Virologica Sinica

, Volume 30, Issue 4, pp 277–289 | Cite as

Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases

  • Na Han
  • James Adams
  • Wei Fang
  • Si-Qing Liu
  • Simon RaynerEmail author
Research Article


Japanese encephalitis is a mosquito borne disease and is the leading cause of viral encephalitis in the Asia-Pacific area. The causative agent, Japanese encephalitis virus (JEV) can be phylogenetically classified into five genotypes based on nucleotide sequence. In recent years, genotype I (GI) has displaced genotype III (GIII) as the dominant lineage, but the mechanisms behind this displacement event requires elucidation. In an earlier study, we compared host variation over time between the two genotypes and observed that GI appears to have evolved to achieve more efficient infection in hosts in the replication cycle, with the tradeoff of reduced infectivity in secondary hosts such as humans. To further investigate this phenomenon, we collected JEV surveillance data on human cases and, together with sequence data, and generated genotype/case profiles from seven Asia-Pacific countries and regions to characterize the GI/GIII displacement event. We found that, when comprehensive and consistent vaccination and surveillance data was available, and the GIII to GI shift occurred within a well-defined time period, there was a statistically significant drop in JEV human cases. Our findings provide further support for the argument that GI is less effective in infecting humans, who represent a dead end host. However, experimental investigation is necessary to confirm this hypothesis. The study highlights the value of alternative approaches to investigation of epidemics, as well as the importance of effective data collection for disease surveillance and control.


flavivirus Japanese encephalitis virus (JEV) bioinformatics epidemiology lineage replacement 


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Copyright information

© Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Na Han
    • 3
    • 4
  • James Adams
    • 2
  • Wei Fang
    • 1
  • Si-Qing Liu
    • 1
  • Simon Rayner
    • 1
    • 2
    Email author
  1. 1.Department of Medical GeneticsOslo University HospitalOsloNorway
  2. 2.State Key Laboratory of Virology, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
  3. 3.State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
  4. 4.Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesHangzhouChina

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