Tissue tropism and molecular characterization of a Japanese encephalitis virus strain isolated from pigs in southwest China

•JEV strains originating from pigs are very limited, and the infection mechanism of JEV was not very clear. The associations between amino acid mutations and virulence of JEV still need to further study.•We isolated a wild strain of JEV in Sichuan province of China, which is the first genotype I JEV strain isolated from swine in this area.•We explored preliminarily the infection mode of JEV by studying the tissue tropism of the isolated strain.•Complete genome sequencing and amino acid mutations analyze can provide support to studying of molecular mechanism of virus infection.

Since September 2012, an epidemic has been spreading among swine in a pig farm located in Sichuan province, southwest China, which has resulted in abortion, stillbirth, and fetal mummification. The brains of stillborn pigs were collected and a previously unknown Japanese encephalitis virus (JEV), namely SCYA201201, was isolated. According to the results of agarose gel diffusion precipitation, indirect immunofluorescence analysis, neutralization testing, reverse transcription PCR (RT-PCR) amplification, and physical and chemical testing, the virus was conformed to have the characteristics of JEV. The virus titer in BHK-21 cells was 108.47 PFU/ml and the median lethal dose (LD50) to 3-week-old and 7-day-old mice was 1.99 log10 and 1.02 log10 PFU/LD50, respectively. The results of tissue tropism for mice showed that the viral load in the brain was significantly higher than other organs, indicating that the isolate was strongly neurotropic. Additionally, the complete genome sequence of the isolate was determined and compared with other JEV strains. Phylogenetic analysis showed that the isolate belongs to genotype I and may be an imported virus. The isolate had 88.4% nucleotide identity with the Chinese vaccine strain SA14-14-2. However, there were 69 amino acid substitutions compared with the strain SA14-14-2. Some substitutions indicated that SCYA201201 was highly neurovirulent and infective, in accordance with the results of animal testing.