Early detection of high-pathogenicity avian influenza viruses (H5 clade 2.3.4.4b) in sediment from wetland habitats preceding an epizootic in wildlife and poultry

Introduction: Environmental surveillance is a promising new strategy for monitoring highly pathogenic avian influenza viruses (HPAIVs), especially panzootic lineages that are spread by migratory birds. In fall 2024, we successfully deployed a surveillance program based on screening sediment specimens from wild bird habitats in British Columbia (BC), Canada. Methods: Surveillance was conducted during the fall migration season at seven wetlands in the Greater Vancouver region. Each site was visited bi-weekly between 5 Sept 2024 and 28 Nov 2024. Twelve sediment specimens were collected per site visit (504 total for the season). Sediment specimens were screened for influenza viruses by RT-qPCR, and positives were further characterized by targeted genomic sequencing. Detection rates in sediment were compared to local HPAIV trends in wildlife and poultry. Phylogenetic analysis was conducted on HPAIV genomic sequences from sediment, wildlife, poultry, and humans in the Pacific Northwest region. Results: HPAIVs from H5 clade 2.3.4.4b were first detected in sediment on 16 Sept. This preceded detections in wildlife, poultry, and a local human case by 17 days, 35 days, and 53 days respectively. Sediment detections increased over the migratory season, peaking the week of Oct 21 with 50% specimen positivity at some sites. Sediment detection trends anticipated subsequent infection trends in wildlife and poultry. Phylogenetic analysis confirmed that HPAIVs in sediment were closely related to those infecting wildlife, poultry, and humans in BC, Alaska, and Washington state. Discussion: Sediment surveillance is a powerful tool that provides early warning of HPAIV incursions during migration seasons.

Kevin Kuchinski, British Columbia Ministry of Agriculture Gabrielle Cortez, University of British Columbia Marzieh Kalhor, University of British Columbia Jake Miller, University of British Columbia Sarah Mansour, British Columbia Centre for Disease Control Natalie Prystajecky, British Columbia Centre for Disease Control Chelsea Himsworth, British Columbia Ministry of Agriculture

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