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An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses

Benjamin Roche12*, John M Drake34 and Pejman Rohani156

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA

2 UMI IRD/UPMC 209 - UMMISCO, 93143, Bondy, France

3 Odum School of Ecology, University of Georgia, Athens, GA 30602, USA

4 Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA

5 Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109 USA

6 Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA

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BMC Bioinformatics 2011, 12:87  doi:10.1186/1471-2105-12-87

Published: 30 March 2011



Influenza A viruses exhibit complex epidemiological patterns in a number of mammalian and avian hosts. Understanding transmission of these viruses necessitates taking into account their evolution, which represents a challenge for developing mathematical models. This is because the phrasing of multi-strain systems in terms of traditional compartmental ODE models either requires simplifying assumptions to be made that overlook important evolutionary processes, or leads to complex dynamical systems that are too cumbersome to analyse.


Here, we develop an Individual-Based Model (IBM) in order to address simultaneously the ecology, epidemiology and evolution of strain-polymorphic pathogens, using Influenza A viruses as an illustrative example.


We carry out careful validation of our IBM against comparable mathematical models to demonstrate the robustness of our algorithm and the sound basis for this novel framework. We discuss how this new approach can give critical insights in the study of influenza evolution.