title: Analysis of single nucleotide polymorphism among Varicella-Zoster Virus and identification of vaccine-specific sites.
abstract: Varicella-zoster virus (VZV) is a causative agent for chickenpox and zoster. Live attenuated vaccines have been developed based on Oka and MAV/06 strains. In order to understand the molecular mechanisms of attenuation, complete genome sequences of vaccine and wild-type strains were compared and single nucleotide polymorphism (SNP) was analyzed. ORF22 and ORF62 contained the highest number of SNPs. The detailed analysis of the SNPs suggested 24 potential vaccine-specific sites. All the mutational events found in vaccine-specific sites were transitional, and most of them were substitution of AT to GC pair. Interestingly, 18 of the vaccine-specific sites of the vaccine strains appeared to be genetically heterogeneous. The probability of a single genome of vaccine strain to contain all 24 vaccine-type sequences was calculated to be less than 4%. The average codon adaptation index (CAI) value of the vaccine strains was significantly lower than the CAI value of the clinical strains.
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju, South Korea.
authors.forename: Jeong Seon
authors.initials: JS
authors.lastname: Jeon
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju, South Korea.
authors.forename: Youn Hee
authors.initials: YH
authors.lastname: Won
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju, South Korea.
authors.forename: In Kyo
authors.initials: IK
authors.lastname: Kim
authors.affiliation: Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea.
authors.forename: Jin Hyun
authors.initials: JH
authors.lastname: Ahn
authors.affiliation: Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea.
authors.forename: Ok Sarah
authors.initials: OS
authors.lastname: Shin
authors.affiliation: Mogam Biotechnology Research Institute, Yongin, South Korea.
authors.forename: Jung Hwan
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Microbiology, Chungbuk National University, Cheongju, South Korea. Electronic address: chlee@chungbuk.ac.kr.
authors.forename: Chan Hee
authors.initials: CH
authors.lastname: Lee
mesh_terms: D000220:Adaptation, Biological; D019943:Amino Acid Substitution; D002644:Chickenpox / Q000276:immunology / Q000517:prevention & control; D019433:Chickenpox Vaccine / Q000276:immunology*; D003062:Codon; D000939:Epitopes / Q000235:genetics* / Q000276:immunology*; D016679:Genome, Viral; D014645:Herpesvirus 3, Human / Q000145:classification / Q000235:genetics* / Q000276:immunology*; D006801:Humans; D054643:INDEL Mutation; D009154:Mutation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D019433:Chickenpox Vaccine; D003062:Codon; D000939:Epitopes
keywords: Genetic heterogeneity; Live attenuated vaccine; Sequence diversity; Single nucleotide polymorphism (SNP); Vaccine-specific sites; Varicella-zoster virus (VZV)