Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Live attenuated influenza virus vaccines by computer-aided rational design

Nature Biotechnology volume 28, pages 723–726 (2010)Cite this article

Subjects

Abstract

Despite existing vaccines and enormous efforts in biomedical research, influenza annually claims 250,000–500,000 lives worldwide1, motivating the search for new, more effective vaccines that can be rapidly designed and easily produced. We applied the previously described synthetic attenuated virus engineering (SAVE)2 approach to influenza virus strain A/PR/8/34 to rationally design live attenuated influenza virus vaccine candidates through genome-scale changes in codon-pair bias. As attenuation is based on many hundreds of nucleotide changes across the viral genome, reversion of the attenuated variant to a virulent form is unlikely. Immunization of mice by a single intranasal exposure to codon pair–deoptimized virus conferred protection against subsequent challenge with wild-type (WT) influenza virus. The method can be applied rapidly to any emerging influenza virus in its entirety, an advantage that is especially relevant when dealing with seasonal epidemics and pandemic threats, such as H5N1- or 2009-H1N1 influenza.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Characterization in tissue culture of synthetic codon pair–deoptimized influenza viruses.
Figure 2: Attenuation of codon pair–deoptimized influenza virus PR83F in BALB/c mice.
Figure 3: Immune responses and protection.

Similar content being viewed by others

Accession codes

Accessions

NCBI Reference Sequence

References

  1. Salomon, R. & Webster, R.G. The influenza virus enigma. Cell 136, 402–410 (2009).

    Article  CAS  Google Scholar 

  2. Coleman, J.R. et al. Virus attenuation by genome-scale changes in codon-pair bias. Science 320, 1784–1787 (2008).

    Article  CAS  Google Scholar 

  3. Palese, P. & Shaw, M.L. in Field's Virology, vol. 2 (eds. D.M. Knipe et al.) 1647–1689, (Lippincott Williams & Wilkins, Philadelphia, 2007).

  4. Steinhauer, D.A. & Skehel, J.J. Genetics of influenza viruses. Annu. Rev. Genet. 36, 305–332 (2002).

    Article  CAS  Google Scholar 

  5. Maassab, H.F. Adaptation and growth characteristics of influenza virus at 25 degrees c. Nature 213, 612–614 (1967).

    Article  CAS  Google Scholar 

  6. Rimmelzwaan, G.F., Fouchier, R.A. & Osterhaus, A.D. Influenza virus-specific cytotoxic T lymphocytes: a correlate of protection and a basis for vaccine development. Curr. Opin. Biotechnol. 18, 529–536 (2007).

    Article  CAS  Google Scholar 

  7. Sant, A.J. et al. Immunodominance in CD4 T-cell responses: implications for immune responses to influenza virus and for vaccine design. Expert Rev. Vaccines 6, 357–368 (2007).

    Article  CAS  Google Scholar 

  8. Hikono, H. et al. T-cell memory and recall responses to respiratory virus infections. Immunol. Rev. 211, 119–132 (2006).

    Article  CAS  Google Scholar 

  9. Swain, S.L. et al. CD4+ T-cell memory: generation and multi-faceted roles for CD4+ T cells in protective immunity to influenza. Immunol. Rev. 211, 8–22 (2006).

    Article  CAS  Google Scholar 

  10. Simonsen, L. et al. Impact of influenza vaccination on seasonal mortality in the US elderly population. Arch. Intern. Med. 165, 265–272 (2005).

    Article  Google Scholar 

  11. Belshe, R.B., Van Voris, L.P., Bartram, J. & Crookshanks, F.K. Live attenuated influenza A virus vaccines in children: results of a field trial. J. Infect. Dis. 150, 834–840 (1984).

    Article  CAS  Google Scholar 

  12. Belshe, R.B. et al. The efficacy of live attenuated, cold-adapted, trivalent, intranasal influenzavirus vaccine in children. N. Engl. J. Med. 338, 1405–1412 (1998).

    Article  CAS  Google Scholar 

  13. Cello, J., Paul, A.V. & Wimmer, E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297, 1016–1018 (2002).

    Article  CAS  Google Scholar 

  14. Gutman, G.A. & Hatfield, G.W. Nonrandom utilization of codon pairs in Escherichia coli. Proc. Natl. Acad. Sci. USA 86, 3699–3703 (1989).

    Article  CAS  Google Scholar 

  15. Moura, G. et al. Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS ONE 2, e847 (2007).

    Article  Google Scholar 

  16. Wimmer, E., Mueller, S., Tumpey, T.M. & Taubenberger, J.K. Synthetic viruses: a new opportunity to understand and prevent viral disease. Nat. Biotechnol. 27, 1163–1172 (2009).

    Article  CAS  Google Scholar 

  17. Hoffmann, E., Neumann, G., Kawaoka, Y., Hobom, G. & Webster, R.G.A. DNA transfection system for generation of influenza A virus from eight plasmids. Proc. Natl. Acad. Sci. USA 97, 6108–6113 (2000).

    Article  CAS  Google Scholar 

  18. Schickli, J.H. et al. Plasmid-only rescue of influenza A virus vaccine candidates. Phil. Trans. R. Soc. Lond. B 356, 1965–1973 (2001).

    Article  CAS  Google Scholar 

  19. Mueller, S., Papamichail, D., Coleman, J.R., Skiena, S. & Wimmer, E. Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J. Virol. 80, 9687–9696 (2006).

    Article  CAS  Google Scholar 

  20. Shizhen, L . Compendium of Materia Medica (Bencao Gangmu, 1593) (Foreign Language Press, 2004).

  21. Hutchinson, E.C., Curran, M.D., Read, E.K., Gog, J.R. & Digard, P. Mutational analysis of cis-acting RNA signals in segment 7 of influenza A virus. J. Virol. 82, 11869–11879 (2008).

    Article  CAS  Google Scholar 

  22. Wang, Z., Tobler, S., Roayaei, J. & Eick, A. Live attenuated or inactivated influenza vaccines and medical encounters for respiratory illnesses among US military personnel. J. Am. Med. Assoc. 301, 945–953 (2009).

    Article  CAS  Google Scholar 

  23. Coffin, J.M. Attenuation by a thousand cuts. N. Engl. J. Med. 359, 2283–2285 (2008).

    Article  CAS  Google Scholar 

  24. Reed, L.J. & Muench, M. A simple method for estimating fifty percent endpoints. Am. J. Hyg. 27, 493–497 (1938).

    Google Scholar 

  25. Quinlivan, M. et al. Attenuation of equine influenza viruses through truncations of the NS1 protein. J. Virol. 79, 8431–8439 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors are indebted to A. García-Sastre and P. Palese for sharing with us their 8-plasmid system for PR8, antibodies, and information. We thank A. Paul and J. Cello for comments on the manuscript. Supported by National Institutes of Health grants AI075219 and AI15122 (EW) and a TRO-Fusion Award by Stony Brook University (S.M. and S.S.).

Author information

Author notes

  1. J Robert Coleman & Dimitris Papamichail

    Present address: Present addresses: Department of Medicine, Division of Infectious Disease, Albert Einstein College of Medicine, Bronx, New York, USA (J.R.C.) and Department of Computer Science, University of Miami, Coral Gables, Florida, USA (D.P.).,

Authors and Affiliations

  1. Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, USA

    Steffen Mueller, J Robert Coleman, Anjaruwee Nimnual, Bruce Futcher & Eckard Wimmer

  2. Department of Computer Science, Stony Brook University, Stony Brook, New York, USA

    Dimitris Papamichail, Charles B Ward & Steven Skiena

Authors
  1. Steffen Mueller
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J Robert Coleman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dimitris Papamichail
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Charles B Ward
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Anjaruwee Nimnual
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bruce Futcher
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Steven Skiena
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Eckard Wimmer
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

S.M. designed and carried out the majority of the study and wrote the paper. J.R.C. and A.N. carried out experiments contributing to Figures 1c and 2. D.P., C.B.W. and S.S. developed computer design and analysis algorithms. B.F. and E.W. contributed to the design of the study and writing of the paper.

Corresponding author

Correspondence to Steffen Mueller.

Ethics declarations

Competing interests

All authors declare they have a patent pending relating to certain aspects of this work.

Supplementary information

Supplementary Text and Figures

Supplementary Figs. 1–3 (PDF 322 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mueller, S., Coleman, J., Papamichail, D. et al. Live attenuated influenza virus vaccines by computer-aided rational design. Nat Biotechnol 28, 723–726 (2010). https://doi.org/10.1038/nbt.1636

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.1636

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research