Computational study of dispersion and extent of mutated and duplicated sequences of the H5N1 influenza neuraminidase over the period 1997-2008

Journal of Chemical Information and Modeling

Volumn 49, Issue 11, 2009, Pages 2627-2638

  Ghosh, Ambarnil ^a   Nandy, Ashesh ^a   Nandy, Papiya ^a   Gute, Brian D ^b   Basak, Subhash C ^b  

^a JADAVPUR UNIVERSITY   (India)

^b UNIVERSITY OF MINNESOTA DULUTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS; STRUCTURAL ANALYSIS; VIRUSES;

C-TERMINAL REGIONS; COMPUTATIONAL STUDIES; INHIBITOR DESIGN; MUTATIONAL CHANGES; NUMERICAL CHARACTERIZATION; POTENTIAL REGION; PROTEIN SEQUENCES; STRUCTURAL SECTIONS;

GENES;

SIALIDASE;

ARTICLE; ENZYMOLOGY; GENETIC RECOMBINATION; GENETICS; INFLUENZA VIRUS A H5N1; MUTATION;

INFLUENZA A VIRUS, H5N1 SUBTYPE; MUTATION; NEURAMINIDASE; RECOMBINATION, GENETIC;

EID: 72949090425     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9001662     Document Type: Article

References (46)

1. Peiris, J. S. M.; Yu, W. C.; Leung, C. W.; Cheung, C. Y.; Ng, W. F.; Nicholls, J. M.; Ng, T. K.; Chan, K. H.; Lai, S. T.; Lim, W. L.; Yuen, K. Y.; Guan, Y. Re-emergence of fatal human influenza A subtype H5N1 disease. Lancet 2004, 363, 617-619.
2. Li, K. S.; Guan, Y.; Wang, J.; Smith, G. J. D.; Xu, K. M.; Duan, L.; Rahardjo, A. P.; Puthavathana, P.; Buranathai, C.; Nguyen, T. D.; Estoepangestie, A. T. S.; Chalsingh, A.; Auewarakul, P.; Long, H. T.; Hanh, N. T. H.; Webby, R. J.; Poon, L. L. M.; Chen, H.; Shortridge, K. F.; Yuen, K. Y.; Webster, R. G.; Peiris, J. S. M. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature (London, U.K.) 2004, 430, 209-213.
3. Chen, H.; Smith, G. J. D.; Li, K. S.; Wang, J.; Fan, X. H.; Rayner, J. M.; Vijaykrishna, D.; Zhang, J. X.; Zhang, L. J.; Guo, C. T.; Cheung, C. L.; Xu, K. M.; Duan, L.; Huang, K.; Qin, K.; Leung, Y. H. C.; Wu, W. L.; Lu, H.R.; Chen, Y.; Xia, N. S.; Naipospos, T. S. P.; Yuen, K. Y.; Hassan, S. S.; Bahri, S.; Nguyen, T. D.; Webster, R. G.; Peiris, J. S. M.; Guan, Y. Establishment of multiple sublineages of H5N1 influenza virus in Asia: Implications for pandemic control. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 2845-2850.
4. Bagchi, S. Bird flu spreading in Asia. Can. Med. Assoc. J. 2008, 178, 1415.
5. World Health Organization (WHO). http://www.who.int/csr/disease/avian- influenza/en/ (accessed March 23, 2009).
6. Wu, W. L.; Chen, Y.; Wang, P.; Song, W.; Lau, S. Y.; Rayner, J. M.; Smith, G. J. D.; Webster, R. G.; Peiris, J. S. M.; Lin, T.; Xia, N.; Guan, Y.; Chen, H. Antigenic profile of avian H5N1 viruses in Asia from 2002 to 2007. J. Virol. 2008, 82, 1798-1807.
7. Johansson, B. E.; Brett, I. C. Changing perspective on immunization against influenza. Vaccine 2007, 25, 3062-3065.
8. Lal, S. K.; Chow, V. T. K. Avian Influenza H5N1 Virus: An emerging global pandemic. Issues Infect. Dis. 2007, 4, 59-77.
9. Tumpey, T. M.; Basler, C. F.; Aguilar, P. V.; Zeng, H.; Solórzano, A.; Swayne, D. E.; Cox, N. J.; Katz, J. M.; Taubenberger, J. K.; Palese, P.; García-Sastre, A. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 2005, 310, 77.
10. Moscona, A. Neuraminidase Inhibitors for Influenza. New Engl. J. Med. 2005, 353, 1363-1373.
11. Mills, C. E.; Robins, J. M.; Bergstrom, C. T.; Lipsitch, M. Pandemic Influenza: Risk of Multiple Introductions and the Need to Prepare for Them. PLoS Med. 2006, 3 (6), 769-773.
12. Hoa, H. T.; Hurt, A. C.; Mosse, J.; Barr, I. Neuraminidase inhibitor drug susceptibility differs between influenza N1and N2 neuraminidase following mutagenesis of two conserved residues. Antiviral Res. 2007, 76, 263-266.
13. Colman, P. M. Design and antiviral properties of influenza virus neuraminidase inhibitors. Pure Appl. Chem. 1995, 67, 1683-1688.
14. Breschkin, J. L. M.; Sahasrabudhe, A.; Blick, T. J.; McDonald, M.; Colman, P. M.; Hart, G. J.; Bethell, R. C.; Varghese, J. N. Mutations in a conserved residue in the influenza virus neuraminidase active site decreases sensitivity to Neu5Ac2en-derived inhibitors. J. Virol. 1998, 72, 2456-2462.
15. The World Health Organization Global Influenza Program Surveillance Network, Evolution of H5N1 Avian Influenza Viruses in Asia. Emerging Infect. Dis. 2005, 11, 1515-1521.
16. Vijaykrishna, D.; Bahl, J.; Riley, S.; Duan, L.; Zhang, J. X.; Chen, H.; Peiris, J. S. M.; Smith, G. J. D.; Guan, Y. Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses. PLoS Pathog. [Online] 2008 2009, 4 (9), e1000161(accessed March 23rd, 10.1371/journal.ppat.1000161).
17. Lam, T. T.-Y.; Hon, C.-C.; Pybus, O. G.; Pond, S. L. K.; Wong, R. T.- Y.; Yip, C.-W.; Zeng, F.; Leung, F. C.-C. Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia. PLoS Pathog. [Online], 2008 2009, 4 (8), e1000130(accessed March 23rd, 10.1371/journal.ppat.1000130).
18. Owoade, A. A.; Gerloff, N. A.; Ducatez, M. F.; Taiwo, J. O.; Kremer, J. R.; Muller, C. P. Replacement of Sublineages of Avian Influenza (H5N1) by Reassortments, Sub-Saharan Africa. Emerging Infect. Dis. 2008, 14, 1731-1735.
19. Bruyere, A.; Wantroba, M.; Flasinski, S.; Dzianott, A.; Bujarski, J. J. Frequent Homologous Recombination Events between Molecules of One RNA Component in a Multipartite RNA Virus. J. Virol. 2000, 74, 4214-4219.
20. He, C.-Q.; Xie, Z.-X.; Han, G.-Z.; Dong, J.-B.; Wang, D.; Liu, J.-B.; Ma, L.-Y.; Tang, X.-F.; Liu, X.-P.; Pang, Y.-S.; Li, G.-R. Homologous Recombination as an Evolutionary Force in the Avian Influenza A Virus. Mol. Biol. EVol. 2009, 26, 177-187.
21. He, C.-Q.; Han, G.-Z.; Wang, D.; Liu, W.; Li, G.-R.; Liu, X.-P.; Ding, N.-Z. Homologous recombination evidence in human and swine influenza-A viruses. Virology 2008, 380, 12-20.
22. Nandy, A.; Gute, B.; Basak, S. C. Graphical representation and numerical characterization of H5N1 avain flu neuraminidase gene sequence. J. Chem. Inf. Model. 2007, 47, 945-951.
23. Varghese, J. N.; Laver, W. G.; Colman, P. M. Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature (London, U.K.) 1983, 303, 35-40.
24. Li, X.; Fang, F.; Song, Y.; Yan, H.; Chang, H.; Sun, S.; Chen, Z. Essential Sequence of Influenza Neuraminidase DNA to Provide Protection Against Lethal Viral Infection. DNA Cell Biol. 2006, 25, 197-205. 10.1089/dna.2006.25. 197. (Pubitemid 43668281)
25. NCBI Influenza Virus Resource. http://www.ncbi.nlm.nih.gov/genomes/FLU/ FLU.html (accessed March 10, 2009).
26. Nandy, A.; Harle, M.; Basak, S. C. Mathematical descriptors of DNA sequences: development and applications. ARKIVOC 2006, 9, 211-238.
27. Liao, B.; Xiang, V.; Zhu, W. Coronavirus phylogeny based on 2D graphical representation of DNA sequence. J. Comput. Chem. 2006, 27, 1196-1202.
28. Nandy, A.; Basak, S. C. Simple numerical descriptor for quantifying effect of toxic substances on DNA sequences. J. Chem. Inf. Comput. Sci. 2000, 40, 915-919.
29. Ghosh, S.; Roy, A.; Adhya, S.; Nandy, A. Identification of new genes in human chromosome 3 contig 7 by graphical representation technique. Curr. Sci. 2003, 84, 1534-1543.
30. Larionov, S.; Loskutov, A.; Ryadchenko, E. Chromosome evolution with naked eye: Palindromic context of the life origin. CHAOS 2008, 18, 013105.
31. Nandy, A.; Nandy, P. On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models. Chem. Phys. Lett. 2003, 368, 102-107.
32. Nandy, A.; Ghosh, A.; Nandy, P. Numerical characterization of protein sequences and application to voltage-gated sodium channel α subunit phylogeny. In Silico Biol. [online] 2009 2009, 9, 0008. http://www.bioinfo.de/ isb/toc-vol-09.html (accessed April 25, 2009).
33. Shinya, K.; Ebina, M.; Yamada, S.; Ono, M.; Kasai, N.; Kawaoka, Y. Avian flu: Influenza virus receptors in the human airway. Nature (London, U.K.) 2006, 440, 435-436.
34. Castrucii, M. R.; Kawaoka, Y. Biologic importance of neuraminidase stalk length in influenza-A virus. J. Virol. 1993, 67, 759-764.
35. Ferraris, O.; Lina, B. Mutations of neuraminidase implicated in neuraminidase inhibitors resistance. J. Clin. Virol. 2008, 41, 13-19.
36. Gaidet, N.; Newman, S. H.; Hagemeijer, W.; Dodman, T.; Cappelle, J.; Hammoumi, S.; Simone, L. D.; Takekawa, J. Y. Duck Migration and Past Influenza A (H5N1) Outbreak Areas. Emerging Infect. Dis. 2008, 14, 1164-1166.
37. Vong, S.; Ly, S.; Mardy, S.; Holl, D.; Buchy, P. Environmental contamination during influenza A virus (H5N1) outbreaks, Cambodia. Emerging Infect. Dis. 2008 2006, 14, 1303-1305.
38. Drake, J. W.; Charlesworth, B.; Charlesworth, D.; Crow, J. F. Rates of spontaneous mutation. Genetics 1998, 148, 1667-1686.
39. Klug, W. S.; Cummings, M. R. 14. Gene Mutation, DNA Repair, and Transposable Elements. In Concepts of Genetics, 7th ed. (First Indian reprints, 2003); Pearson Education (Singapore) Pte. Ltd.: Indian Branch, 482 F.I.E. Patparganj, Delhi 110092, India, 2003; Chapter 14, pp 362-364.
40. Lai, M. M. C. RNA Recombination in animal and plant viruses. Microbiol. Rev. 1992, 56, 61-79.
41. Fields, B. N. Genetics of reovirus. Curr. Top. Microbiol. Immunol. 1981, 91, 1-24.
42. Palese, P. The genes of influenza virus. Cell 1977, 10, 1-10.
43. Matsuoka, Y.; Swayne, D. E.; Thomas, C.; Welti, M. A. R.; Naffakh, N.; Warnes, C.; Altholtz, M.; Donis, R.; Subbarao, K. Neuraminidase stalk length and additional glycosylation of the hemagglutinin influence the virulence of influenza H5N1 viruses for mice. J. Virol. 2009, 83 (9), 4704-4708.
44. Baigent, S. J.; McCauley, J. W. Glycosylation of haemagglutinin and stalk-length of neuraminidase combine to regulate the growth of avian influenza viruses in tissue culture. Virus Res. 2001, 79 (1-2), 177-185.
45. Chan, M. World now at the start of 2009 influenza pandemic; WHO website [online] http://www.who.int/mediacentre/news/statements/2009/h1n1-pandemic- phase6-20090611/en/index.html>?(accessed June 30, 2009).
46. Nandy, A. Mathematical Characterization of DNA Sequences -Towards New Directions. Computational Methods in Science and Engineering, Theory and Computation: Old Problems and New Challenge, Corfu, Greece, 2007; Maroulis, G., Simos, T., Eds.; American Institute of Physics: 2007; CP963, Vol.1, pp 596-602.