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Dynamic Models of Infectious Diseases pp 205–225Cite as

Evaluating the Evolutionary Dynamics of Viral Populations

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Abstract

Phylodynamic techniques combine epidemiological and genetic information to analyze the evolutionary and spatiotemporal dynamics of rapidly evolving pathogens, such as influenza A or human immunodeficiency viruses. We introduce allele dynamics plots (AD-plots) as a method for visualizing the evolutionary dynamics of a gene in a population. Using AD-plots, we propose to identify the alleles that are likely to be subject to directional selection. We analyze the method’s merits with a detailed study of the evolutionary dynamics of seasonal influenza A viruses. AD-plots for the major surface protein of seasonal influenza A (H3N2) and the 2009 swine-origin influenza A (H1N1) viruses show the succession of substitutions that became fixed in the evolution of the two viral populations. They also allow the early identification of those viral strains that later rise to predominance, which is important for the problem of vaccine strain selection. In summary, we describe a technique that reveals the evolutionary dynamics of a rapidly evolving population and allows us to identify alleles and associated genetic changes that might be under directional selection. The method can be applied for the study of influenza A viruses and other rapidly evolving species or viruses.

Adapted from: Steinbrück L, McHardy AC (2011) Allele dynamics plots for the study of evolutionary dynamics in viral populations. Nucleic Acids Res 39(1):e4, by permission of Oxford University Press.

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Author information

Authors and Affiliations

  1. Max Planck Institut Informatik, Saarbrücken, Germany

    Lars Steinbrück

  2. Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123, Saarbrücken, Germany

    Alice Carolyn McHardy

  3. Department for Algorithmic Bioinformatics, Heinrich-Heine-University, Universitätsstr. 1, 40225, Düsseldorf, Germany

    Alice Carolyn McHardy

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  1. Lars Steinbrück
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  2. Alice Carolyn McHardy
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Correspondence to Alice Carolyn McHardy .

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Editors and Affiliations

  1. Foundation for Scientific Research and Technological Innovation, Hyderabad, Andhra Pradesh, India

    V. Sree Hari Rao

  2. University of New Mexico School of Medicine, Albuquerque, New Mexico, USA

    Ravi Durvasula

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Steinbrück, L., McHardy, A.C. (2013). Evaluating the Evolutionary Dynamics of Viral Populations. In: Sree Hari Rao, V., Durvasula, R. (eds) Dynamic Models of Infectious Diseases. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9224-5_8

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