title: Molecular epidemiology of Japanese encephalitis in northern Vietnam, 1964-2011: genotype replacement.
abstract: BACKGROUND
  Japanese encephalitis virus (JEV) is an arthropod-borne virus causing serious public health issues in Asia. JEV consists of five genotypes and recent studies have shown the emergence of JEV genotype I (GI) and its replacement of genotype III (GIII). Using an archival JEV collection, we investigated the molecular evolution of JEV in Vietnam over the last 48 years (1964-2012) in humans, mosquitoes, and pigs, within the global context.
  
  
  METHODS
  The nine JEV isolates from humans, pigs, and mosquitoes sequenced in this study and 29 sequences available in GenBank were used to analyze the envelope (E) protein of the Vietnamese JEVs. A collection of 225 cerebrospinal fluid specimens from patients with suspected Japanese encephalitis (JE) was also tested and genotyped with real-time RT-PCR.
  
  
  RESULTS
  The 38 E genes identified with sequencing and nine Vietnamese JEV strains genotyped with real-time RT-PCR, belonging to two lineages, evolved in accordance with those in the rest of the world. The first GIII strain was detected in humans in Vietnam in 1964, and in mosquitoes in 1979, whereas GI strains were first detected in humans and mosquitoes in 1990 and 1994, respectively. After 2004, GI was the only genotype detected in Vietnam, demonstrating that the GIIII strains had been displaced by GI strains. Five haplotypes were identified in the Vietnamese JEVs, with SKSS predominant. The S123N and S123R substitutions in the E protein were already present in the Vietnamese JEVs.
  
  
  CONCLUSIONS
  This study describes the long evolutionary history of JEV in Vietnam over 34 years, which correlates well with the global evolution of JEV. The Vietnamese GIII strains have been replaced by GI strains in mosquitoes, pigs, and humans. The predominant haplotypes of the Vietnamese strains support this genotype displacement in Vietnam. Further surveillance is required to confirm the disappearance of the GIII strains in nature and the emergence of new pathogens causing encephalitis in Vietnam, after the long-term use of JEV vaccines in that country.
authors.affiliation: National Institute of Hygiene and Epidemiology, Hanoi, 10000, Vietnam. loankobe@gmail.com.
authors.forename: Loan Phuong
authors.initials: LP
authors.lastname: Do
authors.affiliation: National Institute of Hygiene and Epidemiology, Hanoi, 10000, Vietnam. trangminhbui3007@gmail.com.
authors.forename: Trang Minh
authors.initials: TM
authors.lastname: Bui
authors.affiliation: Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan. rainbow@nagaski-u.ac.jp.
authors.forename: Futoshi
authors.initials: F
authors.lastname: Hasebe
authors.affiliation: Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan. moritak@nagasaki-u.ac.jp.
authors.forename: Kouichi
authors.initials: K
authors.lastname: Morita
authors.affiliation: National Institute of Hygiene and Epidemiology, Hanoi, 10000, Vietnam. pnga_arboviruses@yahoo.com.
authors.forename: Nga Thi
authors.initials: NT
authors.lastname: Phan
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D009033:Culicidae / Q000821:virology*; D004664:Encephalitis Virus, Japanese / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D004672:Encephalitis, Japanese / Q000453:epidemiology* / Q000662:veterinary / Q000821:virology; D019143:Evolution, Molecular; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008562:Membrane Glycoproteins / Q000235:genetics; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013552:Swine / Q000821:virology*; D014744:Vietnam / Q000453:epidemiology; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D008562:Membrane Glycoproteins; D012367:RNA, Viral; D014759:Viral Envelope Proteins; C080628:glycoprotein E, Japanese encephalitis virus