EcoHealth

, Volume 6, Issue 3, pp 346–350

Wild Bird’s-eye View of Influenza Virus A(H1N1) Phylogenetic Evolution

  • Antoinette J. Piaggio
  • Larry Clark
  • Alan B. Franklin
  • Sergios-Orestis Kolokotronis
Short Communication

Abstract

Wild bird fecal samples collected and characterized by the USDA as part of a national surveillance effort were sequenced to study the genetic relatedness of avian, swine, and human H1 and N1 subtypes. Our results find that the 2009 H1N1 human outbreak is closely related to swine virus, but falls into different clades in the H1 and N1 trees. Further, there is evidence of multiple viral genetic exchanges between birds and swine. Ongoing research across host species contributes to an understanding of the circulation of influenza viruses.

Keywords

Influenza virus A H1N1 phylogeny evolution surveillance zoonoses 

References

  1. Duan L, Campitelli L, Fan XH, Leung YHC, Vijaykrishna D, Zhang JX, et al. (2007) Characterization of low-pathogenic H5 subtype influenza viruses from Eurasia: implications for the origin of highly pathogenic H5N1 viruses. Journal of Virology 81:7529–7539CrossRefGoogle Scholar
  2. Fouchier RA, Munster MV, Wallensten A, Bestebroer TM, Hersft S, Smith D, et al. (2005) Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. Journal of Virology 79:2814–2822CrossRefGoogle Scholar
  3. Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, et al. (2009) Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325(5937):197-201. doi:10.1126/science.1176225 CrossRefGoogle Scholar
  4. Karasin AI, West K, Carman S, Olsen CW (2004) Characterization of avian H3N3 and H1N1 influenza A viruses isolated from pigs in Canada. Journal of Clinical Microbiology 42:4349–4354CrossRefGoogle Scholar
  5. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33:511–518CrossRefGoogle Scholar
  6. Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution 20:86–93CrossRefGoogle Scholar
  7. McLean R, Hall J, Franklin AB, Sullivan H, VanDalen K, Shriner S, et al. (2007) Avian influenza in wild birds: environmental sampling for the rapid detection of avian influenza viruses. In: Proceedings of the 12th Wildlife Damage Management Conference, Nolte DL, Arjo WM, Stalman D (editors), Bethesda, MD: The Wildlife Society; pp 87–93Google Scholar
  8. Nava GM, Attene-Ramos MS, Ang JK, Escorcia M (2009) Origins of the new influenza A(H1N1) virus: time to take action. Euro Surveillance 14:pii = 19228Google Scholar
  9. Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122–1125CrossRefGoogle Scholar
  10. Spackman E (2008) A brief introduction to the avian influenza virus. In: Avian Influenza Virus, Spackman E (editor), Totowa, NJ: Humana Press; pp 1–6Google Scholar
  11. Spackman E, Senne DA, Myers TJ, Bulaga LL, Garber LP, Perdue ML, et al. (2002) Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes. Journal of Clinical Microbiology 40:3256–3260CrossRefGoogle Scholar
  12. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690CrossRefGoogle Scholar
  13. Stamatakis A, Ott M, Ludwig T (2005) RAxML-OMP: an efficient program for phylogenetic inference on SMPs. In: Proceedings of the 8th International Conference on Parallel Computing Technologies (PaCT2005). Lecture Notes in Computer Science, New York: Springer-Verlag; 3606:288–302Google Scholar
  14. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57:758–771CrossRefGoogle Scholar
  15. Taubenberger JK, Reid AH, Lourens RM, Wang R, Jin G, Fanning TG (2004) Characterization of the 1918 influenza virus polymerase genes. Nature 437:889–893CrossRefGoogle Scholar
  16. Trampuz AJ, Rajesh MP, Smith TF, Baddour LM (2004) Avian influenza: a new pandemic threat? Mayo Clinic Proceedings 79:827–833CrossRefGoogle Scholar
  17. Trifonov V, Khiabanian H, Greenbaum B, Rabadan R (2009a) The origin of the recent swine influenza A(H1N1) virus infecting humans. Eurosurveillance 14:pii = 19193Google Scholar
  18. Trifonov V, Khiabanian H, Rabadan R (2009b) Geographic dependence, surveillance, and origins of the 2009 influenza A(H1N1) virus. New England Journal of Medicine 361:115–119CrossRefGoogle Scholar
  19. U.S. Interagency Strategic Plan (2006) An early detection system for highly pathogenic H5N1 avian influenza in wild migratory birds. Available: http://www.usda.gov/documents/wildbirdstrategicplanpdf.pdf
  20. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiological Reviews 56:152–179Google Scholar
  21. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306–314CrossRefGoogle Scholar

Copyright information

© United States Department of Agriculture 2010

Authors and Affiliations

  • Antoinette J. Piaggio
    • 1
  • Larry Clark
    • 1
  • Alan B. Franklin
    • 1
  • Sergios-Orestis Kolokotronis
    • 2
  1. 1.National Wildlife Research Center, United States Department of AgricultureWildlife ServicesFort CollinsUSA
  2. 2.Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkUSA

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