Isolation of genotypes 1 and 3 of Japanese Encephalitis Virus in Kochi, Japan.

Japanese encephalitis virus (JEV) is a mosquito-borne virus belonging to the JEV serocomplex within the genus Flavivirus, family Flaviviridae. JEV is divided into five genotypes, G1 to G5, based on the envelope (E) protein nucleotide sequence. JEV G3 circulated in Japan until the early 1990s when it was replaced by G1. However, JEV G3 was isolated from swine serum samples (sw/Kochi/1/2004) in Kochi Prefecture, western Japan in 2004. In addition, 2018 isolates from pigs and cows (sw/Kochi/492/2018 and bo/Kochi/211/2018) in the same prefecture were identified as G3. The nucleotide sequencing results of the polyprotein region of sw/Kochi/492/2018 and bo/Kochi/211/2018 differed from those of the sw/Kochi/1/2004 strain described in our previous report. Seven JEV isolates were identified as G1 in the same geographical area as this study. This result indicates that both JEV G1 and G3 are present in the Kochi area.