Importation risks and local transmission of Japanese encephalitis virus in Taiwan

Japanese encephalitis (JE) remains a significant threat to the human, horse, and pig industries throughout the Asia-Pacific region. Emerging genotype V and IV JE virus (JEV) can evade vaccine-induced immunity and exacerbate the disease burden after spreading into JE-naïve or epidemic areas through the movement of mosquitoes, pigs, and birds. This study aimed to assess the risk of viral importation into Taiwan by conducting mosquito-based surveillance. Our phylogenetic results revealed that at least six JEV importation events occurred in Taiwan between 1958 and 2024. Over the past 16 years of mosquito-based surveillance, three imported events of two genotype I (GI) subclusters (Sub I and Sub II) were detected and sustained local transmission in Taiwan from the first identification in 2008 and 2009 to 2024, without evidence of repeated importations. We further identified three distinct evolutionary stages of local GI JEVs: (1) an initial decade (2009-2018) characterized by co-circulation of Sub I and Sub II; (2) a reduction in viral population size, a decline in genetic heterogeneity, and the extinction of Sub II after 2018; and (3) emergence of a novel, dominant Sub I-I cluster bearing the E-V441I substitution in the stem region of envelope (E) protein. Our findings suggest that Taiwan has faced a low risk of JEV importation over the past 67 years. However, when the virus was introduced, it could subsequently establish a long-term circulation and overwinter in Taiwan. These findings underscore the importance of ongoing surveillance of potential JEV overwintering hosts to guide future control strategies.