the accelerated cell spread phenotype. Some of the variations noted with high passage in cell culture are consistent with variations seen in the IE62 gene of the vaccine strains (S628G, R958G and I1260V) that may help in pinpointing variations essential for attenuation. Although VZV has been considered to be one of the most genetically stable human herpesviruses, this initial assessment of genomic VZV cartography provides insight into ORFs with previously unreported variations.

Sensitive and rapid diagnosis of human parvovirus B19 infection by loop-mediated isothermal amplification

BACKGROUND

Human parvovirus B19 (B19) infections exhibit various skin manifestations that are similar to and hence hard to distinguish from many other skin diseases. The virological diagnosis of B19 infection is usually based on time-consuming serological tests and polymerase chain reaction (PCR).

OBJECTIVES

In this study, a DNA amplification method, loop-mediated isothermal amplification (LAMP), was used for the diagnosis of B19 infection and was compared with PCR.

METHODS

Ten patients with acute B19 infection and 16 patients with other skin diseases were enrolled. Sera and pharyngeal swabs were used directly as the templates in LAMP. The LAMP reaction was carried out at 63 degrees C for 1 h in a heat block. The reaction products were judged visually, by adding SYBR Green I into the tubes, and by gel electrophoresis.

RESULTS

B19 DNA was detected by LAMP in 10 sera and all of seven tested pharyngeal swabs of 10 patients with acute B19 infection but not in samples from 16 patients with other skin diseases. The results were in agreement with those obtained by PCR except for one case. The reason for the single discrepancy may be that the sensitivity of LAMP is 10(2) times higher than PCR.

CONCLUSIONS

Detection of B19 DNA by LAMP in serum and especially in the pharynx is a rapid and convenient method for the diagnosis of acute B19 infection.

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.

Close association of predominant genotype of herpes simplex virus type 1 with eczema herpeticum analyzed using restriction fragment length polymorphism of polymerase chain reaction

Herpes simplex virus type 1 (HSV-1) strains belonging to the same genotype can possibly share biological properties and clinical manifestations common to the genotype. We classified previously 66 HSV-1 strains into 35 genotypes (F1-F35) using restriction fragment length polymorphism (RFLP) and F1 and F35 genotypes were revealed to be predominant [Arch. Virol. 13 (1993) 29]. It was found later that the F35 genotype seemed to be closely associated with eczema herpeticum [J. Med. Virol. 49 (1996) 329]. In the present study, a convenient method was developed for classification of two predominant genotypes by RFLP of polymerase chain reaction (RFLP-PCR). Using this method, genotypes of 21 strains isolated from eczema herpeticum were analyzed; seven of 21 strains (33.3%) were of F1 and five of 21 (23.8%) were of F35. Genotypes of 19 strains isolated from facial herpes other than eczema herpeticum were as follows; six of 19 (31.6%) strains were of F1 and one of 19 (5.3%) were of F35. Thus, strains belonging to F35 were appear to have been isolated more frequently from eczema herpeticum (5/21) than from facial herpes (1/19). These ratios showed a statistically significant difference. These results support the hypothesis that F35 strains is clearly associated with eczema herpeticum, in agreement with previous study. This is the first report of PCR-based approach for classification of HSV-1 strains into genotypes seeking an association of a genotype with clinical manifestation.

Varicella-zoster virus immunity and prevention: a conference perspective

This report offers a concise overview of the VZV Conference, highlighting recent developments in the field and speculating on areas of greatest opportunity and need for future work. The goal of eradicating VZV disease will be facilitated by a multifaceted research agenda directed at a fuller comprehension of how the virus replicates, spreads and persists, and how it eludes host immune responses.

Rapid genotyping of varicella-zoster virus vaccine and wild-type strains with fluorophore-labeled hybridization probes

We developed a single-tube rapid method for the detection and differentiation of varicella-zoster virus (VZV) vaccine and wild-type strains that combines rapid-cycle PCR with wild-type-specific fluorescent probe melting profiles for product genotyping. A region including the polymorphic site in VZV open reading frame (ORF) 62 was amplified in the presence of two fluorescence-labeled hybridization probes. During the annealing step of the thermal cycling, both probes bound to their complementary sequences in the amplicon, resulting in resonance energy transfer, thus providing real-time fluorescence monitoring of PCR. Continuous acquisition of fluorescence data during a melting curve analysis at the completion of PCR revealed that loss of fluorescence occurred in a strain-specific manner as the detection probe, which was fully complementary to the wild-type VZV ORF 62 region, melted off the template. Use of this method allowed genotyping of samples within minutes after the completion of PCR, eliminating the need for post-PCR sample manipulation. In addition to reducing the time required to produce a result, this method substantially reduces the risk of contamination of the final product as well as the risk of sample tracking errors. The genotypes of 79 VZV-positive samples determined by this fluorescent resonance energy transfer (FRET) method were identical to the genotypes obtained by conventional PCR and restriction fragment length polymorphism analysis. The genotyping of VZV strains by the FRET method is a rapid and reliable method that is suitable for typing and that is also practical for use for the processing of large numbers of specimens.