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Epidemiology as Related to the Phylogenetic Analysis of the Evolution of the Influenza Virus

The evolution of the influenza virus is characterized by continual changes to its surface structures due to antigenic drift and antigenic shift. The host immune system must alter antibodies in response to the ever-changing virus allowing for the persistence of influenza in a host population. The spread of related strains through a susceptible population with regard to their phylogenetic distance from a parental strain during a season is examined, as well as the within host dynamics. Very little work has been done to integrate phylogenetic analysis of evolution with the epidemiological spread of the influenza virus. In this study, an attempt is made to couple these two scale by using infection rates that are defined as functions of phylogenetic distances between strains. Competition between strains is focused on and strain prevalence for outbreaks during several seasons (2000-2004, inclusive) is examined at various levels: global, regional, and for New York City. Coexistence is found to only be possible between very similar strains, otherwise competitive exclusion or extinction of all strains occurs. Stochastic simulations at the cellular level indicate that the immune system is most effective when the virus has little variability, so the rapid mutation of influenza is an effective strategy in evading the immune system. Similar simulations for the population level show that a strain's prevalence depends largely on the effect on the antigenic structure as a result of the locations of amino acid mutations.

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Amanda Criner, University of Maine
Brandon Hale, Murray State University
Lorena Morales-Paredes, University of Alabama at Huntsville
David Roy Estrella Segura, Arizona State University
Ariel Cintron-Arias, Cornell University