Influenza A viruses have been isolated from many animal species, but wild waterfowl and shorebirds are recognized as their natural reservoirs due to the prevalence of the highest diversity of influenza A virus among these hosts. Influenza A viruses detected over the past century in the majority of mammalian hosts can be phylogenetically traced back to their ancestors in waterfowl or shorebirds. Although many wild bird species may harbor avian influenza viruses, birds belonging to the Anseriformes (ducks, geese, and swans) and Charadriiformes (gulls, terns, and waders) constitute the primary natural virus reservoir. Avian influenza viruses are primarily transmitted via the fecal-oral route, which allows the effective transmission of influenza A viruses between susceptible birds and potentially allows temporal and spatial connectivity of virus populations in different host (sub)populations. Avian influenza viruses are normally asymptomatic in wild birds, or cause mild disease in poultry, and therefore are termed low pathogenic avian influenza (LPAI) viruses. However, the acquisition of a multibasic cleavage site in the hemagglutinin protein genes of H5 and H7 subtype influenza A viruses can cause a highly pathogenic avian influenza (HPAI) virus resulting in severe disease in poultry and wild birds. In this chapter, we review the avian influenza virus literature to discuss the ecology and evolution of LPAI and HPAI viruses in birds.

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Keywords Avian, Ecology, Evolution, Genetics, Influenza, Migration
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Hurt, A.C, Fouchier, R.A.M, & Vijaykrishna, D. (D.). (2017). Ecology and Evolution of Avian Influenza Viruses. In Genetics and Evolution of Infectious Diseases: Second Edition (pp. 621–640). doi:10.1016/B978-0-12-799942-5.00027-5