Archives of Virology

, Volume 152, Issue 1, pp 11–24 | Cite as

The variable codons of H3 influenza A virus haemagglutinin genes

  • M. J. Gibbs
  • P. Wayper
  • M. L. A. Fourment
  • J. T. Wood
  • K. Ohshima
  • J. S. Armstrong
  • A. J. Gibbs


We have analyzed several sets of well-studied haemagglutinin (HA) gene sequences of H3 subtype influenza A viruses to identify codons that are unusually variable, using a simple pairwise sliding window method, DnDscanning. For two of the sets there were results of detailed phylogenetic modeling studies of selection already published. A third set had been the subject of an antigen mapping study, the results of which provide a completely independent benchmark of selected changes in H3 HA genes. Our analyses show that the codons with greatest DnDscan scores (i.e. the most variable) were mostly those reported in the published studies as being positively selected; indeed the DnDscan results matched the antigenic mapping results more closely than did those of the phylogenetic modeling methods. These results suggest that codons under selection can be found even when, as with some sets of virus sequences, a phylogeny is uncertain or cannot be obtained because, for example, the sequences are recombinants, or when selection is not necessarily linked with phylogeny, as in host-switching events. The program DnDscan is available at


Codon Neutral Theory Randomly Evolve Phylogenetic Modeling Window Position 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • M. J. Gibbs
    • 1
  • P. Wayper
    • 1
  • M. L. A. Fourment
    • 1
  • J. T. Wood
    • 2
  • K. Ohshima
    • 3
  • J. S. Armstrong
    • 1
  • A. J. Gibbs
    • 4
  1. 1.School of Botany and Zoology, Faculty of ScienceAustralian National UniversityCanberraAustralia
  2. 2.Statistical Consulting Unit, Graduate Research SchoolAustralian National UniversityCanberraAustralia
  3. 3.Laboratory of Plant Virology, Faculty of AgricultureSaga UniversityJapan
  4. 4.YarralumlaAustralia

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