Reassortment networks and the evolution of pandemic H1N1 swine-origin influenza

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 1, 2012, Pages 214-227

  Bokhari, Shahid H ^a   Pomeroy, Laura W ^a   Janies, Daniel A ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Cray XMT; graph theory; influenza; multithreading; networks; pandemic; reassortment; S OIV; shortest paths; swine flu

Indexed keywords

CRAY XMT; INFLUENZA; MULTI-THREADING; PANDEMIC; REASSORTMENT; S-OIV; SHORTEST PATH; SWINE FLU;

COSTS; DYNAMIC PROGRAMMING; GENES; GRAPH THEORY; MOLECULAR BIOLOGY; NETWORKS (CIRCUITS); SUPERCOMPUTERS; VIRUSES;

COMPUTER VIRUSES;

INFLUENZA A VIRUS; INFLUENZAVIRUS A; SUIDAE;

ANIMAL; ARTICLE; COMPUTER NETWORK; GENETIC REASSORTMENT; GENETICS; HUMAN; INFLUENZA; INFLUENZA VIRUS A H1N1; MOLECULAR EVOLUTION; MUTATION; PANDEMIC; SWINE; VIROLOGY; VIRUS GENOME;

ANIMALS; COMPUTER COMMUNICATION NETWORKS; EVOLUTION, MOLECULAR; GENOME, VIRAL; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA, HUMAN; MUTATION; PANDEMICS; REASSORTANT VIRUSES; SUS SCROFA; SWINE;

EID: 81455143751     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.95     Document Type: Article

References (38)

1. C. Fraser, C.A. Donnelly, S. Cauchemez, W.P. Hanage, M.D. Van Kerkhove, T.D. Hollingsworth, J. Griffin, R.F. Baggaley, H.E. Jenkins, E.J. Lyons, T. Jombart, W.R. Hinsley, N.C. Grassly, F. Balloux, A.C. Ghani, N.M. Ferguson, A. Rambaut, O.G. Pybus, H. Lopez-Gatell, C.M. Alpuche-Aranda, I.B. Chapela, E.P. Zavala, D.M. Guevara, F. Checchi, E. Garcia, S. Hugonnet, and C. Roth, "Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings," Science, vol. 324, no. 5934, pp. 1557-1561, 2009.
2. G. Neumann, T. Noda, and Y. Kawaoka, "Emergence and Pandemic Potential of Swine-Origin H1N1 Influenza Virus," Nature, vol. 459, no. 7249, pp. 931-999, 2009.
3. A.J. Gibbs, J.S. Armstrong, and J.C. Downie, "From Where did the 2009 "Swine-Origin" Influenza A Virus (H1N1) Emerge," J. Virology, vol. 6, p. 207, 2009.
4. F.S. Dawood, S. Jain, L. Finelli, M.W. Shaw, S. Lindstrom, R.J. Garten, L.V. Gubareva, X. Xu, C.B. Bridges, and T.M. Uyeki, "Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans," The New England J. Medicine, vol. 360, no. 25, pp. 2605-2615, 2009.
5. M. Chan, "World Now at the Start of 2009 Influenza Pandemic," www.who.int/mediacentre/news/statements/2009/h1n1-pandemic-phase6-20090611/en/ index.html, 2009.
6. WHO "WHO Pandemic (H1N1) 2009 Update 98," www.who.int/csr/don/ 2010-04-30a/en/index.html, 2009.
7. R.G. Webster, W.J. Bean, O.T. Gorman, T.M. Chambers, and Y. Kawaoka, "Evolution and Ecology of Influenza A Viruses," Microbiological Rev., vol. 56, no. 1, pp. 152-159, 1992.
8. M.I. Nelson and E.C. Holmes, "The Evolution of Epidemic Influenza," Nature Rev. Genetics, vol. 8, no. 3, pp. 196-205, 2007.
9. R.A. Fouchier, V. Munster, A. Wallensten, T.M. Bestebroer, S. Herfst, D. Smith, G.F. Rimmelzwaan, B. Olsen, and A.D. Osterhaus, "Characterization of a Novel Influenza A Virus Hemagglutinin Subtype (H16) Obtained from Black-Headed Gulls," J. Virology, vol. 79, no. 5, pp. 2814-2822, 2005. (Pubitemid 40270559)
10. Y. Guan, D. Vijaykrishna, J. Bahl, H. Zhu, J. Wang, and G.J.D. Smith, "The Emergence of Pandemic Influenza Viruses," Protein and Cell, vol. 1, no. 1, pp. 9-13, Jan. 2010.
11. R. Webster, W. Bean, O. Gorman, T. Chambers, and Y. Kawaoka, "Evolution and Ecology Of Influenza-A Viruses," Microbiological Rev., vol. 56, pp. 152-179, Mar. 1992.
12. N. Zhou, D. Senne, J. Landgraf, S. Swenson, G. Erickson, K. Rossow, L. Liu, K. Yoon, S. Krauss, and R. Webster, "Genetic Reassortment of Avian, Swine, and Human Influenza A Viruses in American Pigs," J. Virology, vol. 73, pp. 8851-8856, Oct. 1999. (Pubitemid 29441754)
13. L. Campitelli, A. Di Martino, D. Spagnolo, G.J. Smith, L. Di Trani, M. Facchini, M.A. De Marco, E. Foni, C. Chiapponi, A.M. Martin, H. Chen, Y. Guan, M. Delogu, and I. Donatelli, "Molecular Analysis of Avian H7 Influenza Viruses Circulating in Eurasia in 1999-2005: Detection of Multiple Reassortant Virus Genotypes," J. General Virology, vol. 89, Pt 1, pp. 48-59, 2008.
14. R. Rabadan, A.J. Levine, and M. Krasnitz, "Non-Random Reassortment in Human Influenza A Viruses," Influenza and Other Respiratory Viruses, vol. 2, no. 1, pp. 9-22, 2008.
15. H. Khiabanian, V. Trifonov, and R. Rabadan, "Reassortment Patterns in Swine Influenza Viruses," PLoS One, vol. 4, no. 10, p. e7366, 2009.
16. D.H. Huson and D. Bryant, "Application of Phylogenetic Networks in Evolutionary Studies," Molecular Biology and Evolution, vol. 23, no. 2, pp. 254-267, 2006. (Pubitemid 43100040)
17. V. Makarenkov and P. Legendre, "From a Phylogenetic Tree to a Reticulated Network," J. Computational Biology, vol. 11, no. 1, pp. 195-212, 2004. (Pubitemid 38429371)
18. D.H. Huson and C. Scornavacca, "A Survey of Combinatorial Methods for Phylogenetic Networks," Genome Biology and Evolution, vol. 3, pp. 23-35, 2011.
19. S.H. Bokhari and D.A. Janies, "Reassortment Networks for Investigating the Evolution of Segmented Viruses," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 288-298, Apr.-June 2010.
20. Y. Bao, P. Bolotov, D. Dernovoy, B. Kiryutin, L. Zaslavsky, T. Tatusova, J. Ostell, and D. Lipman, "The Influenza Virus Resource at the National Center for Biotechnology Information," J. Virology, vol. 82, no. 2, pp. 596-601, Apr.-June 2008.
21. D. Gusfield, Algorithms on Strings, Trees, and Sequences. Cambridge Univ. Press, 1997.
22. A. Cornish-Bowden, "IUPAC-IUB Symbols for Nucleotide Nomenclature," Nucleic Acids Research, vol. 13, pp. 3021-3030, 1985.
23. R. Alverson, D. Callahan, D. Cummings, B. Koblenz, A. Porterfield, and B. Smith, "The Tera Computer System," Proc. Fourth Int'l Conf. Supercomputing, pp. 1-6, 1990.
24. A. Snavely, L. Carter, J. Boisseau, A. Majumdar, K.S. Gatlin, N. Mitchell, J. Feo, and B. Koblenz, "Multi-Processor Performance on the Tera MTA," Proc. IEEE/ACM Conf. Supercomputing, pp. 1-8, 1998.
25. S.H. Bokhari and J.R. Sauer, "Sequence Alignment on the Cray MTA-2," Concurrency and Computation, vol. 16, pp. 823-839, 2004.
26. S. Bokhari and J. Sauer, "Parallel Algorithms for Bioinformatics," Parallel Computing for Bioinformatics, A. Zomaya, ed., pp. 509-529, Wiley, 2006.
27. C.W. Olsen, "The Emergence of Novel Swine Influenza Viruses in North America," Virus Research, vol. 85, no. 2, pp. 199-210, 2002. (Pubitemid 34606914)
28. V. Trifonov, H. Khiabanian, and R. Rabadan, "Geographic Dependence, Surveillance, and Origins of the 2009 Influenza A (H1N1) Virus," The New England J. Medicine, vol. 361, no. 2, pp. 115-119, 2009.
29. C. Kingsford, N. Nagarajan, and S.L. Salzberg, "2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates," PLoS One, vol. 4, no. 7, p. e6402, 2009.
30. G.J. Smith, D. Vijaykrishna, J. Bahl, S.J. Lycett, M. Worobey, O.G. Pybus, S.K. Ma, C.L. Cheung, J. Raghwani, S. Bhatt, J.S. Peiris, Y. Guan, and A. Rambaut, "Origins and Evolutionary Genomics of the 2009 Swine-Origin H1N1 Influenza A Epidemic," Nature, vol. 459, no. 7250, pp. 1122-1125, 2009.
31. A.I. Karasin, M.M. Schutten, L.A. Cooper, C.B. Smith, K. Subbarao, G.A. Anderson, S. Carman, and C.W. Olsen, "Genetic Characterization of H3N2 Influenza Viruses Isolated from Pigs in North America, 1977-1999: Evidence for Wholly Human and Reassortant Virus Genotypes," Virus Research, vol. 68, no. 1, pp. 71-85, 2000. (Pubitemid 30621412)
32. C.W. Olsen, A. Karasin, and G. Erickson, "Characterization of a Swine-Like Reassortant H1N2 Influenza Virus Isolated from a Wild Duck in the United States," Virus Research, vol. 93, no. 1, pp. 115-121, 2003. (Pubitemid 36513893)
33. G.C. Gray, T. McCarthy, A.W. Capuano, S.F. Setterquist, C.W. Olsen, M.C. Alavanja, and C.F. Lynch, "Swine Workers and Swine Influenza Virus Infections," Emerging Infectious Diseases, vol. 13, no. 12, pp. 1871-1878, Dec. 2007. (Pubitemid 350248489)
34. H. Yu, P.-C. Zhang, Y.-J. Zhou, G.-X. Li, J. Pan, L.-P. Yan, X.-X. Shi, H.-L. Liu, and G.-Z. Tong, "Isolation and Genetic Characterization of Avian-Like H1N1 and Novel Ressortant H1N2 Influenza Viruses from Pigs in China," Biochemical and Biophysical Research Comm., vol. 386, no. 2, pp. 278-283, 2009.
35. G. Chen and S. Shih, "Genomic Signatures of Influenza A Pandemic (H1N1) 2009 Virus," Emerging Infectious Diseases, vol. 15, no. 12, pp. 1897-1903, www.cdc.gov/EID/content/15/12/1897.htm, Dec. 2009.
36. W. Ma, A.L. Vincent, K.M. Lager, B.H. Janke, S.C. Henry, R.R.R. Rowland, R.A. Hesse, and J.A. Richt, "Identification and Characterization of a Highly Virulent Triple Reassortant H1N1 Swine Influenza Virus in the United States," Virus Genes, vol. 40, no. 1, pp. 28-36, Feb. 2010.
37. D. Vijaykrishna, L.L. Poon, H.C. Zhu, S.K. Ma, O.T. Li, C.L. Cheung, G.J. Smith, J.S. Peiris, and Y. Guan, "Reassortment of Pandemic H1N1/2009 Influenza A Virus in Swine," Science, vol. 328, no. 5985, p. 1529, June 2010.
38. W. Wheeler, "Fixed Character States and the Optimization of Molecular Sequence Data," Cladistics, vol. 15, pp. 379-385, 1999. (Pubitemid 30203164)