A Brief Introduction to Avian Influenza Virus

  • Erica SpackmanEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2123)


The earliest recorded cases of what was likely high-pathogenicity AIV in poultry were reported in Italy in the 1870s. Avian influenza infection has been recognized in domestic poultry through the modern era of poultry production. Infection of poultry with either low pathogenic (LP) or highly pathogenic (HP) avian influenza viruses (AIVs) can result in substantial economic consequences. Productivity can be reduced directly and indirectly because of disease leading to decreased egg or meat yield, mortality, vaccination costs, and restricted trade. Aquatic birds are the natural hosts for AIV, and infection tends to be subclinical, although some strains of HPAIV can cause losses in domestic ducks. Biosecurity and vaccination are the most common methods of preventing infection of poultry. Approaches to AIV control vary widely, but elimination of the disease in poultry is a common goal. The basics of AIV biology, clinical disease, molecular aspects, and AIV detection are briefly reviewed.

Key words

Avian influenza virus Type A influenza Orthomyxovirus Host range Pathogenesis Molecular characteristics 


  1. 1.
    Lamb RA, Krug RM (2001) Orthomyxoviridae: the viruses and their replication. In: Knipe DM, Howley PM (eds) Fields virology, vol 1, 4th edn. LIppincott, Williams and Wilkins, Philadelphia, PA, pp 1487–1532Google Scholar
  2. 2.
    Tong S, Li Y, Rivailler P, Conrardy C, Castillo DA, Chen LM, Recuenco S, Ellison JA, Davis CT, York IA, Turmelle AS, Moran D, Rogers S, Shi M, Tao Y, Weil MR, Tang K, Rowe LA, Sammons S, Xu X, Frace M, Lindblade KA, Cox NJ, Anderson LJ, Rupprecht CE, Donis RO (2012) A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci U S A 109(11):4269–4274. Scholar
  3. 3.
    Munster VJ, Baas C, Lexmond P, Waldenstrom J, Wallensten A, Fransson T, Rimmelzwaan GF, Beyer WE, Schutten M, Olsen B, Osterhaus AD, Fouchier RA (2007) Spatial, temporal, and species variation in prevalence of influenza A viruses in wild migratory birds. PLoS Pathog 3(5):e61CrossRefGoogle Scholar
  4. 4.
    Dou D, Revol R, Ostbye H, Wang H, Daniels R (2018) Influenza A virus cell entry, replication, virion assembly and movement. Front Immunol 9:1581. Scholar
  5. 5.
    Rott R (1992) The pathogenic determinant of influenza virus. Vet Microbiol 33(1–4):303–310CrossRefGoogle Scholar
  6. 6.
    Khatchikian D, Orlich M, Rott R (1989) Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus. Nature 340(6229):156–157CrossRefGoogle Scholar
  7. 7.
    Orlich M, Gottwald H, Rott R (1994) Nonhomologous recombination between the hemagglutinin gene and the nucleoprotein gene of an influenza virus. Virology 204(1):462–465. Scholar
  8. 8.
    Pasick J, Handel K, Robinson J, Copps J, Ridd D, Hills K, Kehler H, Cottam-Birt C, Neufeld J, Berhane Y, Czub S (2005) Intersegmental recombination between the haemagglutinin and matrix genes was responsible for the emergence of a highly pathogenic H7N3 avian influenza virus in British Columbia. J Gen Virol 86(3):727–731CrossRefGoogle Scholar
  9. 9.
    Suarez DL, Senne DA, Banks J, Brown IH, Essen SC, Lee C, Manvell RJ, Mathieu-Benson C, Moreno V, Pedersen JC, Panigrahy B, Rojas H, Spackman E, Alexander DJ (2004) Recombination resulting in virulence shift in avian influenza outbreak in, Chile. Emerg Infect Dis 10(4):693–699CrossRefGoogle Scholar
  10. 10.
    Berhane Y, Hisanaga T, Kehler H, Neufeld J, Manning L, Argue C, Handel K, Hooper-McGrevy K, Jonas M, Robinson J, Webster RG, Pasick J (2009) Highly pathogenic avian influenza virus A (H7N3) in domestic poultry, Saskatchewan, Canada, 2007. Emerg Infect Dis 15(9):1492–1495. Scholar
  11. 11.
    Killian ML, Kim-Torchetti M, Hines N, Yingst S, DeLiberto T, Lee DH (2016) Outbreak of H7N8 low pathogenic avian influenza in commercial Turkeys with spontaneous mutation to highly pathogenic avian influenza. Genome Announc 4(3):e00457. Scholar
  12. 12.
    Lee DH, Torchetti MK, Killian ML, Berhane Y, Swayne DE (2017) Highly pathogenic avian influenza A(H7N9) virus, Tennessee, USA, March 2017. Emerg Infect Dis 23(11).
  13. 13.
    Maurer-Stroh S, Lee RT, Gunalan V, Eisenhaber F (2013) The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA. Virol J 10:139. Scholar
  14. 14.
    Alexander DJ (2000) A review of avian influenza in different bird species. Vet Microbiol 74(1–2):3–13CrossRefGoogle Scholar
  15. 15.
    Beare AS, Webster RG (1991) Replication of avian influenza viruses in humans. Arch Virol 119(1–2):37–42CrossRefGoogle Scholar
  16. 16.
    Slemons RD, Johnson DC, Osborn JS, Hayes F (1974) Type-A influenza viruses isolated from wild free-flying ducks in California. Avian Dis 18:119–124CrossRefGoogle Scholar
  17. 17.
    Hanson BA, Stallknecht DE, Swayne DE, Lewis LA, Senne DA (2003) Avian influenza viruses in Minnesota ducks during 1998-2000. Avian Dis 47(3 Suppl):867–871CrossRefGoogle Scholar
  18. 18.
    Stallknecht DE, Shane SM, Zwank PJ, Senne DA, Kearney MT (1990) Avian influenza viruses from migratory and resident ducks of coastal Louisiana. Avian Dis 34(2):398–405CrossRefGoogle Scholar
  19. 19.
    Liu D, Zhang Z, He L, Gao Z, Li J, Gu M, Hu J, Wang X, Liu X, Liu X (2018) Characteristics of the emerging chicken-origin highly pathogenic H7N9 viruses: a new threat to public health and poultry industry. J Infect 76(2):217–220. Scholar
  20. 20.
    Uyeki TM (2009) Human infection with highly pathogenic avian influenza A (H5N1) virus: review of clinical issues. Clin Infect Dis 49(2):279–290. Scholar
  21. 21.
    Klenk HD, Rott R, Orlich M (1977) Further studies on the activation of influenza virus by proteolytic cleavage of the haemagglutinin. J Gen Virol 36(1):151–161CrossRefGoogle Scholar
  22. 22.
    OIE (2018) Manual of diagnostic tests and vaccines for terrestrial animals 2018. World Organization for Animal Health (OIE). Accessed 20 Sept 2018
  23. 23.
    Swayne DE, Suarez DL (2000) Highly pathogenic avian influenza. Rev Sci Tech 19(2):463–482CrossRefGoogle Scholar
  24. 24.
    Senne DA, Panigrahy B, Kawaoka Y, Pearson JE, Suss J, Lipkind M, Kida H, Webster RG (1996) Survey of the hemagglutinin (HA) cleavage site sequence of H5 and H7 avian influenza viruses: amino acid sequence at the HA cleavage site as a marker of pathogenicity potential. Avian Dis 40(2):425–437CrossRefGoogle Scholar
  25. 25.
    Nili H, Asasi K (2003) Avian influenza (H9N2) outbreak in Iran. Avian Dis 47(3 Suppl):828–831CrossRefGoogle Scholar
  26. 26.
    Bano S, Naeem K, Malik SA (2003) Evaluation of pathogenic potential of avian influenza virus serotype H9N2 in chickens. Avian Dis 47(3 Suppl):817–822CrossRefGoogle Scholar
  27. 27.
    Bonfante F, Mazzetto E, Zanardello C, Fortin A, Gobbo F, Maniero S, Bigolaro M, Davidson I, Haddas R, Cattoli G, Terregino C (2018) A G1-lineage H9N2 virus with oviduct tropism causes chronic pathological changes in the infundibulum and a long-lasting drop in egg production. Vet Res 49(1):83. Scholar
  28. 28.
    Slomka MJ, Seekings AH, Mahmood S, Thomas S, Puranik A, Watson S, Byrne AMP, Hicks D, Nunez A, Brown IH, Brookes SM (2018) Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. Sci Rep 8(1):7322. Scholar
  29. 29.
    Pantin-Jackwood MJ, Stephens CB, Bertran K, Swayne DE, Spackman E (2017) The pathogenesis of H7N8 low and highly pathogenic avian influenza viruses from the United States 2016 outbreak in chickens, turkeys and mallards. PLoS One 12(5):e0177265. Scholar
  30. 30.
    Kapczynski DR, Pantin-Jackwood M, Guzman SG, Ricardez Y, Spackman E, Bertran K, Suarez DL, Swayne DE (2013) Characterization of the 2012 highly pathogenic avian influenza H7N3 virus isolated from poultry in an outbreak in Mexico: pathobiology and vaccine protection. J Virol.
  31. 31.
    Bowes VA, Ritchie SJ, Byrne S, Sojonky K, Bidulka JJ, Robinson JH (2004) Virus characterization, clinical presentation, and pathology associated with H7N3 avian influenza in British Columbia broiler breeder chickens in 2004. Avian Dis 48(4):928–934CrossRefGoogle Scholar
  32. 32.
    Jones YL, Swayne DE (2004) Comparative pathobiology of low and high pathogenicity H7N3 Chilean avian influenza viruses in chickens. Avian Dis 48(1):119–128CrossRefGoogle Scholar
  33. 33.
    Swayne DE, Perdue ML, Garcia M, Rivera-Cruz E, Brugh M (1997) Pathogenicity and diagnosis of H5N2 Mexican avian influenza viruses in chickens. Avian Dis 41(2):335–346CrossRefGoogle Scholar
  34. 34.
    Lee CW, Swayne DE, Linares JA, Senne DA, Suarez DL (2005) H5N2 avian influenza outbreak in Texas in 2004: the first highly pathogenic strain in the United States in 20 years? J Virol 79(17):11412–11421. Scholar
  35. 35.
    Nili H, Asasi K (2002) Natural cases and an experimental study of H9N2 avian influenza in commercial broiler chickens of Iran. Avian Pathol 31(3):247–252. Scholar
  36. 36.
    Jackwood MW, Suarez DL, Hilt D, Pantin-Jackwood MJ, Spackman E, Woolcock P, Cardona C (2010) Biologic characterization of chicken-derived H6N2 low pathogenic avian influenza viruses in chickens and ducks. Avian Dis 54(1):120–125CrossRefGoogle Scholar
  37. 37.
    Woolcock PR, Suarez DL, Kuney D (2003) Low-pathogenicity avian influenza virus (H6N2) in chickens in California, 2000-02. Avian Dis 47(3 Suppl):872–881CrossRefGoogle Scholar
  38. 38.
    Slemons RD, Swayne DE (1995) Tissue tropism and replicative properties of waterfowl-origin influenza viruses in chickens. Avian Dis 39(3):521–527CrossRefGoogle Scholar
  39. 39.
    Kawaoka Y, Nestorowicz A, Alexander DJ, Webster RG (1987) Molecular analyses of the hemagglutinin genes of H5 influenza viruses: origin of a virulent turkey strain. Virology 158(1):218–227CrossRefGoogle Scholar
  40. 40.
    Garcia M, Crawford JM, Latimer JW, Rivera-Cruz E, Perdue ML (1996) Heterogeneity in the haemagglutinin gene and emergence of the highly pathogenic phenotype among recent H5N2 avian influenza viruses from Mexico. J Gen Virol 77(Pt 7):1493–1504CrossRefGoogle Scholar
  41. 41.
    Pantin-Jackwood MJ, Costa-Hurtado M, Shepherd E, DeJesus E, Smith D, Spackman E, Kapczynski DR, Suarez DL, Stallknecht DE, Swayne DE (2016) Pathogenicity and transmission of H5 and H7 highly pathogenic avian influenza viruses in Mallards. J Virol 90(21):9967–9982. Scholar
  42. 42.
    Lee DH, Bertran K, Kwon JH, Swayne DE (2017) Evolution, global spread, and pathogenicity of highly pathogenic avian influenza H5Nx clade J Vet Sci 18(S1):269–280. Scholar
  43. 43.
    Sturm-Ramirez KM, Ellis T, Bousfield B, Bissett L, Dyrting K, Rehg JE, Poon L, Guan Y, Peiris M, Webster RG (2004) Reemerging H5N1 influenza viruses in Hong Kong in 2002 are highly pathogenic to ducks. J Virol 78(9):4892–4901CrossRefGoogle Scholar
  44. 44.
    Pantin-Jackwood MJ, Costa-Hurtado M, Bertran K, DeJesus E, Smith D, Swayne DE (2017) Infectivity, transmission and pathogenicity of H5 highly pathogenic avian influenza clade (H5N8 and H5N2) United States index viruses in Pekin ducks and Chinese geese. Vet Res 48(1):33. Scholar
  45. 45.
    McQuiston JH, Garber LP, Porter-Spalding BA, Hahn JW, Pierson FW, Wainwright SH, Senne DA, Brignole TJ, Akey BL, Holt TJ (2005) Evaluation of risk factors for the spread of low pathogenicity H7N2 avian influenza virus among commercial poultry farms. J Am Vet Med Assoc 226(5):767–772CrossRefGoogle Scholar
  46. 46.
    Yupiana Y, de Vlas SJ, Adnan NM, Richardus JH (2010) Risk factors of poultry outbreaks and human cases of H5N1 avian influenza virus infection in West Java Province, Indonesia. Int J Infect Dis 14(9):e800–e805. Scholar
  47. 47.
    Fang LQ, de Vlas SJ, Liang S, Looman CW, Gong P, Xu B, Yan L, Yang H, Richardus JH, Cao WC (2008) Environmental factors contributing to the spread of H5N1 avian influenza in mainland China. PLoS One 3(5):e2268. Scholar
  48. 48.
    Jonges M, van Leuken J, Wouters I, Koch G, Meijer A, Koopmans M (2015) Wind-mediated spread of low-pathogenic avian influenza virus into the environment during outbreaks at commercial poultry farms. PLoS One 10(5):e0125401. Scholar
  49. 49.
    Torremorell M, Alonso C, Davies PR, Raynor PC, Patnayak D, Torchetti M, McCluskey B (2016) Investigation into the airborne dissemination of H5N2 highly pathogenic avian influenza virus during the 2015 spring outbreaks in the Midwestern United States. Avian Dis 60(3):637–643. Scholar
  50. 50.
    Sims L, Swayne DE (2017) Avian influenza control strategies. In: Swayne D (ed) Animal influenza, 2nd edn. Wiley Balckwell, Ames, IA, pp 363–377Google Scholar
  51. 51.
    Swayne DE, Kapczynski DR (2017) Vaccines and vaccinationf for avian influenza in poultry. In: Swayne DE (ed) Animal influenza, 2nd edn. Wiley-Blackwell, Ames, IA, pp 378–438Google Scholar
  52. 52.
    Castellan DM, Hinrichs J, Fusheng G, Sawitri E, Dung do H, Martin V, McGrane J, Bandyopadhayay FS, Inui K, Yamage M, Ahmed GM, Macfarlane L, Williams T, Dissanayake R, Akram M, Kalpravidh W, Gopinath CY, Morzaria S (2014) Development and application of a vaccination planning tool for avian influenza. Avian Dis 58(3):437–452. Scholar

Copyright information

© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. 2020

Authors and Affiliations

  1. 1.Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research CenterUS Department of Agriculture, Agricultural Research ServiceAthensUSA

Personalised recommendations