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The evolution of Ebola virus: Insights from the 2013–2016 epidemic

Nature volume 538, pages 193–200 (2016)Cite this article

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Abstract

The 2013–2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Here, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution and spread during the epidemic. We provide basic scientists, epidemiologists, medical practitioners and other outbreak responders with an enhanced understanding of the utility and limitations of pathogen genomic sequencing. This will be crucially important in our attempts to track and control future infectious disease outbreaks.

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Figure 1: Evolution of EBOV during the 2013–2016 outbreak showing the extent and location of virus sampling.
Figure 2: Evolutionary rates of EBOV compared to those of other RNA viruses.
Figure 3: Examples of violations of the Ebola virus molecular clock.
Figure 4: Illustration of different measures of genomic variation.

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Acknowledgements

We thank all the African doctors, nurses, scientists, and outbreak responders who worked to control the 2013–2016 EVD epidemic, some of whom tragically died in the process. We also thank the EBOV genome sequence data producers for making their data publicly available, S. Schaffner for suggestions and reading of the manuscript, and L. M. Carvalho for donating evolutionary rate data. E.C.H. is funded by an NHMRC Australia Fellowship (AF30). G.D. is supported by EU (FP7/2007-2013) Grant Agreement no. 278433-PREDEMICS and the Mahan Postdoctoral Fellowship from the Computational Biology Program at Fred Hutchinson Cancer Research Center. A.R. is supported by EU (FP7/2007-2013) Grant Agreement no. 278433-PREDEMICS, H2020 Grant Agreement no. 643476-COMPARE, and a Wellcome Trust Strategic Award (VIZIONS; 093724). K.G.A. is a PEW Biomedical Scholar, and his work is supported by an NIH National Center for Advancing Translational Studies Clinical and Translational Science Award UL1TR001114, and NIAID contract HHSN272201400048C.

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Authors and Affiliations

  1. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, 2006, New South Wales, Australia

    Edward C. Holmes

  2. Fred Hutchinson Cancer Research Center, Seattle, 98109, Washington, USA

    Gytis Dudas

  3. Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK

    Gytis Dudas & Andrew Rambaut

  4. Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3FL, UK

    Andrew Rambaut

  5. Fogarty International Center, National Institutes of Health, MSC 2220 Bethesda, Maryland, 20892, USA

    Andrew Rambaut

  6. Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, San Diego, 92037, California, USA

    Kristian G. Andersen

  7. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, San Diego, 92037, California, USA

    Kristian G. Andersen

  8. Scripps Translational Science Institute, La Jolla, San Diego, 92037, California, USA

    Kristian G. Andersen

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  1. Edward C. Holmes
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Correspondence to Edward C. Holmes or Kristian G. Andersen.

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Nature thanks C. Drosten, P. Lemey, G. Palacios and T. Sadler for their contribution to the peer review of this work.

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Holmes, E., Dudas, G., Rambaut, A. et al. The evolution of Ebola virus: Insights from the 2013–2016 epidemic. Nature 538, 193–200 (2016). https://doi.org/10.1038/nature19790

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