Descriptive Epidemiology and Phylodynamics of the “First Wave” of an Outbreak of Highly Pathogenic Avian Influenza (H5N1 Clade 2.3.4.4b) in British Columbia and the Yukon, Canada, April to September 2022

Abstract

Highly pathogenic avian influenza (HPAI) is a viral disease that causes significant rates of morbidity and mortality in domestic poultry and wild birds, with occasional spillover into mammals, including humans. Beginning in November 2021, Canada experienced its longest and largest outbreak of HPAI in history. A portion of this outbreak (H5N1, clade 2.3.4.4b) occurred in western Canada, specifically in British Columbia (B.C.) and the Yukon, between April 12 and September 11, 2022, which was classified as the “first wave” in this region. Wild birds and mammals identified through passive surveillance and suspect domestic poultry flocks were screened for avian influenza virus (AIV), typed H5 by qPCR, and positive cases were whole genome sequenced. Descriptive epidemiological and phylodynamic analyses were performed to: (1) understand the taxonomic and geographic extent of wild species involved; and (2) examine the origins and probable transmission networks of HPAI viruses introduced into B.C./Yukon by comparing local viruses with those circulating elsewhere in North America. This outbreak included 21 species of wild birds, 2 species of wild mammals, 4 commercial, and 12 domestic small flock infected premises. Canada geese (Branta canadensis) and bald eagles (Haliaeetus leucocephalus) were the most common wild species detected. We demonstrate that north-south avian migration via the Pacific Flyway is the probable route of multiple incursions into this region. Phylogenetic analysis of the hemagglutinin (HA) segment revealed that the B.C./Yukon viruses detected formed five distinct genetic clusters which were maintained across the whole genome. Although, the genome segments were predominantly Eurasian in origin, NP and PB2 segments from all samples, as well as NS and PB1 segments from Cluster 3, had North American origins. Overall, we demonstrate the utility of genomic epidemiology to inform HPAI transmission dynamics across Western Canada and discuss potential knowledge gaps that exist in passive surveillance strategies for HPAI.