A simple measure of the dynamics of segmented genomes: an application to influenza

  • Authors:

  • Stéphane Aris-Brosou

  • Affiliations:

  • Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON, Canada and Department of Mathematics and Statistics, University of Ottawa

  • Venue:
  • RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
  • Year:
  • 2010

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Abstract

The severity of influenza epidemics, which can potentially become a pandemic, has been very difficult to predict. However, past efforts were focusing on gene-by-gene approaches, while it is acknowledged that the whole genome dynamics contribute to the severity of an epidemic. Here, putting this rationale into action, I describe a simple measure of the amount of reassortment that affects influenza at a genomic scale during a particular year. The analysis of 530 complete genomes of the H1N1 subtype, sampled over eleven years, shows that the proposed measure explains 58% of the variance in the prevalence of H1 influenza in the US population. The proposed measure, denoted nRF, could therefore improve influenza surveillance programs at a minimal cost.