Complete genome sequence analysis of Japanese encephalitis virus attenuated SA14-14-2-B3 vaccine strain.

The complete genome sequence of Japanese encephalitis virus (JEV) SA14-14-2-B3 strain was amplified by RT-PCR using eight pairs of primers designed according to the published sequence of JEV. The genome consisted of 10 977 nt, encoding a poly-protein of 3 432 amino acids (aa) residues. Sequence comparison showed that it had high level identities with the vaccine strain SA14-14-2, SA (A) and wildtype strain SA14, with 99.8 %, 99.9 % and 99.4 % homologies at nucleotide level and 99.7 %, 99.8 % and 99.1 % homologies at amino acid level, respectively. The sequence identities with HEN0701 and KV1899 of porcine origin was relatively lower, with 88.5 % similarities in nucleotide and 96.6 %, 97.6 % in amino acids. There was a G-base insertion at the site of 10 700 nt in SA14-14-2-B3 strain. Phylogenetic analysis showed that the SA14-14-2-B3 strain had a closest genetic relationship with SA14 virus strains SA14, SA14-14-2, SA (A), SA (V), and Beijing-1, p3, WHe, HW isolates, but a low genetic similarity with HEN0701 and KV1899 isolates. Phylogenetic relationship based on the E gene indicated that the SA14-14-2-B3 strain belonged to JEV genotype Ⅲ.