Japanese Encephalitis Virus Genotype Replacement, Taiwan, 2009–2010

Yi-Ying Chen¹, Yi-Chin Fan¹, Wu-Chun Tu¹, Rey-Yi Chang, Chen-Chang Shih, In-Houng Lu, Maw-Shien Chien, Wei-Cheng Lee, Ter-Hsin Chen, Gwong-Jen Chang, and Shyan-Song Chiou

Author affiliations: National Chung Hsing University, Taichung, Taiwan (Y.-Y. Chen, Y.-C. Fan, W.-C. Tu, M.-S. Chien, W.-C. Lee, T.-H. Chen, S.-S. Chiou); National Dong Hwa University, Hualien, Taiwan (R.-Y. Chang, I.-H. Lu); Mennonite Christian Hospital, Hualien (C.-C. Shih); Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (G.-J. Chang)

Abstract

Genotype I of Japanese encephalitis virus first appeared in Taiwan in 2008. Phylogenetic analysis of 37 viruses from pig farms in 2009–2010 classified these viruses into 2 unique subclusters of genotype I viruses and suggested multiple introductions and swift replacement of genotype III by genotype I virus in Taiwan.

Japanese encephalitis virus (JEV), a mosquito-borne flavivirus, is a common cause of viral encephalitis in southern and eastern Asia. Pigs are a readily available virus amplifying host, and Culex tritaeniorhynchus mosquitoes, the primary transmission vector of JEV, breed predominantly in rice paddies (1). Molecular epidemiologic studies have found that the introduction of JEV into subtropical regions from tropical regions, possibly associated with the Pacific flyway of spring migratory birds, may contribute to annual JEV epidemics and epizootics in subtropical regions (2).

Phylogenetic reconstruction, based on capsid and precursor membrane or envelope (E) structural protein genes of JEV, supports an Indonesian origin and further classifies JEV into 6 genotypes (3,4). The genotype III (GIII) virus is most widely distributed in the temperate zone and is the genotype most frequently associated with JEV outbreaks and epidemics in eastern and Southeast Asian countries (4). Genotype I (GI) JEV, which originated in Indonesia and circulated in Thailand and Cambodia during the 1970s, appeared in South Korea and Japan during the 1990s. The replacement of GIII by GI was swift, completed in just a few years in Japan, South Korea, Thailand, and Vietnam (2,5–7). The introduction of GI JEV into Japan may have followed a south-to-north or west-to-east route and has been reported to have come from Southeast Asia and mainland People’s Republic of China (8). However, events leading to replacement, including introduction, transition dynamics, and interplay between the 2 virus genotypes, are still unclear. The only 2 remaining GI-free island countries, the Philippines and Taiwan, provide a location where the transmission dynamics of these 2 JEV genotypes can be elucidated. GI JEV was first detected in northern Taiwan during the winter of 2008 by the Centers for Disease Control, Taiwan (CDC-Taiwan) (9); however, GIII JEV remained the dominant virus in Taiwan that year.

Suggested citation for this article: Chen Y-Y, Fan Y-C, Tu W-C, Chang R-Y, Shih C-C, Lu I-H, et al. Japanese encephalitis virus genotype replacement, Taiwan, 2009–2010. Emerg Infect Dis [serial on the Internet] 2011 Dec [date cited]. http://dx.doi.org/10.3201/eid1712.110914