Whole genome sequence analysis of an emerging Japanese encephalitis virus (genotype Ⅴ) strain isolated in mainland China / 中华微生物学和免疫学杂志

ABSTRACT

Abstract] Objective To analyze the molecular characteristics of the full-length genome of a new-ly isolated genotypeⅤJapanese encephalitis virus (JEV) strain (XZ0934) in China and the first genotypeⅤJEV strain ( Muar) isolated in Malaya 60 years ago.Methods Several softwares including ClustalX 2.0.9, DNAStar 7.1, Bioedit 7.2.5 and MEGA6.06 were used to conduct sequence alignments and phylo-genetic analysis.Results The full-length genomes of XZ0934 strain (isolated in Tibet, China in 2009) and Muar strain (isolated in Malaya in 1952) were composed of 10 983 and 10 988 nucleotides, respective-ly.The XZ0934 strain was highly similar with the Muar strain showing the homology of 90.6%in nucleotide (nt) and 98.3%in amino acid (aa).The open reading frame (ORF) of the two genotype Ⅴ JEV strains encoded 3433 aa while the ORF of other four genotypes (Ⅰ-Ⅳ) (10 299 nt) encoded 3432 aa.Compared with JEV strains of other genotypes, a serine were inserted into the NS4A gene of JEV strains genotype Ⅴand 10-14 nucleotides were inserted into the downstream of the ORF stop codon in 3′-untranslated region. Phylogenetic analysis of E sequences of all JEV strains genotypedⅠ-Ⅴrevealed that in the cluster of geno-typeⅤ, XZ0934 and 10-1827 ( isolated from mosquitoes in South Korea, 2010) stains formed a branch and were divergent from that of Muar strain indicating that there were molecular genetic differences among geno-typeⅤJEV strains after a 60 years hiatus.Conclusion The two genotypeⅤJEV strains showed high lev-els of identity in nucleotide sequences and amino acid sequences with serine insertion in the NS4A gene. However, there were molecular genetic differences between genotypeⅤJEV strains isolated after a 60 years hiatus.