Cloning and sequencing of complete cDNA of Japanese encephalitis virus YL strain in Taiwan.

We determined the complete nucleotide sequence of the YL strain of Japanese encephalitis virus and its amino acid sequence was deduced. Our results displayed that the genome of YL strain contained a single open reading frame of 10,296 nucleotides (nts) which was flanked by untranslated region (UTR) containing 95 bases at the 5'-end and 586 bases at the 3'-end, respectively. Comparison of sequences showed that the overall amino acid sequence and 3' UTR of YL were similar to those of the virulent strain JaGAr0l. However, some significant amino acid differences of viral envelope (E) protein were observed between YL and JaGAr01; the amino acid sequence of E protein in YL strain possessed RGG(387-389) tripeptide instead of RGD(387-389) in JaGAr01 and in other strains; and another amino acid is K(138) in YL, not E(138) found in others. These differences suggested that the YL strain impairs in viral attachment to the cell surface and loses neuroinvasiveness, and therefore this strain was used as a live attenuated vaccine.