Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case

DNA Research

Volumn 18, Issue 2, 2011, Pages 125-136

  Iwasaki, Yuki ^a   Abe, Takashi ^a   Wada, Kennosuke ^a   Itoh, Masae ^a   Ikemura, Toshimichi ^a  

^a NAGAHAMA INSTITUTE OF BIO SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

codon usage; influenza virus; oligonucleotide composition; pandemic; self organizing map

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; CODON; GENE CLUSTER; GENE SEQUENCE; HOST; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; NONHUMAN; PANDEMIC INFLUENZA; PREDICTION; SEASONAL INFLUENZA; SEQUENCE ALIGNMENT; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN;

ANIMALS; BASE SEQUENCE; BIRDS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; CODON; GENOME, VIRAL; HOST SPECIFICITY; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA IN BIRDS; INFLUENZA, HUMAN; MODELS, GENETIC; OLIGONUCLEOTIDES; PANDEMICS; REPRODUCIBILITY OF RESULTS; SEASONS; SEQUENCE HOMOLOGY, NUCLEIC ACID; TIME FACTORS;

ANIMALIA; AVES; INFLUENZA A VIRUS; ORTHOMYXOVIRIDAE;

EID: 79954568885     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsr005     Document Type: Article

References (37)

1. Bush, R.M., Bender, CA, Subbarao, K., Cox, N.J. and Fitch, W.M. 1999, Predicting the evolution of human influenza A, Science, 286, 1921-5. (Pubitemid 129515893)
2. Suzuki, Y and Gojobori, T. 1999,A method for detecting positive selection at single amino acid sites, Mol. Biol. Evol., 16, 1315-28. (Pubitemid 29473226)
3. Igarashi, M., Ito, K., Yoshida, R., et al. 2010, Predicting the antigenic structure of the pandemic (H1N1) 2009 influenza virus hemagglutinin, PLoS One, 5, e8553.
4. Nei, M. 1987, Molecular Evolutionary Genetics, Columbia University Press: New York.
5. Kumar, S., Nei, M., Dudley, J. and Tamura, K. 2008, MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences, Brief Bioinform., 9, 299-306. (Pubitemid 351890826)
6. Abe, T., Kanaya, S., Kinouchi, M., et al. 2003, Informatics for unveiling hidden genome signatures, Genome Res., 13, 693-702. (Pubitemid 36511927)
7. Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S. and Ikemura, T. 2005, Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples, DNA Res., 12, 281-90.
8. Kohonen,T. 1982,Self-organized formation of topologi-cally correct feature maps, Biol. Cybern., 43, 59-69.
9. Kohonen, T., Oja, E., Simula, O., Visa, A. and Kangas, J. 1996, Engineering applications of the self-organizing map, Proc IEEE, 84, 1358-84.
10. Karlin, S., Campbell, A.M. and Mrazek, J. 1998, Comparative DNA analysis across diverse genomes, Annu. Rev. Genet., 32, 185-225. (Pubitemid 29045312)
11. Uchiyama, T., Abe, T., Ikemura, T. and Watanabe, K. 2005, Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes, Nat. Biotechnol., 23, 88-93. (Pubitemid 41724630)
12. Hayashi, H., Abe, T., Sakamoto, M., et al. 2005, Direct cloning of genes encoding novel xylanases from human gut, Can. J. Microbiol., 51, 251-9. (Pubitemid 41039390)
13. Kosaka, T., Kato, S., Shimoyama, T., et al. 2008, The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota, Genome Res., 18, 442-8. (Pubitemid 351347087)
14. Wilmes, P., Andersson, A.F., Lefsrud, M.G., et al. 2008, Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal, ISME J., 2, 853-64.
15. Dick, G.J., Andersson, A.F., Baker, B.J., et al. 2009, Community-wide analysis of microbial genome sequence signatures, Genome Biol., 10, R85.
16. Centers for Disease Control and Prevention. 2009, Swine influenza A (H1N1) infection in two children\South California, March-April 2009, Morb. Mortal. Wkly Rep., 58, 400-2.
17. Smith, G.J., Vijaykrishna, D., Bahl, J., et al. 2009, Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic, Nature, 459, 1122-5.
18. Garten, R.J., Davis, C.T., Russell, CA, et al. 2009, Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans, Science, 325, 197-201.
19. Hirahata, M., Abe, T., Tanaka, N., et al. 2006, Genome information broker for viruses, Nucl. Acids Res., 35, D339-42.
20. Bao, Y 2008, The influenza virus resource at the National Center for Biotechnology Information, J. Virol., 82, 596-601.
21. Kanaya, S., Kinouchi, M., Abe, T., et al. 2001, Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome, Gene, 276, 89-99. (Pubitemid 32925263)
22. García-Sastre,A 2001, Inhibition of interferon-mediated antiviral responses by influenza Aviruses and other nega-tive-strand RNAviruses, Virology, 279, 375-84. (Pubitemid 34161101)
23. Voinnet, O. 2005, Induction and suppression of RNA silencing: insights from viral infections, Nat Rev. Genet., 6, 206-20. (Pubitemid 40293031)
24. Nelson, M.I. and Holmes, E.C. 2007, The evolution of epidemic influenza, Nat Rev. Genet., 8, 196-205.
25. Alexey, A. and Moelling, K. 2007, Dicer is involved in protection against influenza A virus infection, J. Gen. Virol., 88, 2627-35. (Pubitemid 47555013)
26. Rabadan, R., Levine, A.J. and Robins, H. 2006, Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes, J. Virol., 80, 11887-91. (Pubitemid 44788900)
27. Wong, E.H., Smith, D.K., Rabadan, R., Peiris, M. and Poon, L.L. 2010, Codon usage bias and the evolution of influenza A viruses, BMC Evol. Biol., 10, 253.
28. Ikemura, T 1981, Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes,J. Mol. Biol., 146, 1-21. (Pubitemid 11144185)
29. Ikemura, T 1985, Codon usage and transfer RNA content in unicellular and multicellular organisms, Mol. Biol. Evol., 2, 1 3-34.
30. Sharp, P.M. and Matassi, G. 1994, Codon usage and genome evolution, Curr. Opin. Gen. Dev., 4, 851-60.
31. Sueoka, N. 1995, Intrastrand parity rules of DNA base composition and usage biases of synonymous codons, J. Mol. Evol., 40, 318-25.
32. Domingo, E. and Holland, J.J. 1997, RNAvirus mutations and fitness for survival, Annu. Rev. Microbiol., 51, 151-78.
33. Greenbaum, B.D., Levine, AJ., Bhanot, G. and Rabadan, R. 2008, Patterns of evolution and host gene mimicry in influenza and other RNAviruses, PLoS Pathog., 4, e1000079.
34. Itzstein, M.V 2007,The war against influenza: discovery and development of sialidase inhibitors, Nat Rev. Drug Discov., 6, 967-74.
35. Le, Q.M., Kiso, M., Someya, K., et al. 2005, Avian flu: isolation of drug-resistant H5N1 virus, Nature, 437, 1108. (Pubitemid 41509341)
36. Fodor, E., Devenish, L., Engelhardt, O.G., et al. 1999, Rescue of influenza A virus from recombinant DNA, J. Virol., 73, 9679-82. (Pubitemid 29487131)
37. Yamada, S., Hatta, M., Staker, B. L., et al.2010, Biological and structural characterization of a host-adapting aminoacid in influenzavirus,PLoS Pathog.,6,e1001034.