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sector_ico_Agrifood_trans Agrifood

Genomic Analysis of Wetland Sediment as a Tool for Avian Influenza Virus Surveillance in Wild Waterfowl

  • Project Leaders: Chelsea Himsworth, Agatha Jassem, Natalie Prystajecky, William Hsiao
  • Institutions: University of British Columbia (UBC)
  • Budget: $310450
  • Program/Competition: Emerging Issues
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2015
  • Status: Closed

In 2014/2015 an outbreak of highly pathogenic Avian Influenza (AI) struck British Columbia. A total of 13 poultry farms were affected and approximately 240,000 birds died or were destroyed to control the outbreak. The economic impact of a similar outbreak that occurred in the same location in 2004 was close to $600M.

Wild waterfowl are known to be the reservoir for AI, and although wild bird AI surveillance programs were already in place in Canada and the USA, it was limited to collecting and testing individual wild birds. To improve the surveillance to include environmental monitoring, in 2015 the BC Ministry of Agriculture, BC Centre for Disease Control Public Health Laboratory, and University of British Columbia joined forces to develop a new approach – a genomics-based test that identifies and characterizes AI viruses (AIV) in wetland sediments.

The project team collected 300 sediment samples from 15 wetlands within the Fraser Valley during the above outbreak, plus 45 samples from ‘mini wetlands’ (i.e., outdoor areas where wild waterfowl were observed to congregate) on infected farms.  The preliminary results showed a detection rate to be up to 37 times more sensitive when compared to the current BC Ministry of Agriculture surveillance program. In addition, a diverse array of AI viruses was identified and characterized in these samples, suggesting early widespread of viruses in waterfowl populations. This showed the potential for early detection, in advance of the outbreak, had this technology been available. A Phase II project working on refinement and validations of this genomics tool with the aim of eventual implementation were funded under Genome BC’s User Partnership Program.