Japanese encephalitis virus (JEV), closely related to dengue, Zika, yellow fever and West Nile viruses, remains neglected and not well characterized1. JEV is the leading causative agent of encephalitis, and is responsible for thousands of deaths each year in Asia. Humoral immunity is essential for protecting against flavivirus infections and passive immunization has been demonstrated to be effective in curing disease2,3. Here, we demonstrate that JEV-specific monoclonal antibodies, 2F2 and 2H4, block attachment of the virus to its receptor and also prevent fusion of the virus. Neutralization of JEV by these antibodies is exceptionally potent and confers clear therapeutic benefit in mouse models. A single 20 μg dose of these antibodies resulted in 100% survival and complete clearance of JEV from the brains of mice. The 4.7 Å and 4.6 Å resolution cryo-electron microscopy structures of JEV–2F2-Fab and JEV–2H4-Fab complexes, together with the crystal structure of 2H4 Fab and our recent near-atomic structure of JEV4, unveil the nature and location of epitopes targeted by the antibodies. Both 2F2 and 2H4 Fabs bind quaternary epitopes that span across three adjacent envelope proteins. Our results provide a structural and molecular basis for the application of 2F2 and 2H4 to treat JEV infection.

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We thank Y. Chen, Z. Yang and B. Zhou for SPR technical support; X. Huang, B. Zhu and Z. Guo for cryo-EM technical support; and M.S. Diamond, S. Lok and D. Stuart for providing comments on the paper. The cryo-EM datasets were collected at the Center for Biological Imaging, Institute of Biophysics; the X-ray diffraction datasets were collected at beam line BL18U of the Shanghai Synchrotron Facility. Work was supported by the Ministry of Science and Technology 973 Project (grant no. 2014CB542800); the National Key Research and Development Program of China (no. 2016YFC1200400); the National Science Foundation, grant no. 81330036, no. 31570717, no. 81171557 and no.81520108019; the Strategic Priority Research Program of the Chinese Academy of Sciences, grant no. XDB08020200; and US NIH grants R01 AI1 12381 and R21 AI09464. X.W. is supported by the Young Elite Scientist sponsorship of CAST and program C of “One Hundred Talented People” of the Chinese Academy of Sciences.

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Author notes

  1. Xiaodi Qiu and Yingfeng Lei contributed equally to this work.


  1. National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing , China

    • Xiaodi Qiu
    • , Pan Yang
    • , Qiang Gao
    • , Nan Wang
    • , Lei Cao
    • , Shuai Yuan
    • , Xiaofang Huang
    • , Junjie Hu
    • , Xiangxi Wang
    •  & Zihe Rao
  2. University of Chinese Academy of Sciences, Beijing, China

    • Xiaodi Qiu
    • , Pan Yang
    •  & Nan Wang
  3. Department of Microbiology, The Fourth Military Medical University, Xian, Shanxi, China

    • Yingfeng Lei
    • , Wenyu Ma
    • , Tianbing Ding
    • , Fanglin Zhang
    • , Xingan Wu
    •  & Zhikai Xu
  4. Sinovac Biotech Co., Ltd, Beijing, China

    • Qiang Gao
  5. State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China

    • Lei Cao
  6. Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China

    • Yongqiang Deng
    •  & Chengfeng Qin
  7. Program in Viruses and Emerging Pathogens, Infectious Diseases Institute; Center for Retrovirus Research, Department of Veterinary Biosciences, Microbial Infection and Immunity, and Microbiology, Ohio State University, Columbus, OH, USA

    • Shan-Lu Liu
  8. Laboratory of Structural BiolspringDE@2017ogy, School of Medicine, Tsinghua University, Beijing, China

    • Zihe Rao


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X.Q., Y.L., P.Y., N.W., Q.G. and X.Wa. performed the experiments; W.M., X.W., T.D. and F.Z. provided the reagents; X.Wa., Y.L., Z.X. and Z.R. designed the study; all authors analysed the data; and X.Wa., Y.L., Z.X., S.-L.L. and Z.R. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Xiangxi Wang or Zhikai Xu or Zihe Rao.

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