Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains

BMC Infectious Diseases

Volumn 13, Issue 1, 2013, Pages

  Iwasaki, Yuki ^a   Abe, Takashi ^b   Wada, Yoshiko ^a   Wada, Kennosuke ^a   Ikemura, Toshimichi ^a  

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

^b NIIGATA UNIVERSITY   (Japan)

Author keywords

Big data; Bioinformatics; H1N1 09; Host tropism; Influenza virus; Oligonucleotide composition; Pandemic; Self organization map; Virus invasion; Zoonotic virus

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; BATCH LEARNING SELF ORGANIZING MAP; BIOINFORMATICS; CONTROLLED STUDY; GENETIC PROCEDURES; GENOME ANALYSIS; INFLUENZA VIRUS A; INFLUENZA VIRUS B; NONHUMAN; NUCLEIC ACID ANALYSIS; PREDICTION; PROCESS DEVELOPMENT; SEQUENCE ANALYSIS; SPECIES COMPARISON; STRAIN DIFFERENCE; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS STRAIN;

EID: 84882410631     PISSN: None     EISSN: 14712334     Source Type: Journal    
DOI: 10.1186/1471-2334-13-386     Document Type: Article

References (27)

1. Karlin S, Campbell AM, Mrazek J. Comparative DNA analysis across diverse genomes. Annu Rev Genet 1998, 32:185-225. 10.1146/annurev.genet.32.1.185, 9928479.
2. Gentles AJ, Karlin S. Genome-scale compositional comparisons in eukaryotes. Genome Res 2001, 11:540-546. 10.1101/gr.163101, 311039, 11282969.
3. Kohonen T. Self-organized formation of topologi- cally correct feature maps. Biol Cybern 1982, 43:59-69.
4. Kohonen T, Oja E, Simula O, Visa A, Kangas J. Engineering applications of the self-organizing map. Proc IEEE 1996, 84:1358-1384.
5. Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nishi T, Mori H, Ikemura T. 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 2001, 276:89-99. 10.1016/S0378-1119(01)00673-4, 11591475.
6. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. Informatics for unveiling hidden genome signatures. Genome Res 2003, 13:693-702. 10.1101/gr.634603, 430167, 12671005.
7. Abe T, Sugawara H, Kanaya S, Ikemura T. Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a large-scale Self-Organizing Map constructed with the Earth Simulator. Journal of the Earth Simulator 2006, 6:17-23.
8. Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res 2005, 12:281-290.
9. Centers for Disease Control and Prevention Swine influenza A (H1N1) infection in two children-South California, March-April 2009. Morb Mortal Wkly Rep 2009, 58:400-402. Centers for Disease Control and Prevention.
10. Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009, 459:1122-1125. 10.1038/nature08182, 19516283.
11. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, et al. Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans. Science 2009, 2009(325):197-201.
12. Bush RM, Bende CA, Subbarao K, Cox NJ, Fitch WM. Predicting the evolution of human influenza A. Science 1999, 286:1921-1925. 10.1126/science.286.5446.1921, 10583948.
13. Suzuki Y, Gojobori T. A method for detecting positive selection at single amino acid sites. Mol Biol Evol 1999, 16:1315-1328. 10.1093/oxfordjournals.molbev.a026042, 10563013.
14. Iwasaki Y, Abe T, Wada K, Itoh M, Ikemura T. Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case. DNA Res 2011, 18:125-136. 10.1093/dnares/dsr005, 3077041, 21444341.
15. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. The influenza virus resource at the National Center for Biotechnology Information. J Virol 2008, 82:596-601. 10.1128/JVI.02005-07, 2224563, 17942553.
16. García-Sastre A. Inhibition of interferon-mediated antiviral responses by influenza A viruses and other negative-strand RNA viruses. Virology 2001, 279:375-384. 10.1006/viro.2000.0756, 11162793.
17. Voinnet O. Induction and suppression of RNA silencing: insights from viral infections. Nat Rev Genet 2005, 6:206-220. 10.1038/nrg1555, 15703763.
18. Alexey A, Moelling K. Dicer is involved in protection against influenza A virus infection. J Gen Virol 2007, 88:2627-2635. 10.1099/vir.0.83103-0, 17872512.
19. Rabadan R, Levine AJ, Robins H. Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes. J Virol 2006, 80:11887-11891. 10.1128/JVI.01414-06, 1642607, 16987977.
20. Greenbaum BD, Levine AJ, Bhanot G, Rabadan R. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 2008, 4:e1000079. 10.1371/journal.ppat.1000079, 2390760, 18535658.
21. Berhane Y, Ojkic D, Neufeld J, Leith M, Hisanaga T, Kehler H, Ferencz A, Wojcinski H, Cottam-Birt C, Suderman M, Handel K, Alexandersen S, Pasick J. Molecular characterization of pandemic H1N1 influenza viruses isolated from turkeys and pathogenicity of a human pH1N1 isolate in turkeys. Avian Dis 2010, 54(4):1275-1285. 10.1637/9422-061410-Reg.1, 21313850.
22. Suzuki Y. Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol Biol Evol 2004, 21:2352-2359. 10.1093/molbev/msh249, 15356273.
23. Suzuki Y. Natural selection on the influenza virus genome. Mol Biol Evol 2006, 23:1902-1911. 10.1093/molbev/msl050, 16818477.
24. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 1985, 2:13-34.
25. Domingo E, Holland JJ. RNA virus mutations and fitness for survival. Annu Rev Microbiol 1997, 51:151-178. 10.1146/annurev.micro.51.1.151, 9343347.
26. Nelson MI, Holmes EC. The evolution of epidemic influenza. Nat Rev Genet 2007, 8:196-205. 10.1038/nrg2053, 17262054.
27. Abe T, Kanaya S, Uehara H, Ikemura T. A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses. DNA Res 2009, 16:287-298. 10.1093/dnares/dsp018, 2762413, 19801558.