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Journal of Mathematical Chemistry

, Volume 51, Issue 8, pp 2238–2255 | Cite as

Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses

  • Vladimir R. Perovic
Original Paper

Abstract

The highly pathogenic avian influenza virus (HPAIV) A subtype H5N1 is causing threat to human health over the years. Phylogenetic analysis is an important tool for analyzing the evolution of influenza. A novel phylogenetic algorithm based on a new protein distance measure derived from the informational spectrum method (ISM) has been presented. The new phylogenetic approach allows assessment of functional evolution of protein sequences. The new ISM-based phylogenetic approach has been found to overcome some drawbacks of other phylogenetic approaches, particularly concerning sensitivity to a single mutation, deletion and the position of the mutation. The ISM-based approach applied to hemagglutinin subunit 1 protein (HA1) of HPAIV A subtype H5N1 viruses in Egypt between 2006 and 2011, revealed clear clustering in two groups, with one growing group of H5N1 viruses after 2009 with increased number of human infections with H5N1. Four group-specific mutations are identified which are important for increased human tropism and the pandemic potential.

Keywords

Protein sequence Phylogenetic analysis H5N1 influenza virus Electron-ion interaction potential Informational spectrum method 

Notes

Acknowledgments

This work was supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia (Grant No. 173001).

Supplementary material

10910_2013_212_MOESM1_ESM.jpg (2.7 mb)
Online Resource 1. Comparison of the standard and ISM-based phylogenetic analyses; High resolution trees are generated the same as in Fig. 3 with more details.
10910_2013_212_MOESM2_ESM.jpg (2.7 mb)
Online Resource 2. High resolution phylogenetic tree constructed using the ISM-based method. HA1 sequences are colored according to years they were isolated.

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Institute of Nuclear Sciences Vinca, Center for Multidisciplinary ResearchUniversity of BelgradeBelgradeSerbia

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