Alignment free characterization of the influenza-A hemagglutinin genes by the ISSCOR method

C R Biol. 2012 Mar;335(3):180-93. doi: 10.1016/j.crvi.2012.01.001. Epub 2012 Feb 24.

Abstract

Analyses and visualizations by the ISSCOR method of the influenza virus hemagglutinin genes of three different A-subtypes revealed some rather striking temporal (for A/H3N3), and spatial relationships (for A/H5N1) between groups of individual gene subsets. The application to the A/H1N1 set revealed also relationships between the seasonal H1, and the swine-like novel 2009 H1v variants in a quick and unambiguous manner. Based on these examples we consider the application of the ISSCOR method for analysis of large sets of homologous genes as a worthwhile addition to a toolbox of genomics-it allows a rapid diagnostics of trends, and possibly can even aid an early warning of newly emerging epidemiological threats.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, Viral / genetics
  • Codon / genetics
  • Computer Simulation
  • Epidemiologic Methods
  • Genes, Viral / genetics*
  • Genomics / methods*
  • Hemagglutinins, Viral / genetics*
  • Humans
  • Influenza A Virus, H1N1 Subtype / genetics
  • Influenza A Virus, H3N2 Subtype / genetics
  • Influenza A Virus, H5N1 Subtype / genetics
  • Influenza A virus / genetics*
  • Least-Squares Analysis
  • Monte Carlo Method
  • Multigene Family
  • Principal Component Analysis
  • Seasons
  • Stochastic Processes
  • Swine

Substances

  • Antigens, Viral
  • Codon
  • Hemagglutinins, Viral