Avian Influenza Virus Sample Types, Collection, and Handling

  • Mary Lea KillianEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2123)


Successful detection of avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be considered prior to sample collection. Sera are acceptable samples for ELISA or agar gel immunodiffusion tests, but not for real-time RT-PCR. Likewise, swabs and/or tissues are acceptable for real-time RT-PCR and virus isolation. The sample type will also depend on the type of birds that are being tested; oropharyngeal swabs from gallinaceous poultry and cloacal swabs from waterfowl are the preferred specimens for most diagnostic tests, although it is optimal to collect swabs from both locations, if possible. In addition to collecting the appropriate sample for the tests to be performed, selecting the right materials for sample collection (i.e., type of swab) is very important. This chapter will outline the collection of different specimen types and procedures for proper specimen handling.

Key words

Avian influenza diagnostics Avian influenza Virus detection Specimen collection Sample processing 


  1. 1.
    Swayne DE, Suarez DL, Sims LD (2013) Influenza. In: Swayne D (ed) Diseases of poultry, 13th edn. Blackwell, Ames, IA, pp 181–218CrossRefGoogle Scholar
  2. 2.
    WHO manual on animal influenza diagnosis and surveillance (2002). World Health Organization, Geneva, SwitzerlandGoogle Scholar
  3. 3.
    Swayne DE, Senne D, Suarez DL (2008) Avian influenza. In: Dufour-Zavala L, Swayne DE, Glisson J et al (eds) Isolation and identification of avian pathogens, 5th edn. American Association of Avian Pathologists, Jacksonville, FL, pp 128–134Google Scholar
  4. 4.
    Spackman E, Pedersen JC, McKinley ET, Gelb J Jr (2013) Optimal specimen collection and transport methods for the detection of avian influenza virus and Newcastle disease virus. BMC Vet Res 9:35. Scholar
  5. 5.
    Johnson FB (1990) Transport of viral specimens. Clin Microbiol Rev 3(2):120–131CrossRefGoogle Scholar
  6. 6.
    Busquets N, Abad FX, Alba A, Dolz R, Allepuz A, Rivas R, Ramis A, Darji A, Majo N (2010) Persistence of highly pathogenic avian influenza virus (H7N1) in infected chickens: feather as a suitable sample for diagnosis. J Gen Virol 91(Pt 9):2307–2313. Scholar
  7. 7.
    Fereidouni SR, Globig A, Starick E, Harder TC (2012) Effect of swab matrix, storage time, and temperature on detection of avian influenza virus RNA in swab samples. Avian Dis 56(4 Suppl):955–958CrossRefGoogle Scholar
  8. 8.
    Daum LT, Worthy SA, Yim KC, Nogueras M, Schuman RF, Choi YW, Fischer GW (2011) A clinical specimen collection and transport medium for molecular diagnostic and genomic applications. Epidemiol Infect 139(11):1764–1773. Scholar
  9. 9.
    Keeler SP, Ferro PJ, Brown JD, Fang X, El-Attrache J, Poulson R, Jackwood MW, Stallknecht DE (2012) Use of FTA sampling cards for molecular detection of avian influenza virus in wild birds. Avian Dis 56(1):200–207CrossRefGoogle Scholar
  10. 10.
    Beck JR, Swayne DE, Davison S, Casavant S, Gutierrez C (2003) Validation of egg yolk antibody testing as a method to determine influenza status in white leghorn hens. Avian Dis 47(3 Suppl):1196–1199CrossRefGoogle Scholar
  11. 11.
    Murphy FA, Gibbs EPJ, Horzinek MC, Studdert MJ (1999) Veterinary virology. Elsevier Science, AmsterdamGoogle Scholar
  12. 12.
    OIE (2018) Manual of diagnostic tests and vaccines for terrestrial animals 2018. World Organization for Animal Health (OIE). Accessed 20 Sept 2018
  13. 13.
    Avian samples collection for infleunza A and Newcastle disease (2016)Google Scholar
  14. 14.
    Kramer MH, Harris DJ (2010) Avian blood collection. J Exot Pet Med 19:82–86. 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.Avian Viruses Section, Diagnostic Virology Laboratory, National Veterinary Services LaboratoriesUS Department of AgricultureAmesUSA

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