Whole genome sequence analysis of an emerging Japanese encephalitis virus (genotype V) strain isolated in mainland China

Abstract

Objective To analyze the molecular characteristics of the full-length genome of a newly isolated genotype Ⅴ Japanese encephalitis virus (JEV) strain (XZ0934) in China and the first genotype Ⅴ JEV 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 phylogenetic 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, respectively. 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 Ⅴ and 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 genotyped Ⅰ-Ⅴrevealed that in the cluster of genotypeⅤ, 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 genotype Ⅴ JEV strains after a 60 years hiatus. Conclusion The two genotypeⅤ JEV strains showed high levels of identity in nucleotide sequences and amino acid sequences with serine insertion in the NS4A gene. However, there were molecular genetic differences between genotype Ⅴ JEV strains isolated after a 60 years hiatus. Key words: Japanese encephalitis virus; GenotypeⅤ; Molecular phylogenetic analysis