Article | Published:

Neutralization mechanism of human monoclonal antibodies against Rift Valley fever virus

Abstract

Rift Valley fever virus (RVFV) is a mosquito-borne pathogen that causes substantial morbidity and mortality in livestock and humans. To date, there are no licensed human vaccines or therapeutics available. Here, we report the isolation of monoclonal antibodies from a convalescent patient, targeting the RVFV envelope proteins Gn and Gc. The Gn-specific monoclonal antibodies exhibited much higher neutralizing activities in vitro and protection efficacies in mice against RVFV infection, compared to the Gc-specific monoclonal antibodies. The Gn monoclonal antibodies were found to interfere with soluble Gn binding to cells and prevent infection by blocking the attachment of virions to host cells. Structural analysis of Gn complexed with four Gn-specific monoclonal antibodies resulted in the definition of three antigenic patches (A, B and C) on Gn domain I. Both patches A and B are major neutralizing epitopes. Our results highlight the potential of antibody-based therapeutics and provide a structure-based rationale for designing vaccines against RVFV.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Data availability

The crystal structures of Gn complexed with the Fab form of the monoclonal antibodies R12, R13 and R15 and the scFv of R17 have been deposited in the Protein Data Bank under accession codes 6IEK, 6IEA, 6IEB and 6IEC, respectively. The data that support the findings of this study are available from the corresponding author upon request.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

References

  1. 1.

    Daubney, R., Hudson, J. R. & Garnham, P. C. Enzootic hepatitis or Rift Valley fever. An undescribed virus disease of sheep cattle and man from East Africa. J. Pathol. Bacteriol. 34, 545–579 (1931).

  2. 2.

    Nanyingi, M. O. et al. A systematic review of Rift Valley Fever epidemiology 1931–2014. Infect. Ecol. Epidemiol. 5, 28024 (2015).

  3. 3.

    Rift Valley Fever (RVF). World Organisation for Animal Health http://www.oie.int/en/animal-health-in-the-world/animal-diseases/rift-valley-fever (2019).

  4. 4.

    Rift Valley Fever. World Health Organization http://www.who.int/csr/don/archive/disease/rift_valley_fever/en/ (2018).

  5. 5.

    Shoemaker, T. et al. Genetic analysis of viruses associated with emergence of Rift Valley fever in Saudi Arabia and Yemen, 2000–01. Emerg. Infect. Dis. 8, 1415–1420 (2002).

  6. 6.

    Liu, J. et al. The first imported case of Rift Valley fever in China reveals a genetic reassortment of different viral lineages. Emerg. Microbes Infect. 6, e4 (2017).

  7. 7.

    Mansfield, K. L. et al. Rift Valley fever virus: A review of diagnosis and vaccination, and implications for emergence in Europe. Vaccine 33, 5520–5531 (2015).

  8. 8.

    Adams, M. J. et al. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017). Arch. Virol. 162, 2505–2538 (2017).

  9. 9.

    Knipe, D. M. & Howley, P. M. Fields Virology 6th edn (Wolters Kluwer/Lippincott Williams & Wilkins Health, 2013).

  10. 10.

    de Boer, S. M. et al. Acid-activated structural reorganization of the Rift Valley fever virus Gc fusion protein. J. Virol. 86, 13642–13652 (2012).

  11. 11.

    Dessau, M. & Modis, Y. Crystal structure of glycoprotein C from Rift Valley fever virus. Proc. Natl Acad. Sci. USA 110, 1696–1701 (2013).

  12. 12.

    Zhu, Y. et al. The post-fusion structure of the Heartland virus Gc glycoprotein supports taxonomic separation of the bunyaviral families Phenuiviridae and Hantaviridae. J. Virol. 92, e01558–01517 (2017).

  13. 13.

    Wu, Y. et al. Structures of phlebovirus glycoprotein Gn and identification of a neutralizing antibody epitope. Proc. Natl Acad. Sci. USA 114, E7564–E7573 (2017).

  14. 14.

    Halldorsson, S. et al. Shielding and activation of a viral membrane fusion protein. Nat. Commun. 9, 349 (2018).

  15. 15.

    Huiskonen, J. T., Overby, A. K., Weber, F. & Grunewald, K. Electron cryo-microscopy and single-particle averaging of Rift Valley fever virus: evidence for GN–GC glycoprotein heterodimers. J. Virol. 83, 3762–3769 (2009).

  16. 16.

    Lagerqvist, N. et al. Characterisation of immune responses and protective efficacy in mice after immunisation with Rift Valley Fever virus cDNA constructs. Virol. J. 6, 6 (2009).

  17. 17.

    de Boer, S. M. et al. Rift Valley fever virus subunit vaccines confer complete protection against a lethal virus challenge. Vaccine 28, 2330–2339 (2010).

  18. 18.

    Wallace, D. B. et al. Protective immune responses induced by different recombinant vaccine regimes to Rift Valley fever. Vaccine 24, 7181–7189 (2006).

  19. 19.

    Faburay, B. et al. A recombinant Rift Valley fever virus glycoprotein subunit vaccine confers full protection against Rift Valley fever challenge in sheep. Sci. Rep. 6, 27719 (2016).

  20. 20.

    Papin, J. F. et al. Recombinant Rift Valley fever vaccines induce protective levels of antibody in baboons and resistance to lethal challenge in mice. Proc. Natl Acad. Sci. USA 108, 14926–14931 (2011).

  21. 21.

    Heise, M. T. et al. An alphavirus replicon-derived candidate vaccine against Rift Valley fever virus. Epidemiol. Infect. 137, 1309–1318 (2009).

  22. 22.

    Wang, Q. et al. Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus. Sci. Transl. Med. 8, 369ra179 (2016).

  23. 23.

    Smith, D. R. et al. The pathogenesis of Rift Valley fever virus in the mouse model. Virology 407, 256–267 (2010).

  24. 24.

    Gao, G. F. From "A"IV to "Z"IKV: Attacks from emerging and re-emerging pathogens. Cell 172, 1157–1159 (2018).

  25. 25.

    Shi, Y., Wu, Y., Zhang, W., Qi, J. & Gao, G. F. Enabling the ‘host jump’: structural determinants of receptor-binding specificity in influenza A viruses. Nat. Rev. Microbiol. 12, 822–831 (2014).

  26. 26.

    Hofmann, H. et al. Severe fever with thrombocytopenia virus glycoproteins are targeted by neutralizing antibodies and can use DC-SIGN as a receptor for pH-dependent entry into human and animal cell lines. J. Virol. 87, 4384–4394 (2013).

  27. 27.

    Yamashita, T. et al. Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure. Proc. Natl Acad. Sci. USA 106, 12986–12991 (2009).

  28. 28.

    Nderitu, L. et al. Sequential Rift Valley fever outbreaks in eastern Africa caused by multiple lineages of the virus. J. Infect. Dis. 203, 655–665 (2011).

  29. 29.

    Bird, B. H., Khristova, M. L., Rollin, P. E., Ksiazek, T. G. & Nichol, S. T. Complete genome analysis of 33 ecologically and biologically diverse Rift Valley fever virus strains reveals widespread virus movement and low genetic diversity due to recent common ancestry. J. Virol. 81, 2805–2816 (2007).

  30. 30.

    Frank, A. L., Six, H. R. & Marchini, A. Human monoclonal antibodies to influenza virus: IgG subclass and light chain distribution. Viral Immunol. 2, 31–36 (1989).

  31. 31.

    Kirchenbaum, G. A., Allen, J. D., Layman, T. S., Sautto, G. A. & Ross, T. M. Infection of ferrets with influenza virus elicits a light chain-biased antibody response against hemagglutinin. J. Immunol. 199, 3798–3807 (2017).

  32. 32.

    Kraus, A. A., Messer, W., Haymore, L. B. & De Silva, A. M. Comparison of plaque- and flow cytometry-based methods for measuring dengue virus neutralization. J. Clin. Microbiol. 45, 3777–3780 (2007).

  33. 33.

    Chen, M. et al. A flow cytometry-based assay to assess RSV-specific neutralizing antibody is reproducible, efficient and accurate. J. Immunol. Methods 362, 180–184 (2010).

  34. 34.

    Schmaljohn, C. S. et al. Baculovirus expression of the M genome segment of Rift Valley fever virus and examination of antigenic and immunogenic properties of the expressed proteins. Virology 170, 184–192 (1989).

  35. 35.

    Keegan, K. & Collett, M. S. Use of bacterial expression cloning to define the amino-acid-sequences of antigenic determinants on the G2-glycoprotein of Rift-Valley fever virus. J. Virol. 58, 263–270 (1986).

  36. 36.

    Zhang, Q. et al. Potent neutralizing monoclonal antibodies against Ebola virus infection. Sci. Rep. 6, 25856 (2016).

  37. 37.

    Liao, H. X. et al. High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies. J. Virol. Methods 158, 171–179 (2009).

  38. 38.

    Ehrenmann, F., Kaas, Q. & Lefranc, M. P. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res. 38, D301–D307 (2010).

  39. 39.

    Zhang, W. et al. Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus. Protein Cell 1, 459–467 (2010).

  40. 40.

    Zhou, M. et al. Screening and identification of severe acute respiratory syndrome-associated coronavirus-specific CTL epitopes. J. Immunol. 177, 2138–2145 (2006).

  41. 41.

    Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

  42. 42.

    Read, R. J. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D 57, 1373–1382 (2001).

  43. 43.

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

  44. 44.

    Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

  45. 45.

    Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).

Download references

Acknowledgements

We thank G. Salazar (University of Texas Health Science Center at Houston) for her critical editing of the manuscript. We acknowledge L. Zhang and Q. Zhang (Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University) for their instruction and help with isolating single B cells. We thank the staff of the BL19U1 beamline at Shanghai Synchrotron Radiation Facility (Shanghai, People’s Republic of China) for assistance during data collection. We are grateful to J. Jia (Institute of Biophysics, Chinese Academy of Sciences) for technical support of BDAria II manipulation and Y. Chen and Z. Yang (Institute of Biophysics, Chinese Academy of Sciences) for technical help with BIAcore experiments. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDB29040201), the National Science and Technology Major Projects for ‘Major New Drugs Innovation and Development’ (grant no. 2018ZX09711003-002-001), the National Science and Technology Major Project (grant nos. 2016ZX10004222-008 and 2018ZX10101004-001), the External Cooperation Program of CAS (153211KYSB20160001) and the National Natural Science Foundation of China (NSFC, grant nos. 31872745, 31502078 and 81502972). Y.S. is supported by the National Science and Technology Major Project (grant no. 2018ZX10101004-001). G.F.G. is also supported by the External Cooperation Program of CAS (grant no. 153211KYSB20160001). Q.W. is supported by Young Elite Scientist Sponsorship Program by China Association for Science and Technology (grant no. 2015QNRC001), the Youth Innovation Promotion Association CAS (grant no. 2018119) and the grant from China Scholarship Council (grant no. 201704910327). Y.W. is supported by the Youth Innovation Promotion Association CAS (grant no. 2016086). J.Y. and G.F.G. are supported by the foundation of the NSFC Innovative Research Group (grant no. 81621091).

Author information

Q.W., Z.T., G.F.G. and J.Y. initiated and coordinated the project. Q.W., Y.W., Z.T., G.F.G. and J.Y. designed the experiments. Q.W., T.M., Y.W., Z.T. and H.Y. conducted the experiments with the assistance of Z.Z., L.W., R.S. and M.Y. F.G., J.Q. and Y.C. collected the crystallographic data and solved the structures. Z.C. and H.Z. coordinated the isolation of peripheral blood mononuclear cells from the RVFV patient. M.L., C.Q., G.F.G. and J.Y. coordinated the viral experiments. T.M. and G.W. manipulated the viruses with the help of Y.B., J.S. and H.J. Q.W., Y.W., Z.T., Z.A., Y.S., G.F.G. and J.Y. analysed the data. Q.W. wrote the manuscript. Y.W., G.W., Z.A., J.W., T.D.Y., Y.S., W.J.L., G.F.G. and J.Y. helped revise the manuscript.

Competing interests

The authors declare no competing interests.

Correspondence to George F. Gao or Jinghua Yan.

Supplementary information

Supplementary Information

Supplementary Tables 1–4, Supplementary Figures 1–14, Supplementary References and the legend for the Supplementary Dataset.

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark
Fig. 1: Binding characteristics of RVFV monoclonal antibodies.
Fig. 2: Protection potency of monoclonal antibodies against RVFV infection in vitro and in vivo.
Fig. 3: Interference of Gn–cell and RVFV–cell interactions by Gn monoclonal antibodies.
Fig. 4: Molecular determinants of four human neutralizing Gn monoclonal antibodies.
Fig. 5: The detailed atomic interaction at the Gn/monoclonal antibody interface.
Fig. 6: Identification of neutralizing hotspots located on Gn DI.