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

Abstract

Following the detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada, in late 2021, avian influenza virus (AIV) surveillance in wild birds was scaled up across Canada. Herein, we present the 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. The key objectives of the surveillance program were to (i) identify the presence, distribution, and spread of HPAIV and other AIVs; (ii) identify wild bird morbidity and mortality associated with HPAIV; (iii) identify the range of wild bird species infected by HPAIV; and (iv) genetically 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 the presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across interagency partners.

Importance: We present the results of Canada's Interagency Surveillance Program for Avian Influenza in Wild Birds in the year following the first detection of highly pathogenic avian influenza virus (HPAIV) H5N1 on the continent. The surveillance program tested over 17,000 wild birds, both sick and apparently healthy, which revealed spatiotemporal and taxonomic patterns in HPAIV prevalence and mortality across Canada. The significant shift in the presence and distribution of HPAIV in Canada's wild birds underscores the need for sustained investment in wild bird surveillance and collaboration across One Health partners.

Keywords: H5N1; avian influenza; highly pathogenic avian influenza virus; low pathogenicity avian influenza virus; reservoir; surveillance; wild birds.

Fig 1

Timeline of events between November 2021 and 2022 following the first confirmed case of the H5N1 clade 2.3.4.4b highly pathogenic avian influenza virus in Canada. The timeline is stratified by flyway (Pacific, Central, Mississippi, and Atlantic) and province/territory (BC, British Columbia; YK, Yukon; AB, Alberta; SK, Saskatchewan; NT. Northwest Territories; MB, Manitoba; ON, Ontario; NU, Nunavut; QC, Quebec; NB, New Brunswick; NS, Nova Scotia; NL, Newfoundland and Labrador; and PE, Prince Edward Island), which are denoted with colors. The first wild bird sample and domestic premises confirmed to be HPAIV-positive in each province are indicated with an icon. The identity of the HPAIV detected is indicated with color outline. Unusual wild bird mortalities are indicated with a solid black line spanning the relevant period of time (AGWT, American Green-winged Teal; ARTE, Arctic Tern; ATPU, Atlantic Puffin; AWPE, American White Pelican; BLKI, Black-legged Kittiwake; CACG, Cackling Goose; CANG, Canada Goose; COEI, Common Eider; COMU, Common Murre; COTE, Common Tern; DCCO, Double-crested Cormorant; EAGR, Eared Grebe; NOGA, Northern Gannet; RAZO, Razorbill; RBME, Red-breasted Merganser; ROGO, Ross’ Goose; SNGO, Snow Goose; and WEGR, Western Grebe).

Fig 2

Distribution of (A) sick and dead wild birds submitted and tested, (B) live and hunter-harvested wild birds tested for avian influenza virus, (C) the number of sick and dead wild birds confirmed or suspected to be positive for highly pathogenic avian influenza virus, and (D) the proportion of live and hunter-harvested wild bird samples confirmed or suspected to be positive for HPAIV in Canada between November 2021 and December 2022, based on RT-PCR. Internal boundaries indicate the watershed (i.e., sub-sub-drainage area) where samples were received for testing. Shapefile was downloaded from the National Hydro Network (43) on 19 October 2022 and was clipped to the land boundary.

Fig 3

Number of sick and dead wild birds submitted for testing and suspected or confirmed highly pathogenic avian influenza virus or low pathogenicity avian influenza virus positive in Canada between November 2021 and November 2022. Color shading reflects general administrative migratory flyway routes (orange, Pacific; green, Central; blue, Mississippi; and yellow, Atlantic).

Fig 4

Wild birds tested for avian influenza virus between November 2021 and November 2022 across Canada obtained through (A) morbidity and mortality surveillance and (B) live and hunter-harvested surveillance.

Fig 5

Breakdown of sick and dead wild bird samples that were confirmed or suspected highly pathogenic avian influenza virus positive between November 2021 and November 2022 across Canada stratified by taxonomic order and species functional group. The data are shown as a treemap; the area of each rectangle is proportional to the number of wild bird samples that were confirmed or suspected HPAIV positive. [GA, Galliformes; CO, Columbiformes; PR, Procellariiformes (N = 2); unlabeled Passeriformes; other (N = 4); unlabeled Charadriiformes, Sandpipers and Allies (N = 2)]. The data shown here reflect the samples that were tested and therefore do not represent the number of birds that died from HPAIV.

Fig 6

Number of live and hunter-harvested wild birds submitted for testing and suspected or confirmed highly pathogenic avian influenza virus or low pathogenicity avian influenza virus positive in Canada between November 2021 and November 2022. Color reflects migratory flyway routes (orange, Pacific; green, Central; blue, Mississippi; and yellow, Atlantic).

Fig 7

Avian influenza viruses characterized from wild birds sampled during the first year of the outbreak (November 2021–November 2022) in the (A) Pacific Flyway, (B) Central Flyway, (C) Mississippi Flyway, and (D) Atlantic Flyway, stratified by surveillance component and month. AIV detected included wholly Eurasian, wholly North American, and 10 reassortant viruses, the genetic composition of which is described in Table 1.

Fig 8

Time-calibrated maximum likelihood phylogenetic tree of 1,166 HPAIV H5N1 viruses collected from wild bird hosts between November 2021 and 2022. Tree branches are colored according to the flyway in which the sample was collected. Host taxonomic order is represented by colored bars at tree tips. The geographic origin of genome segments 1–8 (either Eurasian or North American) for all tree tips is represented by red and gray bars (from left to right: PB2, PB1, PA, HA, NP, NA, M, and NS). First H5N1 2.3.4.4b detections following the initial incursions into Canada are annotated.

Fig 9

Distribution of avian influenza viruses characterized from wild birds sampled during the first year of the H5N1 outbreak (November 2021–November 2022) across Canada. Viruses detected included those with (A) wholly Eurasian or North American origins, and (B–D) and 10 reassortants, the genetic composition of which is described in Table 1. Provinces and territories are colored by the predominant migratory bird flyway.