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Bioinformatics Advance Access published online on July 10, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm354
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

A Quantitative Genotype Algorithm Reflecting H5N1 Avian Influenza Niches

Xiu-Feng Wan 1,*,¶, Feng Luo 2, Michael Emch 3 and Ruben Donis 4

1Department of Microbiology, Miami University, Oxford, OH 45056, 2School of Computing, Clemson University, Clemson, SC 29634, 3Department of Geography, University of North Carolina, Chapel Hill, NC 27516, 4Influenza Division, Centers for Disease Prevention and Control, Atlanta, GA 30333.
Current address: Molecular Virology and Vaccine Branch, Influenza Division, Centers for Disease Prevention and Control, Atlanta, GA 30333.

*To whom correspondence should be addressed. Xiu-Feng Wan, E-mail: wanhenry{at}yahoo.com or fvq7{at}cdc.gov


  Abstract

Motivation: Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza prevention and control. Most of the current methods that are available are based on multiple sequence alignment and phylogenetic tree construction, which are time consuming and limited by the number of taxa. Arbitrarily defining genotypes further complicates the interpretation of genotyping results. Methods: In this study, we describe a quantitative influenza genotyping algorithm based on the theory of quasispecies. First, the complete composition vector (CCV) was utilized to calculate the pairwise evolutionary distance between genotypes. Next, Hierarchical Bayesian Modeling using the Gibbs Sampling algorithm was applied to identify the segment genotype threshold, which is used to identify influenza segment genotype through a modularity calculation. The viral genotype was defined by combining eight segment genotypes based on the genetic reassortment feature of influenza A viruses. Results: We applied this method for H5N1 avian influenza viruses and identified 107 niches among 283 viruses with a complete genome set. The diversity of viral genotypes, and their correlation with geographic locations suggests that these viruses form local niches after being introduced to a new ecological environment through poultry trade or bird migration. This novel method allows us to define genotypes in a robust, quantitative, as well as hierarchical manner. Contacts: wanx{at}muohio.edu

Associate Editor: Prof. Keith Crandall

Received on January 24, 2007; revised on June 28, 2007; accepted on July 1, 2007

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Z.-M. Zhao, K. F. Shortridge, M. Garcia, Y. Guan, and X.-F. Wan
Genotypic diversity of H5N1 highly pathogenic avian influenza viruses
J. Gen. Virol., September 1, 2008; 89(9): 2182 - 2193.
[Abstract] [Full Text] [PDF]


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