title: An agent-based model to study the epidemiological and evolutionary dynamics of Influenza viruses.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA. benjamin.roche@ird.fr
authors: Benjamin
authors: B
authors: Roche
authors: John M
authors: JM
authors: Drake
authors: Pejman
authors: P
authors: Rohani
mesh_terms: D005075:Biological Evolution; D006801:Humans; D009980:Influenza A virus / Q000235:genetics*; D007251:Influenza, Human / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D008954:Models, Biological; D015203:Reproducibility of Results