A genomics-based test identifies and characterizes avian influenza viruses in wetland sediments. (CNW Group/Genome British Columbia)
A genomics-based test identifies and characterizes avian influenza viruses in wetland sediments.

Genomic test may improve avian influenza surveillance

British Columbia research improves ability to detect and predict avian flu outbreaks.

In 2014-15 an outbreak of highly pathogenic avian influenza struck British Columbia, and a total of 13 poultry farms were affected and approximately 240,000 birds died or were destroyed to control the outbreak. Subsequently, the disease was detected in the U.S. where more than 48 million birds were lost and the outbreak was estimated to have cost $3.3 billion and resulted in shortages and price increases for certain poultry products.

Wild waterfowl are known to be the reservoir for avian influenza virus, and although wild bird surveillance programs were already in place in Canada and the U.S., it was limited to collecting and testing individual wild birds, according to an announcement from Genome British Columbia (Genome BC).

To improve the surveillance to include environmental monitoring, in 2015 the British Columbia Ministry of Agriculture, British Columbia 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 avian influenza viruses (AIV) in wetland sediments.

This work, funded in part by Genome BC and led by Drs. Chelsea Himsworth, Jane Pritchard, William Hsiao, Natalie Prystajecky and Agatha Jassem, successfully demonstrated that this novel approach worked, as AIV was detected in a significant proportion of sediment samples, compared to less than 1% rate of detection in the current Canadian national wild bird influenza surveillance program. Additionally, the outbreak virus was found in wetlands throughout the Fraser Valley, information that could have been used to mitigate the outbreak had this technology been available.

To further evaluate this novel surveillance approach, a new project, "Genomic Analysis of Wetland Sediment as a Tool for Avian Influenza Surveillance & Prevention," represents a combined investment of more than $2.5 million from funders and delivery partners including Genome BC, the British Columbia Ministry of Agriculture, the Canadian Food Inspection Agency, Agriculture & Agri-Food Canada, Investment Agriculture Foundation of British Columbia and the Sustainable Poultry Farming Group.

This phase follows on from previous work and is looking at what steps are required to move the technology from a successful proof-of-concept initiative to implementation. This includes scientific validation of technology, as well as its incorporation into provincial and national wild waterfowl influenza surveillance programs. Genome BC said it is anticipated that this innovative approach will be adopted nationally and internationally for surveillance of AIV and/or other diseases associated with wildlife.

"This investment allows Dr. Himsworth and the team to refine and validate the (avian influenza) sediment surveillance with genomics technologies, methodology and field approach," said Dr. Catalina Lopez-Correa, chief scientific officer and vice president, sectors, at Genome BC. "Most importantly, it allows for the identification of the optimal combination of surveillance techniques for maximum efficiency and efficacy."

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