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Avian Influenza (AI) is a viral disease that can cause significant morbidity and mortality in domestic poultry. AI outbreaks, and associated eradication efforts, have negative impacts on the economy and food security. In 2014 an AI outbreak in Canada and the US was estimated to have cost over $3B.

Wild waterfowl are the reservoir for AI (shedding virus in their feces) and the focus of AI surveillance programs around the world. Thus far, these programs have been centered on testing of individual wild birds – an approach with significant limitations due to the practical and financial impediments of collecting wild waterfowl samples. These programs were in place during the 2014 but failed to predict outbreaks in either country.

In response to the outbreak Genome BC sponsored a pilot study that brought together experts from the Ministry of Agriculture, Foods and Fisheries in partnership and the BC Centre for Disease Control to test a commercial targeted resequencing platform for the isolation and sequencing of a specific set of viral genes to identify the 2014 AI outbreak virus in wetland sediments. This innovative genomic approach demonstrated that the AI virus was widespread in wetlands throughout the Fraser Valley and likely could have been detected in advance of the outbreak had this approach been available.

The follow-on User Partnership Program project was designed to refine the AI sediment surveillance technology and methodology, to validate the sediment surveillance approach in the field, and to identify the optimal combination of AI surveillance techniques for maximum efficiency and efficacy. The multidisciplinary team surpassed these aims by creating and optimizing a novel targeted resequencing platform. The novel methodology was validated in field studies over two years by demonstrating that the level of detection of AI sequences in sediment samples was superior to the gold standard approach using difficult to obtain samples from live and hunter-killed birds. The success of this endeavor was the impetus for a new collaboration among the Ministries of Health, Agriculture, and Environment. The longer-term goal of this collaboration is to create a One Health Genomics Centre that will dramatically increase genomics capacity in the province and make BC a global leader in One Health approaches to genomic-based pathogen surveillance.