Full-length Genomes And Phylogenetic Analysis Of Japanese Encephalitis Virus Isolates From Swine In Henan

Japanese encephalitis virus (JEV) is an arbovirus belonging to the family Flaviviridae. It is maintained in a zoonotic cycle involving pigs, ardeid birds and Culex species of mosquitoes. Humans are accidental dead end hosts of JEV infection because they cannot sustain high viraltiters. This cycle involves pigs as the major reservoir amplifying host, water birds as carriers and mosquitoes as vectors, causing serious economic losses to the pig industry.Sequence analysis of the whole genome can understand the overall information of genome and molecular virulence characteristics. It is also important for molecular epidemiology of JE. The genome is approximately11kb in length, containing short5′and3′non-coding regions, single-stranded, positive sense in polarity, capped at the5′-terminus and lacks a poly(A) tail at the3′-terminus. The genome order has been determined as5’-Cap-C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-3′. The genome is translated into a single large polyprotein which is processed co-and post-translationally into three structural proteins:nucleocapsid protein (C), membrane protein (M), and envelope glycoprotein (E), as well as seven non-structural proteins: NS1through NS5. Up to now, the completed whole genome sequencing of strains is approximately130in China, GenBank published genome sequence of the JEV strains is only63. The paper about JEV strains isolated from swine is few, there are only five domestic strains. Sequence analysis of the genomic can learn more about the complete genome and molecular evolution regular of JEV strains isolated from swine.In order to learn more about the complete genome and molecular evolution regular of Japanese encephalitis virus (JEV) strains isolated from swine, the full-length genome sequences of three JEV isolates, namely as BSF.ZZ-1, BSF.ZZ-3and CSF.XZ-2D isolated from swine were analyzed in this paper. The results show that the length of the complete genomes of BSF.ZZ-1, BSF.ZZ-3and CSF.XZ-2D was10977nt,10977nt and10976nt, respectively. There is an insert base of "G" at the 10701nt site in the genomes of both BSF.ZZ-1and BSF.ZZ-3. Compared to the virulent strain SA14-14-2, the homologies of nucleotide and amino acid sequences of of BSF.ZZ-1is99.8%and99.1%, respectively. The homologies of nucleotide sequences of CSF.XZ-2D and BSF.ZZ-3are99.7%, and the homologies of amino acid sequences are99.2%and99.1%, respectively. However, compared to the virulent strain SA14, the homologies of nucleotide and amino acid sequences of BSF.ZZ-1, CSF.XZ-2D and BSF.ZZ-3are99.4%and99.0%, respectively. Compared to the isolates HW(HW1), HWe(HW2) and SH0601from swine, the homologies of the present three isolates are all more than98.0%. Phylogenetic analysises with other30reference isolates covering all five JEV genotypes indicated that BSF.ZZ-1, CSF.XZ-2D and BSF.ZZ-3located in a same evolutionary branch, belonging to the genotype Ⅲ.