Transmission dynamics of highly pathogenic avian influenza virus at the wildlife-poultry-environmental interface: A case study

Abstract

Avian influenza viruses (AIVs) regularly circulate between wild and domestic bird populations. Following several high-profile outbreaks, highly pathogenic AIVs (HPAIV) with zoonotic potential have been the subject of increasing attention. While we know that HPAIV is transmitted between domestic birds, wildlife, and the environment, little is known about persistence and spillover/back at these interfaces. We integrated the test results of samples collected on and around an infected domestic poultry premise (IP) where H5N1 HPAIV was confirmed in a flock of poultry in 2022 in Southern Ontario, Canada to explore the transmission cycle of AIVs in wildlife and the environment. We sampled a captive flock of Mallards (Anas platyrhynchos) that resided on site, sediment samples collected from water bodies on site, and examined samples collected through surveillance within a 100 km radius of the IP from live wild ducks and sick and dead wildlife. We found serologic evidence of H5 exposure in the captive mallards that resided on site despite no evidence of morbidity or mortality in these birds and no PCR positive detections from samples collected at two different timepoints. Genetic material from the same H5N1 HPAIV subtype circulating in the domestic birds and from low pathogenicity avian influenza viruses were detected in wetlands on site. The results of live and sick and dead surveillance conducted within a 100 km radius confirmed that the virus was circulating in wildlife before and after IP confirmation. These results suggest that biosecurity remains the most critical aspect of minimising spillover/back risk in a virus that has been shown to circulate in asymptomatic wild birds and persist in the surrounding environment.

Keywords: Avian influenza virus; Canada; Domestic poultry; Environment; H5N1; Highly pathogenic avian influenza virus (HPAIV); Mallard; Migratory birds; Spillback; Spillover; Wild bird surveillance; Wild-domestic interface.

Fig. 1

Timeline of events in relation to the detection of Highly Pathogenic Avian Influenza Virus (HPAIV) on the infected premise (IP). The date of the detection at the IP is referred to as 0, with days before and after represented as integers.

Fig. 2

The number of sick and dead wildlife that were found and submitted to the Canadian Wildlife Health Cooperative (black dashed line) within 100 km of a domestic premises in the eight weeks prior to and following the date of detection of highly pathogenic avian influenza on that premises (i.e., Day 0). The number of sick and dead wildlife that were H5 positive on RT-PCR at the National Centre for Foreign Animal Disease is shown by the red line. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

Avian influenza virus genomic material was recovered from five ponds on the infected premise. Two visits were made six months apart, during which superficial sediment specimens were collected from three sub-locations within each pond. Genomic material from the haemagglutinin (HA) and neuraminidase (NA) genome segments was recovered and subtyped using a custom targeted genomic sequencing method. Heatmap shading depicts the percentage of sub-locations within the indicated pond that were positive for the indicated HA or NA subtype.

Fig. 4

Phylogenetic relationships between HPAI H5N1s collected from the infected premise and local wildlife surveillance. Phylogenetic tree was constructed using all 8 segments of the IAV genome. Genomes recovered from live hosts are depicted by circular leaves while those recovered from dead hosts are depicted with “X” leaves. The tree branch line-type represents the viral host status when sampled (sick/dead or live) and branch color represents host origin (either wild or domestic). Ancestral states for host origin and status are reconstructed across all nodes of the tree. Fragmentary HPAI H5 sequences recovered from ponds on the premise were aligned to HA segment sequences from the bird-origin HPAI genomes composing the tree, and the best match(es) for each fragment were determined based on alignment bitscores. Each bird-origin HPAI genome in the tree was allocated a score based on the number of pond fragments for whom it was their best match as well as the identity and length of its alignments with those fragments. These scores are indicated in the heatmap next to the tree. The branch length scale bar indicates number of mutations across all 8 segments of the IAV genome.

Fig. S1

Schematic of the wetland ponds present on the infected premise. The poultry barn was approximately 100 m from the nearest pond. Premise mallards were fed daily on the shoreline of that same pond. The black numbers are the pond identifiers assigned during sampling, and the small letters denote where sediment samples were collected. The colours of the markers indicate the presence/absence of AIV detections on Day 12 (red = positive, grey = negative).

Fig. S2

Results of a) rNP and b) rH5 cELISA on premise mallard blood samples. The black line indicates the laboratory determined percent inhibition (%) threshold above which is considered a positive result.