J Vet Sci.  2013 Mar;14(1):27-36. 10.4142/jvs.2013.14.1.27.

Molecular characterization of Japanese encephalitis virus strains prevalent in Chinese swine herds

  • 1Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China. gztong@shvri.ac.cn


Japanese encephalitis virus (JEV) is the leading cause of viral encephalitis in Asia and domestic pigs serve as the amplifying hosts. In the present study, the full genomic sequences of two JEV strains (HEN0701 and SH0601) isolated from pigs in China were determined and compared with other 12 JEV strains deposited in GenBank. These two strains had an 88.8% nucleotide sequence similarity and 97.9% deduced amino acid sequence homology. HEN0701 had high nucleotide sequence and high amino acid sequence identity with genotype I (GI) strains, while SH0601 had high nucleotide sequence and high amino acid sequence identity with GIII strains at both the gene and full genome levels. Further phylogenetic analysis showed that HEN0701 belonged to the JEV GI group and SH0601 was classified as a GIII strain. Analysis of codon usage showed there were a few differences between the GI and GIII strains in nucleotide composition and codon usage for the open reading frames.


genotype; Japanese encephalitis virus; phylogenetic analysis

MeSH Terms

Cell Line
Encephalitis Virus, Japanese/classification/*genetics
Encephalitis, Japanese/epidemiology/*veterinary/virology
Gene Expression Regulation, Viral/physiology
Genome, Viral
Molecular Epidemiology
Swine Diseases/epidemiology/*virology


  • Fig. 1 Neighbor-joining phylogenetic tree for JEV envelope genes rooted with the West Nile virus (WNV) strain Mex03. Numbers on the branches indicate bootstrap support (1,000 replicates). The GenBank accession number, origin, country/province, and year of isolation of each strain are noted. Sw: derived from swine, Mo: derived from mosquito, Hu: derived from human.

  • Fig. 2 Alignment of the 3' UTR variable region. Nucleotide sequences of the 3' UTRs from 18 JEV strains were aligned with MegAlign (DNAStar, USA). A dash indicates a missing nucleotide. Nucleotides of each strain that differ from those of HEN0701 are marked with grey shading. The variable region consists of 73 nucleotides (nt) immediately downstream of the stop codon in the JEV genomic 3' UTRs.

  • Fig. 3 RNA structures of the 3'- and 5'-end sequences of the HEN0701 and SH0601 genomes. (A) 149 nt 5'-end sequences of the HEN0701 strain. (B) 149-nt 5'-end sequences of the SH0601 strain. (C) 117-nt 3'-end sequences of the HEN0701 strain. (D) 117-nt 3'-end sequences of the SH0601 strain. (E) Interaction between the 5'- and 3'-end sequences of HEN0701. (F) Interaction between the 5'- and 3'-end sequences of SH0601.

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