Environment: a potential source of animal and human infection with influenza A (H5N1) virus

Influenza Other Respir Viruses. 2012 Nov;6(6):442-8. doi: 10.1111/j.1750-2659.2012.00338.x. Epub 2012 Feb 17.


Background: Very little is known regarding the persistence of highly pathogenic avian influenza H5N1 viruses in natural settings during outbreaks in tropical countries, although environmental factors may well play a role in the persistence and in the transmission of H5N1 virus.

Objective: To investigate various environmental compartments surrounding outbreak areas as potential sources for H5N1 virus transmission.

Methods: Environmental specimens were collected following outbreaks of avian influenza in Cambodia between April 2007 and February 2010. The methods used to concentrate H5N1 virus from water samples were based either on agglutination of the virus with chicken red blood cells or on adsorption on glass wool, followed by an elution-concentration step. An elution-concentration method was used for mud specimens. All samples that tested positive by real-time RT-PCRs (qRT-PCRs) targeting the HA5, M and NA1 genes were inoculated into embryonated hen eggs for virus isolation.

Results: Of a total of 246 samples, 46 (19%) tested positive for H5N1 by qRT-PCRs. Viral RNA was frequently detected in dust, mud and soil samples from the farms' environment (respectively, 46%, 31% and 15%). Samples collected from ponds gave a lower proportion of positive samples (6%) as compared to those collected from the farms (24%). In only one sample, infectious virus particles were successfully isolated.

Conclusion: During H5N1 virus outbreaks, numerous environmental samples surrounding outbreak areas are contaminated by the virus and may act as potential sources for human and/or animal contamination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cambodia / epidemiology
  • Chickens
  • Influenza A Virus, H5N1 Subtype / isolation & purification*
  • Influenza in Birds / epidemiology
  • Influenza in Birds / virology
  • RNA, Viral / genetics
  • Real-Time Polymerase Chain Reaction
  • Sewage / virology*
  • Virology / methods
  • Water Microbiology*


  • RNA, Viral
  • Sewage