Genomic Characteristics and E Protein Bioinformatics Analysis of JEV Isolates from South China from 2011 to 2018

Japanese encephalitis is a mosquito-borne zoonotic epidemic caused by the Japanese encephalitis virus (JEV). JEV is not only the leading cause of Asian viral encephalitis, but also one of the leading causes of viral encephalitis worldwide. To understand the genetic evolution and E protein characteristics of JEV, 263 suspected porcine JE samples collected from South China from 2011 to 2018 were inspected. It was found that 78 aborted porcine fetuses were JEV-nucleic-acid-positive, with a positive rate of 29.7%. Furthermore, four JEV variants were isolated from JEV-nucleic-acid-positive materials, namely, CH/GD2011/2011, CH/GD2014/2014, CH/GD2015/2015, and CH/GD2018/2018. The cell culture and virus titer determination of four JEV isolates showed that four JEV isolates could proliferate stably in Vero cells, and the virus titer was as high as 10^8.5 TCID 50/mL. The whole-genome sequences of four JEV isolates were sequenced. Based on the phylogenetic analysis of the JEV E gene and whole genome, it was found that CH/GD2011/2011 and CH/GD2015/2015 belonged to the GIII type, while CH/GD2014/2014 and CH/GD2018/2018 belonged to the GI type, which was significantly different from that of the JEV classical strain CH/BJ-1/1995. Bioinformatics tools were used to analyze the E protein phosphorylation site, glycosylation site, B cell antigen epitope, and modeled 3D structures of E protein in four JEV isolates. The analysis of the prevalence of JEV and the biological function of E protein can provide a theoretical basis for the prevention and control of JEV and the design of antiviral drugs.