an agent-based model to study the epidemiological and evolutionary dynamics of influenza viruses一个基于主体的模型来研究流感病毒的流行病学和演化动力学.pdfVIP

Roche et al. BMC Bioinformatics 2011, 12:87 /1471-2105/12/87 SOFTWARE Open Access An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses Benjamin Roche1,2*, John M Drake3,4 and Pejman Rohani1,5,6 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. 1 Background virus strains [8,2,9,3,10]. The overlap between epidemio- The ecology and evolution of influenza viruses, espe- logical and evolutionary time scales [1], the observed cially in human and avian populations, have received immune drift in human populations [2,3], and the high considerable attention over the last decade [1-3]. It is mutation rate [1] make it essential to integrate a large increasingly recognised that