Avian influenza viruses in wild birds in Canada following incursions of highly pathogenic H5N1 virus from Eurasia in 2021/2022

Abstract

Following detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada in late 2021, avian influenza surveillance in wild birds was scaled-up across Canada. Herein, we present results of Canada’s Interagency Surveillance Program for Avian Influenza in wild birds during the first year (November 2021 – November 2022) following the incursions of HPAIV from Eurasia. Key objectives of the surveillance program were to (i) detect the presence, distribution and spread of HPAIV and other avian influenza viruses (AIVs), (ii) detect wild bird morbidity and mortality associated with HPAIV, (iii) identify the range of wild bird species infected by HPAIV, and (iv) characterize detected AIV. A total of 6,246 sick and dead wild birds were tested, of which 27.4% were HPAIV positive across 12 taxonomic orders and 80 species. Geographically, HPAIV detections occurred in all Canadian provinces and territories, with the highest numbers in the Atlantic and Central flyways. Temporally, peak detections differed across flyways, though the national peak occurred in April 2022. In an additional 11,295 asymptomatic harvested or live captured wild birds, 5.2% were HPAIV positive across 3 taxonomic orders and 19 species. Whole genome sequencing identified HPAIV of Eurasian origin as most prevalent in the Atlantic flyway, along with multiple reassortants of mixed Eurasian and North American origins distributed across Canada, with moderate structuring at the flyway scale. Wild birds were victims and reservoirs of HPAIV H5N1 2.3.4.4b, underscoring the importance of surveillance encompassing samples from sick and dead, as well as live and harvested birds to provide insights into the dynamics and potential impacts of the HPAIV H5N1 outbreak. This dramatic shift in presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across One Health partners.

Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses

“…Those that survived infection in 2022, particularly Northern Gannets, Common Murres and Common Eiders, likely retained some level of immune protection in the year that followed (J. Provencher and J. Giacinti, unpublished data) which we posit explains the lower reported mortalities. Additionally, after more than a year of circulation across the continent, the ancestral virus responsible for high rates of mortality in 2022 (e.g., wholly Eurasian strain), has given rise to many reassortant HPAI viruses (Alkie et al 2023, Giacinti et al 2023, Signore et al in prep). The extensive circulation of these genetically distinct reassortants, along with pre-existing immunity to HPAI, resulted in vastly different patterns of transmission, disease, and mortality than what occurred in 2022.…”

“…The large Greater Snow Goose population (estimated at 900,000 in 2015; Lefebvre et al 2017) means that our documented event involving 1,643 mortalities is not concerning from a conservation perspective. However, it is worth noting that notable mortalities in the hundreds or thousands have also been reported for Lesser Snow Geese in the Central Flyway and Pacific Flyway (Giacinti et al, 2023). Given the apparent susceptibility of all subspecies of Snow Geese to HPAI, efforts to collate mortality reports and disease surveillance data may be warranted if repeated mortality events from HPAI occur seasonally.…”

“…In North America, the first confirmed case of HPAI clade 2.3.4.4b H5N1 in a wild bird was detected in a Great Black-backed Gull ( Larus marinus ) in late 2021 in Newfoundland, Canada (Caliendo et al, 2022). Since then, mass mortality events in seabirds (e.g., Pelecaniformes, Suliformes, and Charadriiformes), sea ducks (e.g., American Common Eider; Somateria mollissima ), and geese (Anseriformes; waterfowl) have been documented (Avery-Gomm et al, 2024; Giacinti et al, 2023). To date, the largest mortalities associated with HPAI in North America have been in eastern Canada, where at least 40,391 wild birds died during the 2022 HPAI outbreak between April and September 2022 (Avery-Gomm et al, 2024).…”

Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland

“…The collated dataset included information on species, date, location (coordinates), observer information, and total observed mortality. Reported mortalities were attributed to HPAI if a species tested positive for the HPAI H5N1 clade 2.3.4.4b virus in eastern Canada between April 1 and September 30, 2022 (Giacinti et al 2023). For reports with less specific taxonomic identity (e.g., unknown gull), HPAI was presumed to be the cause of mortality if more than 50% of that group of species commonly observed within the area tested positive for HPAIV.…”

“…The first reported instance of widespread mortality in seabirds in Canada due to this virus occurred among American Common Eiders ( Somateria mollissima ) in Québec, Canada in May 2022 and was immediately followed by observations of sick and dead Northern Gannets ( Morus bassanus ) on the shores of the Gulf of St. Lawrence (Avery-Gomm et al 2024). These first outbreaks among colonial-nesting seabirds signaled the onset of extensive mass mortality that occurred throughout eastern Canada from May to September 2022 (Giacinti et al 2023; Avery-Gomm et al 2024).…”