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Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients

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Abstract

Varicella-zoster virus (VZV) is a causative agent of chickenpox in primary infection and shingles after its reactivation from latency. Complete or almost-complete genomic DNA sequences for various VZV strains have been reported. Recently, clinical VZV strains were isolated from Korean patients whose genome was sequenced using high-throughput sequencing technology. In this study, we analyzed single nucleotide polymorphism (SNP) of VZV strains to genetically characterize Korean clinical isolates. Phylogenetic analyses revealed that three Korean strains, YC01, YC02, and YC03, were linked to clade 2. Comprehensive SNP analysis identified 86 sites specific for the 5 VZV clades. VZV strains isolated from Korea did not form a phylogenetic cluster. Rather, YC02 and YC03 clustered strongly with Chinese strain 84-7 within clade 2, more specifically cluster 2a. Signature sequences for the cluster 2a were identified and found to play an important role in the separation of cluster 2a strains from other clade 2 strains, as shown in substitution studies. Further genetic analysis with additional strains isolated from Japan, China, and other Asian countries would provide a novel insight into the significance of two distinct subclades within clade 2.

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References

  • Barrett-Muir, W., Scott, F.T., Aaby, P., John, J., Matondo, P., Chaudhry, Q.L., Siqueira, M., Poulsen, A., Yaminishi, K., and Breuer, J. 2003. Genetic variation of varicella-zoster virus: evidence for geographical separation of strains. J. Med. Virol. 70, Suppl 1, S42–47.

    Article  CAS  PubMed  Google Scholar 

  • Breuer, J., Grose, C., Norberg, P., Tipples, G., and Schmid, D.S. 2010. A proposal for a common nomenclature for viral clades that form the species varicella-zoster virus: summary of VZV Nomenclature Meeting 2008, Barts and the London School of Medicine and Dentistry, 24-25 July 2008. J. gen. Virol. 91, 821–828.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chow, V.T., Tipples, G.A., and Grose, C. 2013. Bioinformatics of varicella-zoster virus: single nucleotide polymorphisms define clades and attenuated vaccine genotypes. Infect. Genet. Evol. 18, 351–356.

    Article  CAS  PubMed  Google Scholar 

  • Creed, R., Satyaprakash, A., and Ravanfar, P. 2009. Varicella zoster vaccines. Dermatol. Ther. 22, 143–149.

    Article  PubMed  Google Scholar 

  • Depledge, D.P., Kundu, S., Jensen, N.J., Gray, E.R., Jones, M., Steinberg, S., Gershon, A., Kinchington, P.R., Schmid, D.S., Balloux, F., et al. 2014. Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans. Mol. Biol. Evol. 31, 397–409.

    Article  CAS  PubMed  Google Scholar 

  • Faga, B., Maury, W., Bruckner, D.A., and Grose, C. 2001. Identification and mapping of single nucleotide polymorphisms in the varicella-zoster virus genome. Virology 280, 1–6.

    Article  CAS  PubMed  Google Scholar 

  • Flatt, A. and Breuer, J. 2012. Varicella vaccines. Br. Med. Bull. 103, 115–127.

    Article  CAS  PubMed  Google Scholar 

  • Gershon, A.A. 2013. Varicella zoster vaccines and their implications for development of HSV vaccines. Virology 435, 29–36.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gershon, A.A., and Gershon, M.D. 2013. Pathogenesis and current approaches to control of varicella-zoster virus infections. Clin. Microbiol. Rev. 26, 728–743.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grose, C. 2012. Pangaea and the out-of-africa model of varicellazoster virus evolution and phylogeography. J. Virol. 86, 9558–9565.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta, R.S. 1998. What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol. Microbiol. 29, 695–707.

    Article  CAS  PubMed  Google Scholar 

  • Jeon, J.S., Won, Y.H., Kim, I.K., Ahn, J.H., Shin, O.S., Kim, J.H., and Lee, C.H. 2016. Analysis of single nucleotide polymorphism among Varicella-Zoster Virus and identification of vaccine-specific sites. Virology 496, 277–286.

    Article  CAS  PubMed  Google Scholar 

  • Jiang, L., Gan, L., Chen, J., and Wang, M. 2013. Genetic analysis of clinical VZV isolates collected in China reveals a more homologous profile. Biomed. Res. Int. 2013, 681234.

    PubMed  PubMed Central  Google Scholar 

  • Kim, K.H., Choi, Y.J., Song, K.H., Park, W.B., Jeon, J.H., Park, S.W., Kim, H.B., Kim, N.J., and Oh, M.D. 2011b. Genotype of varicella-zoster virus isolates in South Korea. J. Clin. Microbiol. 49, 1913–1916.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim, J.I., Jung, G.S., Kim, Y.Y., Ji, G.Y., Kim, H.S., Wang, W.D., Park, H.S., Park, S.Y., Kim, G.H., Kwon, S.N., et al. 2011a. Sequencing and characterization of Varicella-zoster virus vaccine strain SuduVax. Virol. J. 8, 547.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • LaRussa, P., Lungu, O., Hardy, I., Gershon, A., Steinberg, S.P., and Silverstein, S. 1992. Restriction fragment length polymorphism of polymerase chain reaction products from vaccine and wildtype varicella-zoster virus isolates. J. Virol. 66, 1016–1020.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li, X.L., Wang, X.X., and Zhang, Z.Y. 2010. Sequencing of whole genome of varicella-zoster virus 84-7 strain. Chinese J. Biol. 1, 003.

    Google Scholar 

  • Liu, J., Wang, M., Gan, L., Yang, S., and Chen, J. 2009. Genotyping of clinical varicella-zoster virus isolates collected in China. J. Clin. Microbiol. 47, 1418–1423.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loparev, V.N., Argaw, T., Krause, P.R., Takayama, M., and Schmid, D.S. 2000. 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. J. Clin. Microbiol. 38, 3156–3160.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Loparev, V.N., Gonzalez, A., Deleon-Carnes, M., Tipples, G., Fickenscher, H., Torfason, E.G., and Schmid, D.S. 2004. Global identification of three major genotypes of varicella-zoster virus: longitudinal clustering and strategies for genotyping. J. Virol. 78, 8349–8358.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loparev, V.N., Rubtcova, E.N., Bostik, V., Govil, D., Birch, C.J., Druce, J.D., Schmid, D.S., and Croxson, M.C. 2007. Identification of five major and two minor genotypes of varicella-zoster virus strains: a practical two-amplicon approach used to genotype clinical isolates in Australia and New Zealand. J. Virol. 81, 12758–12765.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McGeoch, D.J. 2009. Lineages of varicella-zoster virus. J. gen. Virol. 90, 963–969.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Norberg, P., Depledge, D.P., Kundu, S., Atkinson, C., Brown, J., Haque, T., Hussaini, Y., MacMahon, E., Molyneaux, P., Papaevangelou, V., et al. 2015. Recombination of globally circulating varicella-zoster virus. J. Virol. 89, 7133–7146.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Park, C.S., Lee, D.H., Lee, K.M., and Lee, C.H. 2008. Characterization and signature pattern analysis of Korean clade of HIV-1 using nef gene sequences. J. Microbiol. 46, 88–94.

    Article  CAS  PubMed  Google Scholar 

  • Peters, G.A., Tyler, S.D., Carpenter, J.E., Jackson, W., Mori, Y., Arvin, A.M., and Grose, C. 2012. The attenuated genotype of varicellazoster virus includes an ORF0 transitional stop codon mutation. J. Virol. 86, 10695–10703.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peters, G.A., Tyler, S.D., Grose, C., Severini, A., Gray, M.J., Upton, C., and Tipples, G.A. 2006. A full-genome phylogenetic analysis of varicella-zoster virus reveals a novel origin of replication-based genotyping scheme and evidence of recombination between major circulating clades. J. Virol. 80, 9850–9860.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quinlivan, M., Hawrami, K., Barrett-Muir, W., Aaby, P., Arvin, A., Chow, V.T., John, T.J., Matondo, P., Peiris, M., Poulsen, A., et al. 2002. The molecular epidemiology of varicella-zoster virus: evidence for geographic segregation. J. Infect. Dis. 186, 888–894.

    Article  CAS  PubMed  Google Scholar 

  • Sauerbrei, A., Eichhorn, U., Gawellek, S., Egerer, R., Schacke, M., and Wutzler, P. 2003. Molecular characterisation of varicellazoster virus strains in Germany and differentiation from the Oka vaccine strain. J. Med. Virol. 71, 313–319.

    Article  CAS  PubMed  Google Scholar 

  • Schmidt-Chanasit, J. and Sauerbrei, A. 2011. Evolution and worldwide distribution of varicella-zoster virus clades. Infect. Genet. Evol. 11, 1–10.

    Article  PubMed  Google Scholar 

  • Sohn, Y.M., Park, C.Y., Hwang, K.K., Woo, G.J., and Park, S.Y. 1994. Safety and immunogenicity of live attenuated varicella virus vaccine (MAV/06 strain). J. Korean Pediatr. Soc. 37, 1405–1413.

    Google Scholar 

  • Takahashi, M., Otsuka, T., Okuno, Y., Asano, Y., and Yazaki, T. 1974. Live vaccine used to prevent the spread of varicella in children in hospital. Lancet 2, 1288–1290.

    Article  CAS  PubMed  Google Scholar 

  • Toi, C.S. and Dwyer, D.E. 2010. Prevalence of varicella-zoster virus genotypes in Australia characterized by high-resolution melt analysis and ORF22 gene analyses. J. Med. Microbiol. 59, 935–940.

    Article  CAS  PubMed  Google Scholar 

  • Wagenaar, T.R., Chow, V.T., Buranathai, C., Thawatsupha, P., and Grose, C. 2003. The out of Africa model of varicella-zoster virus evolution: single nucleotide polymorphisms and private alleles distinguish Asian clades from European/North American clades. Vaccine 21, 1072–1081.

    Article  CAS  PubMed  Google Scholar 

  • Yamanishi, K. 2008. Molecular analysis of the Oka vaccine strain of varicella-zoster virus. J. Infect. Dis. 197 Suppl 2, S45–48.

    Article  CAS  PubMed  Google Scholar 

  • Zell, R., Taudien, S., Pfaff, F., Wutzler, P., Platzer, M., and Sauerbrei, A. 2012. Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination. J. Virol. 86, 1608–1622.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea

    Min Ho Kim, Jeong Seon Jeon, In Kyo Kim, Ji Seon Park & Chan Hee Lee

  2. Department of Microbiology, College of Medicine, Yeungnam University, Daegu, 42415, Republic of Korea

    Hosun Park

  3. Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, 08308, Republic of Korea

    Ok Sarah Shin

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  1. Min Ho Kim
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  2. Jeong Seon Jeon
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  3. In Kyo Kim
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  4. Ji Seon Park
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  5. Hosun Park
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  6. Ok Sarah Shin
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  7. Chan Hee Lee
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Correspondence to Chan Hee Lee.

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Kim, M.H., Jeon, J.S., Kim, I.K. et al. Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients. J Microbiol. 55, 665–672 (2017). https://doi.org/10.1007/s12275-017-7171-3

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  • DOI: https://doi.org/10.1007/s12275-017-7171-3

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