Molecular evidence of Japanese encephalitis virus in poultry: Need to further elucidate JEV epidemiology.

Japanese encephalitis (JE) is a re-emerging viral zoonotic disease transmitted primarily by the bite of infected Culex mosquitoes with ardeid birds as reservoir host for JE virus (JEV). Swine being the amplifier host have been studied extensively, however the role of domestic poultry in JEV epidemiology remains unexplored. Therefore, the present study was undertaken with the aim of quantifying JE viral load and to identify the circulating genotype of JEV in domestic chicken and duck population of India. A total of 206 chicken and 76 duck samples collected across five JE endemic states of India representing three geographical zones were screened using TaqMan real time RT-PCR targeting JEV envelope gene. Positive samples were further amplified using nested RT-PCR targeting the C/PrM gene of JEV and confirmed by sequencing followed by phylogenetic analysis of the amplified products to infer their genetic relationship with other JEV isolates. A total of 53 chicken samples and 9 duck samples were positive for JEV RNA with viral load ranging from 9 to 1.33 × 10⁵ copies/reaction for chickens and 32 to 1.23 × 10⁴ copies/reaction for ducks. Phylogenetic analysis of the partial C/PrM gene sequences (n = 11) revealed dominance of Genotype III in domestic birds. Two novel amino acid insertions, Serine at C87 and Arginine at C94 positions, were detected in one sequence. The findings of this study suggests that domestic poultry might act as reservoir or amplifier host for the virus, however further studies are required to elucidate their role in JEV transmission to humans.