Skip Navigation


Bioinformatics Advance Access first published online on July 10, 2007
This version published online on July 18, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm354
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary data
Right arrowOA All Versions of this Article:
23/18/2368    most recent
btm354v2
btm354v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Wan, X.-F.
Right arrow Articles by Donis, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wan, X.-F.
Right arrow Articles by Donis, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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,¶, Guorong Chen 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@muohio.edu

Associate Editor: Prof. Keith Crandall

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Gen. Virol.Home page
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]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.