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Tracking virus outbreaks in the twenty-first century

Nature Microbiology volume 4, pages 10–19 (2019)Cite this article

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Abstract

Emerging viruses have the potential to impose substantial mortality, morbidity and economic burdens on human populations. Tracking the spread of infectious diseases to assist in their control has traditionally relied on the analysis of case data gathered as the outbreak proceeds. Here, we describe how many of the key questions in infectious disease epidemiology, from the initial detection and characterization of outbreak viruses, to transmission chain tracking and outbreak mapping, can now be much more accurately addressed using recent advances in virus sequencing and phylogenetics. We highlight the utility of this approach with the hypothetical outbreak of an unknown pathogen, ‘Disease X’, suggested by the World Health Organization to be a potential cause of a future major epidemic. We also outline the requirements and challenges, including the need for flexible platforms that generate sequence data in real-time, and for these data to be shared as widely and openly as possible.

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Fig. 1: Outbreak scenarios and the resulting phylogenetic trees of virus genomes from sampled human cases.
Fig. 2: Transmission chain tracking during outbreaks using virus genomics.
Fig. 3: Integration and testing predictors of phylogeographic spread.

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Acknowledgements

We thank G. Dudas and S. Knemeyer for help with figure creation. N.D.G. is supported by NIH training grant 5T32AI007244-33. P.L. and A.R. acknowledge funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725422-ReservoirDOCS) and from the Wellcome Trust Collaborative Award (grant number 206298/Z/17/Z—ARTICnetwork). P.L. acknowledges support by the Research Foundation—Flanders (‘Fonds voor Wetenschappelijk Onderzoek - Vlaanderen’, G066215N, G0D5117N and G0B9317N). O.G.P. is supported by the European Union’s Seventh Framework Programme (FP7/2007-2013)/European Research Council (614725-PATHPHYLODYN) and by the Oxford Martin School. E.C.H. is supported by an ARC Australian Laureate Fellowship (FL170100022). K.G.A. is a Pew Biomedical Scholar, and is supported by NIH NCATS CTSA UL1TR002550, NIAID contract HHSN272201400048C, NIAID R21AI137690, NIAID U19AI135995, and The Ray Thomas Foundation.

Author information

Authors and Affiliations

  1. Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA

    Nathan D. Grubaugh & Kristian G. Andersen

  2. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA

    Nathan D. Grubaugh

  3. Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA

    Jason T. Ladner

  4. Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium

    Philippe Lemey

  5. Department of Zoology, University of Oxford, Oxford, UK

    Oliver G. Pybus

  6. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

    Andrew Rambaut

  7. Fogarty International Center, National Institutes of Health, Bethesda, MD, USA

    Andrew Rambaut

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

    Edward C. Holmes

  9. Scripps Research Translational Institute, La Jolla, CA, USA

    Kristian G. Andersen

Authors
  1. Nathan D. Grubaugh
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  2. Jason T. Ladner
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  3. Philippe Lemey
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  4. Oliver G. Pybus
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  5. Andrew Rambaut
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  6. Edward C. Holmes
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  7. Kristian G. Andersen
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Contributions

All listed authors have contributed to the conceptualization, writing and preparation of the manuscript.

Corresponding authors

Correspondence to Jason T. Ladner, Andrew Rambaut or Edward C. Holmes.

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The authors declare no competing interests.

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Grubaugh, N.D., Ladner, J.T., Lemey, P. et al. Tracking virus outbreaks in the twenty-first century. Nat Microbiol 4, 10–19 (2019). https://doi.org/10.1038/s41564-018-0296-2

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