Developing a platform to rapidly monitor changes in influenza virus strain composition from environmental samples in the critical Windsor-Essex border region to prepare for future viral spillover events with pandemic potential

To better understand how influenza virus infections in wild bird populations relate to influenza outbreaks in farm animals and people, this project takes a One Health approach to create a novel platform that efficiently monitors and compares virus genome sequences from infections in these different populations over time. The project aims to address Priority Area 2 by adapting recent advances in the methods validated for monitoring virus sequences in wastewater to overcome the technical challenges posed by the diversity and complexity of influenza virus sequences expected in wild bird populations. During the one-year term of the catalyst grant, we aim to develop and test a virus sampling and genome sequence analysis workflow targeting environmental samples from key sites identified within the Windsor-Essex border region, an area with particular significance for migratory birds at the confluence of two of the four major flyways in North America. The interdisciplinary expertise in our team will address the critical challenges of (1) identifying productive sites to monitor viral infections in migratory and non-migratory wild bird populations, (2) effectively concentrating and isolating viral particles from challenging environmental samples and direct-from-bird samples and (3) refining complementary hybridization probe-capture and targeted amplicon workflows to facilitate genome sequence analysis for a diverse range of influenza virus subtypes. This work will establish and validate a novel and sustainable surveillance platform at a border region that acts as a critical gateway for the entry of viruses and other pathogens into Canada. We will work closely with members of the CBRF-supported INSPIRE network to integrate this surveillance platform into a broader public policy decision-making structure to help leaders in government and industry to make policy decisions using information about viral infections in wildlife, farm animals and humans from a One Health perspective.