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Open Access Highly Accessed Methodology

Detecting transmission and reassortment events for influenza A viruses with genotype profile method

Changzheng Dong*, Liya Ying and Dongfang Yuan

Author Affiliations

School of Medicine, Ningbo University, Ningbo, 315211, China

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Virology Journal 2011, 8:395  doi:10.1186/1743-422X-8-395

Published: 9 August 2011

Abstract

Evolutionary events of transmission and reassortment for influenza A viruses were traditionally detected by phylogenetic analysis for influenza viruses' eight gene segments. Because the phylogenetic analysis can be complex, we developed genotype profile method which packaged the phylogenetic algorithms to analyze combination patterns of gene segments and integrated epidemiology knowledge. With the method, the analysis of reassortment and transmission becomes a simple and reliable process that combines genotypes, which is identical for the biological process of the virus. An application called IVEE that implements the method is available for all academic users to apply the method http://snptransformer.sourceforge.net webcite. Furthermore, we found that a previous summary of the reassortment events in swine influenza A viruses may be inaccurate.

Keywords:
influenza A virus; genotype; genotype profile method; reassortment; transmission; phylogenetic analysis; gene segment; IVEE