1. Microbiology and Infectious Disease

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

  1. Fiona Tulloch
  2. Nicky J Atkinson
  3. David J Evans
  4. Martin D Ryan
  5. Peter Simmonds  Is a corresponding author
  1. University of St Andrews, United Kingdom
  2. University of Edinburgh, United Kingdom
  3. University of Warwick, United Kingdom
https://doi.org/10.7554/eLife.04531
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  1. Fiona Tulloch
  2. Nicky J Atkinson
  3. David J Evans
  4. Martin D Ryan
  5. Peter Simmonds
(2014)
RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies
eLife 3:e04531.
https://doi.org/10.7554/eLife.04531
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Abstract

Mutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation efficiency has been advocated as a method to generate safe, attenuated virus vaccines. However, selection for disfavoured CPs leads to unintended increases in CpG and UpA dinucleotide frequencies that also attenuate replication. We designed and phenotypically characterised mutants of the picornavirus, echovirus 7, in which these parameters were independently varied to determine which most influenced virus replication. CpG and UpA dinucleotide frequencies primarily influenced virus replication ability while no fitness differences were observed between mutants with different CP usage where dinucleotide frequencies were kept constant. Contrastingly, translation efficiency was unaffected by either CP usage or dinucleotide frequencies. This mechanistic insight is critical for future rational design of live virus vaccines and their safety evaluation; attenuation is mediated through enhanced innate immune responses to viruses with elevated CpG/UpA dinucleotide frequencies rather the viruses themselves being intrinsically defective.

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Author details

  1. Fiona Tulloch

    School of Biology, University of St Andrews, St Andrews, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  2. Nicky J Atkinson

    Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  3. David J Evans

    School of Life Sciences, University of Warwick, Coventry, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  4. Martin D Ryan

    School of Biology, University of St Andrews, St Andrews, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  5. Peter Simmonds

    Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
    For correspondence
    Peter.Simmonds@ed.ac.uk
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2014, Tulloch et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Fiona Tulloch
  2. Nicky J Atkinson
  3. David J Evans
  4. Martin D Ryan
  5. Peter Simmonds
(2014)
RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies
eLife 3:e04531.
https://doi.org/10.7554/eLife.04531

Share this article

https://doi.org/10.7554/eLife.04531

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Further reading

    1. Microbiology and Infectious Disease

    Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection

    Eleanor Gaunt, Helen M Wise ... Peter Simmonds
    Research Advance Updated

    Previously, we demonstrated that frequencies of CpG and UpA dinucleotides profoundly influence the replication ability of echovirus 7 (Tulloch et al., 2014). Here, we show that that influenza A virus (IAV) with maximised frequencies of these dinucleotides in segment 5 showed comparable attenuation in cell culture compared to unmodified virus and a permuted control (CDLR). Attenuation was also manifested in vivo, with 10-100 fold reduced viral loads in lungs of mice infected with 200PFU of CpG-high and UpA-high mutants. However, both induced powerful inflammatory cytokine and adaptive (T cell and neutralising antibody) responses disproportionate to their replication. CpG-high infected mice also showed markedly reduced clinical severity, minimal weight loss and reduced immmunopathology in lung, yet sterilising immunity to lethal dose WT challenge was achieved after low dose (20PFU) pre-immunisation with this mutant. Increasing CpG dinucleotide frequencies represents a generic and potentially highly effective method for generating safe, highly immunoreactive vaccines.