J Vet Sci.  2004 Sep;5(3):197-205.

Molecular characterization of full-length genome of Japanese encephalitis virus (KV1899) isolated from pigs in Korea

  • 1National Veterinary Research and Quarantine Service, Ministry of Agriculture and Forestry, Anyang 430-824, Korea. yangdk@nvrqs.go.kr
  • 2Department of Veterinary Internal Medicine, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea.


We have determined the complete nucleotide and deduced amino acid sequences of the Japanese encephalitis virus (JEV) strain KV1899, isolated from a fattening pig in Korea. In comparison with 22 fully sequenced JEV genomes currently available, we found that the 10,963-nucleotide RNA genome of KV1899 has a 13-nucelotide deletion in the 3' non-translated variable region and 53 unique nucleotide sequences including 3' non-translated region (NTR). Its single open reading frame has a total of 28 amino acid substitutions. Comparison of the KV1899 genomic sequence with those of the 21 fully sequenced JEV strains in published databases showed nucleotide homology ranging from 97.4% (Ishikawa strain) to 87.0% (CH2195 strain). Amino acid homology with KV1899 strain ranged from 96.4% (K94P05) to 91.0% (GP78). The KV1899 showed the highest nucleotide homology with Ishikawa strain and the highest amino acid homology with K94P05. We performed an extensive E gene based phylogenetic analysis on a selection of 41 JEV isolates available from the GenBank. Compared with Anyang strain, isolated from a pig in 1969, that is current live vaccine strain for swine in Korea, the homology of nucleotide sequence in envelope gene was only 87.1%. The prM gene of the isolate was closely related with those of Ishikawa and K94P05 strains, which were grouped into genotype I of JEV.


Japanese encephalitis virus; Complete genome sequence; Phylogenetic analysis

MeSH Terms

3' Untranslated Regions/chemistry/genetics
Amino Acid Sequence
Base Sequence
Encephalitis Virus, Japanese/*genetics
Encephalitis, Japanese/*veterinary/virology
*Genome, Viral
Membrane Glycoproteins/chemistry/genetics
Molecular Sequence Data
RNA, Viral/chemistry/genetics
Reverse Transcriptase Polymerase Chain Reaction/veterinary
Sequence Alignment
Swine Diseases/*virology
Viral Envelope Proteins/chemistry/genetics
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