Genomic analysis and geographic visualization of the spread of avian influenza (H5N1)

Systematic Biology

Volumn 56, Issue 2, 2007, Pages 321-329

  James, Daniel ^a   Hill, Andrew W ^b   Guralnick, Robert ^b,c   Habib, Farhat ^a   Waltari, Eric ^d   Wheeler, Ward C ^d  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ANTIBIOTIC RESISTANCE; ARTICLE; AVIAN INFLUENZA; BIOLOGICAL MODEL; BIRD; DISEASE TRANSMISSION; GENETICS; GENOMICS; GENOTYPE; GEOGRAPHY; INFLUENZA VIRUS A H5N1; MOLECULAR EVOLUTION; MUTATION; TIME; VIROLOGY; VIRUS GENOME;

ANIMALS; BIRDS; DRUG RESISTANCE, VIRAL; EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOMICS; GENOTYPE; GEOGRAPHY; INFLUENZA A VIRUS, H5N1 SUBTYPE; INFLUENZA IN BIRDS; MODELS, BIOLOGICAL; MUTATION; TIME FACTORS;

EID: 34347222638     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701266848     Document Type: Review

References (40)

1. Blythman, J. 2006. So who's really to blame for bird flu? The Guardian. June 7. www.guardian.co.uk/birdflu/story/0,1791954,00.html
2. Bogner, P., I. Capua, N. Cox, D. Lipman, et al., 2006. A global initiative on sharing avian flu data. Nature 442:981. (Pubitemid 44330240)
3. Boltz, D. A., B. Douangngeun, S. Sinthasak, P. Phommachanh, S. Rolston, H. Chen, Y. Guan, J. Peiris, G. Smith, and R. Webster. 2006. H5N1 influenza viruses in Lao People's Democratic Republic. Emerg. Infect. Dis. 12:1593-1595. (Pubitemid 44570908)
4. Brahmbhatt, M. 2005. Avian influenza: Economic and social impacts. web.worldbank.org/WBSITE/EXTERNAL/NEWS/0,,contentMDK:20663668-pagePK:34370-piPK: 42770-theSitePK:4607,00.html
5. Chen, H., G. Smith, K. Li, J. Wang, X. Fan, J. Rayner, D. Vijaykrishna, J. Zhang, L. Zhang, C. Guo, C. Cheung, K. Xu, L. Duan, K. Huang, K. Qin, Y. Leung, W. Wu, H. Lu, Y. Chen, N. Xia, T. Naipospos, K. Yuen, S. Hassan, S. Bahri, T. Nguyen, R. Webster, J. Peiris, and Y. Guan. 2006. Establishment of multiple sublineages of H5N1 influenza virus in Asia: Implications for pandemic control. Proc. Natl. Acad. Sci. USA 103:2845-2850.
6. Chen, H., G. Smith, S. Zhang, K. Qin, J. Wang, K. Li, R. Webster, J. Peiris, and Y. Guan. 2005. Avian flu H5N1 virus outbreak in migratory waterfowl. Nature 436:191-192. (Pubitemid 41021261)
7. Ducatez, M., C. Olinger, A. Owoade, De Landtsheer S., W. Ammerlaan, H. Niesters, A. D. Osterhaus, R. Fouchier, and C. Muller. 2006. Avian Flu: Multiple introductions of H5N1 in Nigeria. Nature 442:37. (Pubitemid 44064202)
8. Edgar, R. C. 2004. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5:113.
9. Enserink, M. 2006. Avian influenza: As H5N1 keeps spreading, a call to release more data. Science 311:1224.
10. Gerberding, J. 2005. Pandemic planning and preparedness. www.cdc.gov/Washington/testimony/in05262005.htm
11. Ghedin, E., N. Sengamalay, M. Shumway, J. Zaborsky, T. Feldblyum, V. Subbu, D. Spiro, J. Sitz, H. Koo, P. Bolotov, D. Dernovoy, T. Tatusova, Y. Bao, K. St. George, J. Taylor, D. Lipman, C. Fraser, J. Taubenberger, and S. Salzberg. 2005. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437:1162-1166. (Pubitemid 41509354)
12. Gilbert, M., P. Chaitaweesub, T. Parakamawongsa, S. Premashthira, T. Tiensin, W. Kalpravidh. H. Wagner, and J. Slingenberghet. 2006. Free-grazing ducks and highly pathogenic avian influenza, Thailand. Emerg. Infect. Dis. 11:1664-1672.
13. Goloboff, P., S. Farris, and K. Nixon. 2005. TNT: Tree analysis using new technologies. www.zmuc.dk/public/phylogeny/TNT
14. Karesh, W, R. Cook, E. Bennett, and J. Newcomb. 2005. Wildlife trade and global disease emergence. Emerg. Infect. Dis. 11:1000-1002. (Pubitemid 40883100)
15. Kilpatrick, A. M., A. A. Chmura, D. W. Gibbons, R. C. Fleischer, P. P. Marra, and P. Daszak,2006. Predicting the global spread of H5N1 avian influenza. Proc. Natl. Acad. Sci. USA 103:19368-19373. (Pubitemid 46026037)
16. Kobasa, D., S. Kodihalli, L. Ming, M. Castrucci, I. Donatelli, Y. Suzuki, T. Suzuki, and Y. Kawaoka,1999. Amino acid residues contributing to the substrate specificity of the influenza a virus neuraminidase. J. Virol. 78:6743-6751. (Pubitemid 29327857)
17. Li, K., Y. Guan, J. Wang, G. Smith, K. Xu, L. Duan, A. Rahardjo, P. Puthavathana, C. Buranathai, T. Nguyen, A. Estoepangestie, A. Chaisingh, P. Auewarakul, H. Long, N. Hanh, R. Webby, L. Poon, H. Chen, K. Shortridge, K. Yuen, R. Webster, and J. Peiris. 2004. Genesis of a highly pathogenic and potentially pandemic H5N1 influenza virus in eastern Asia. Nature 430:209-213. (Pubitemid 38902429)
18. Lipatov, A., E. Govorkova, R. Webby, H. Ozaki, M. Peiris, Y. Guan, L. Poon, and R. Webster. 2004. Influenza: Emergence and control. J. Virol. 78:8951-8959. (Pubitemid 39096507)
19. Maddison, W. P. 1990. A method for testing the correlated evolution of two binary characters: Are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution. 44:539-557.
20. Maddison, W. P., and Maddison, D. R. 2003. MacClade (version 4.06): Analysis of phylogeny and character evolution. Sinauer, Sunderland, Massachusetts.
21. Melville, D. S., and K. F. Shortridge. 2006. Spread of H5N1 avian influenza virus: An ecological conundrum. Lett. Appl. Microbiol. 42:435-437.
22. Normile, D. 2006a. Wild birds only partly to blame in spreading H5N1. Science 312:1451.
23. Normile, D. 2006b. South Korean flu mystery. Science 314:1371.
24. Obenauer, J., J. Denson, P. Mehta, X. Su, S. Mukatira, D. Finkelstein, X. Xu, J. Wang, Ma, J., Y. Fan, K. Rakestraw, R. G. Webster, E. Hoffmann, S. Krauss, J. Zheng, Z. Zhang, and C. Naeve. 2006. Large-scale sequence analysis of avian influenza isolates science. 311:1576-1580.
25. OIE (World Organization for Animal Health). 2006. Highly pathogenic avian influenza in the Republic of Korea, http://www.oie.int/eng/info/hebdo/ais-68. htm#Sec6
26. Olsen B., V. Munster, A. Wallensten, J. Waldenström, A. Osterhaus, and R. Fouchier, 2006. Global patterns of influenza a virus in wild birds. Science 21:384-388.
27. Rosenthal, E. 2006. Bird flu virus may be spread by smuggling. New York Times, April 15.
28. Salzberg, S., E. Ghedin, and D. Spiro. 2006. Shared data are key to beating threat from flu. Nature 440:605.
29. Shinya, K., S. Hamm, M. Hatta, H. Ito, T. Ito, and Y. Kawaoka. 2004. PB2 amino acid at position 627 affects replicative efficiency, but not cell tropism, of Hong Kong H5N1 influenza A viruses in mice. Virology 320:258-266 (Pubitemid 38315152)
30. Shortridge, K. 1999. Poultry and the influenza H5N1 outbreak in Hong Kong, 1997: Abridged chronology and virus isolation. Vaccine 17:S26-S29. (Pubitemid 29366930)
31. Smith, G. J. D., X. H. Fan, J. Wang, K. S. Li, K. Qin, J. X. Zhang, D. Vijaykrishna, C. L. Cheung, K. Huang, J. M. Rayner, J. S. M. Peiris, H. Chen, R. G. Webster, and Y. Guan. 2006a. Emergence and predominance of an H5N1 influenza variant in China. Proc. Natl. Acad. Sci. USA 103:16936-16941. (Pubitemid 44737356)
32. Smith, G. J. D., T. S. P. Naipospos, T. D. Nguyen, M. D. de Jong, D. Vijaykrishna, T. B. Usman, S. S. Hassan, T. V. Nguyen, T. V. Dao, N. A. Bui, Y. H. Leung, C. L. Cheung, J. M. Rayner, J. X. Zhang, L. J. Zhang, L. L. Poon, K. S. Li, V. C. Nguyen, T. T. Hien, J. Farrar, R. G. Webster, H. Chen, J. S. Peiris, and Y. Guan. 2006b. Evolution and adaptation of H5N1 influenza virus in avian and human hosts in Indonesia and Vietnam. Virology 350:258-268. (Pubitemid 44218982)
33. Stevens, J., O. Blixt, T. Tumpey, J. Taubenberger, J. Paulson, and I. Wilson. 2006. Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science 312:404-410.
34. Subbarao, E. K., W. London, and B. R. Murphy. 1993. A single amino acid in the PB2 gene of influenza A virus is a determinant of host range. J. Virol. 67:1761-1764. (Pubitemid 23088345)
35. Van Borm, S., I. Thomas, G. Hanquet, B. Lambrecht, M. Boschmans, G. Dupont, M. Decaestecker, R. Snacken, and van den T. Berg,2005. Highly pathogenic H5N1 influenza virus in smuggled Thai eagles, Belgium. Emerg. Infect. Dis. 11:702-705. (Pubitemid 40586394)
36. Webster, R. G., W. Bean, O. Gorman, T. Chambers, and Y. Kawaoka.1992. Evolution and ecology of influenza A viruses. Microbiol. Rev. 56:152-179.
37. Webster, R. G., and Govorkova 2006. H5N1 influenza - Continuing evolution and spread. N. Engl. J. Med. 355:2174-2177.
38. Wheeler, W. C. 1996. Optimization alignment: The end of multiple sequence alignment in phylogenetics? Cladistics 12:1-9.
39. Wheeler, W. C, J. Delaet, D. Gladstein, and A. Varon. 2005. POY (version 3.012). Phylogeny reconstruction via optimization of DNA and other data; research.amnh.org/scicomp/projects/poy.php
40. WHO. 2006. Cumulative number of confirmed human cases of avian influenza A/(H5N1) reported to WHO. 1 March 2007. http://www.who.int/csr/disease/ avianjnfluenza/country/cases-table-2007-03-01/en/index.html