Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus

Bioinformatics

Volumn 25, Issue 18, 2009, Pages 2309-2317

  Xia, Zhen ^a   Jin, Gulei ^a   Zhu, Jun ^a   Zhou, Ruhong ^a,b,c  

^a ZHEJIANG UNIVERSITY   (China)

^b IBM T J WATSON RESEARCH CENTER   (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; HEMAGGLUTININ;

ALGORITHM; AMINO ACID SEQUENCE; ANTIGENIC MODULATION; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; GENETIC DRIFT; GENETIC REASSORTMENT; INFLUENZA VIRUS A H3N2; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENETIC TREE; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VIRAL GENETICS; VIRUS MUTATION;

EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; HUMANS; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN;

ORTHOMYXOVIRIDAE;

EID: 69849095989     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp423     Document Type: Article

References (43)

1. Bao,Y. et al. (2008) The influenza virus resource at the National Center for Biotechnology Information. J. Virol., 82, 596-601.
2. Bush,R.M. et al. (1999a) Predicting the evolution of human influenza A. Science, 286, 1921-1925.
3. Bush,R.M. et al. (1999b) Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol. Biol. Evol., 16, 1457-1465.
4. Butte,A.J. and Kohane,I.S. (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput., 5, 418-429.
5. Butte,A.J. et al. (2000) Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl Acad. Sci. USA, 97, 12182-12186.
6. Chen,R. and Holmes,E.C. (2006) Avian influenza virus exhibits rapid evolutionary dynamics. Mol. Biol. Evol., 23, 2336-2341.
7. Cox,N.J. and Subbarao,K. (2000) Global epidemiology of influenza: Past and present. Annu. Rev. Med., 51, 407-421.
8. Das,P. et al. (2009) Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity. J. Comput. Chem., 30, 1654-1663.
9. DeLano,W.L. (2008) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.
10. Du,X. et al. (2008) Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution. Genome Res. 18, 178-187.
11. Edgar,R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
12. Faith,J.J. et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol., 5, e8.
13. Fitch,W.M. et al. (1997) Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl Acad. Sci. USA, 94, 7712-7718.
14. Fouchier,R.A. et al. (2005) Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. J. Virol., 79, 2814-2822.
15. Gamblin,S.J. et al. (2004) The structure and receptor binding properties of the 1918 influenza hemagglutinin. Science, 303 1838-1842.
16. Glaser,F. et al. (2003) ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
17. Ha,Y. et al. (2003) X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus. Virology, 309, 209-218.
18. Hilleman,M.R. (2002) Realities and enigmas of human viral influenza: pathogenesis, epidemiology and control. Vaccine, 20, 3068-3087.
19. Holmes,E.C. et al. (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol., 3, e300.
20. Horimoto,T. and Kawaoka,Y. (2005) Influenza: Lessons from past pandemics, warnings from current incidents. Nat. Rev. Microbiol., 3, 591-600.
21. Huelsenbeck,J.P. and Dyer,K.A. (2004) Bayesian estimation of positively selected sites. J. Mol. Evol., 58, 661-672.
22. Koelle,K. et al. (2006) Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science, 314, 1898-1903.
23. Landau,M. et al. (2005) ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, W299-W302.
24. Li,C. and Wong,W.H. (2003) DNA-Chip Analyzer (dChip). Springer, New York.
25. Margolin,A.A. et al. (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7 (Suppl. 1), S7.
26. Nelson,M.I. et al. (2006) Stochastic processes are key determinants of short-term evolution in influenza a virus. PLoS Pathog., 2, e125.
27. Nielsen,R. and Yang,Z. (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929-936.
28. Plotkin,J.B. and Dushoff,J. (2003) Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proc. Natl Acad. Sci. USA, 100, 7152-7157.
29. Rambaut,A. et al. (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature, 453, 615-619.
30. Shih,A.C. et al. (2007) Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc. Natl Acad. Sci. USA, 104, 6283-6288.
31. Smith,D.J. et al. (2004) Mapping the antigenic and genetic evolution of influenza virus. Science, 305, 371-376.
32. Stevens,J. et al. (2006) Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science, 312, 404-410.
33. Suzuki,Y. (2004) New methods for detecting positive selection at single amino acid sites. J. Mol. Evol., 59, 11-19.
34. Suzuki,Y. and Gojobori,T. (1999) A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol., 16, 1315-1328.
35. Tamura,K. et al. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
36. van Nimwegen,E. (2006) Epidemiology. Influenza escapes immunity along neutral networks. Science, 314, 1884-1886.
37. Webster,R.G. et al. (1982) Molecular mechanisms of variation in influenza viruses. Nature, 296, 115-121.
38. Webster,R.G. et al. (1992) Evolution and ecology of influenza A viruses. Microbiol. Rev., 56, 152-179.
39. Weis,W. et al. (1988) Structure of the influenza virus haemagglutinin complexed with its receptor, sialic acid. Nature, 333, 426-431.
40. Weis,W.I. et al. (1990) Refinement of the influenza virus hemagglutinin by simulated annealing. J. Mol. Biol., 212, 737-761.
41. Yang,Z. et al. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 155, 431-449.
42. Yang,Z. and Swanson,W.J. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol., 19, 49-57.
43. Zhou,R. et al. (2008) Single mutation induced h3n2 hemagglutinin antibody neutralization: A free energy perturbation study. J. Phys. Chem. B, 112, 15813-15820.