As part of initiatives driven by the British Columbia Wildlife Avian Influenza Surveillance Program, we screened oropharyngeal and cloacal swab specimens collected from wild bird carcasses using quantitative reverse transcription PCR targeting a conserved region in the matrix gene and subjected positive samples (cycle threshold <36) to whole-genome sequencing (3). Sequences underwent subtyping, genotyping and phylogenetic analysis as previously described (3).

During October 3, 2024–November 8, 2024, there were 57 detections of HPAI H5N1clade 2.3.4.4b virus in wild birds in British Columbia, including 6 detections of genotype A3 and 51 detections of genotype D1.1 (Figure 1, panel A). Of note, A3 viruses identified in BC in 2024 were more closely related to A3 viruses from Japan (2024) than A3 viruses from British Columbia in 2023, suggesting that they represent a new HPAI incursion from East Asia (Appendix Figure). Most (68.6%, 35/51) detections occurred in the Fraser Valley. Across the province, detections occurred predominantly in cackling geese (Branta hutchinsii; 35.3%, 18/51), followed by Canada geese (Branta canadensis; 17.6%, 9/51) and snow geese (Anser caerulenscens; 15.7%, 8/51); 1–3 detections each occurred in American wigeons (Mareca americana), bald eagles (Haliaeetus leucocephalus), barred owls (Strix varia), great blue herons (Ardea herodias), great horned owls (Bubo virginianus), green-winged teals (Anas carolinensis), northern pintails (Anas acuta), peregrine falcons (Falco peregrinus), and red-tailed hawks (Buteo jamaicensis).

Figure 2

Figure 2. Phylogenetic analysis of concatenated full genome sequences of clade 2.3.4.4b genotype D1.1 detections in wild birds, poultry, and a human from a study of highly pathogenic avian influenza A(H5N1) in...

On November 8, 2024, we confirmed a diagnosis of influenza caused by HPAI H5N1 clade 2.3.4.4b genotype D1.1 in a teenager from the Fraser Valley (5). The sequence we obtained from this patient was most closely related to viruses detected in wild birds (Figure 2). The D1.1 lineage strain of the virus has also been associated with all but one of the 60 poultry outbreaks that occurred in British Columbia during October 21–November 30, 2024 (4).

Figure 3

Figure 3. Phylogenetic relationships and possible origins of the neuraminidase (NA) segment (Am4N1) of the clade 2.3.4.4b D1.1 genotype detected in fall 2024 as part of a study of highly pathogenic avian...

The D1.1 genotype contained 4 Eurasian lineage segments (hemagglutinin, matrix, nonstructural, and polymerase basic 1) that were related to the 2023 BC A3 lineage viruses and 4 segments from North American lineage viruses (neuraminidase [NA], nucleoprotein, polymerase acidic, and polymerase basic 2), including an NA segment not previously associated with HPAI H5N1 clade 2.3.4.4b viruses in British Columbia (Table). Although the 2024 D1.1 lineage viruses and the 2023 A3 lineage viruses shared a recent common ancestor, the 2024 D1.1 lineage viruses displayed less genetic divergence than expected over that intervening time (Figure 1, panel B). Phylodynamic analysis using BEAST (https://beast.community) and sequences from National Center for Biotechnology Information and GISAID (https://www.gisaid.org) databases revealed that the closest relative to the D1.1 Am4N1 NA segment was an H1N1 virus detected in a mallard (A/mallard/BC/AIV-PHL-2360/2024) from the British Columbia interior on August 20, 2024, and that the reassortment event involving that segment may have occurred in fall 2023 (Figure 3) (6). That H1N1 virus belongs to a lineage of earlier H1N1 viruses also detected in mallards and was distantly related to another H1N1 detected in Alberta (A/Mallard/AB/539/2023). Of note, several Am4N1 segments from D1.1 viruses in poultry from the same British Columbia outbreak (A/chicken/BC/FAV-0289-002/2024, A/chicken/BC/FAV-0284-001/2024, A/turkey/BC/FAV-0306-1/2024) had a mutation associated with antiviral resistance, NA-H275Y (7); however, that mutation was not detected in any of the wild bird sequences.

The once dominant B genotypes associated with the HPAI H5N1 clade 2.3.4.4b virus incursion via the Eastern Atlantic Flyway do not appear to be circulating in wild birds within the Pacific Flyway as of fall 2024 (despite the continuing presence of genotype B3.13 in cattle in the western United States [8]) (Table). Instead, a novel genotype, D1.1, has emerged that is the result of a reassortment among the A3 genotypes originally introduced via the Pacific Flyway and >1 North American lineage avian influenza viruses. This virus spilled over into poultry in British Columbia and infected 1 human and has also been detected in parts of the United States south of British Columbia (Figure 2).

Compared with A3 viruses detected a year earlier, the hemagglutinin segment of the D1.1 viruses had acquired fewer net substitutions than expected, despite sharing a relatively recent common ancestor (Figure 1, panel B). This finding could suggest that the D1.1 genotype or its ancestors may have been preserved in an environmental reservoir—e.g., in frozen wetlands in the high arctic (9)—in the summer of 2024 before being reintroduced into migratory birds in the fall. Alternatively, this viral lineage may be particularly well adapted to certain wild bird species or populations, resulting in circulation with minimal evolutionary pressure. This finding has implications for the use of molecular clock theory in phylodynamic modeling of HPAI viruses.

We note that D1.1 appears to be unique among the HPAI H5N1 clade 2.3.4.4b genotypes due to the acquisition of a North American lineage NA segment. The Am4N1 NA segment likely originated from a reassortment event involving waterfowl in western Canada, potentially within British Columbia. Further studies are needed to determine where and when the other reassorted segments were acquired.

Of interest, the prevalence of environmental HPAI H5N1 virus clade 2.3.4.4b detections based on genomic analysis of wetland sediment was far greater in fall 2024 than for data from fall 2023 (10). This phenomenon could suggest that a great number of birds were infected with D1.1 compared with other genotypes in previous years, that the genotype is associated with greater viral shedding, or both. The NA segment encodes the enzyme required for viral release from infected cells (11). Certain NA lineages, therefore, might increase viral shedding in wild birds. Considering the explosive wave of poultry outbreaks observed in British Columbia in late 2024, it would be prudent to investigate whether the Am4N1 NA segment has a functional impact on host-virus interactions. In addition, it will be important to determine the implications of D1.1 for host range and infectivity, given that the virus detected in the human case was most closely related to those found in wild birds, suggesting the potential for direct or indirect transmission from wild birds to humans.