Spatiotemporal patterns of low and highly pathogenic avian influenza virus prevalence in murres in Canada from 2007 to 2022—a case study for wildlife viral monitoring

Wild birds are natural reservoirs of avian influenza virus (AIV), but until 2005 they appeared to be mostly refractory to serious disease caused by infection with highly pathogenic AIV (HPAIV; Liu et al. 2005). However, since 2022, frequent outbreaks, high mortality, and intercontinental spread of HPAIV subtype H5N1 lineage A/goose/Guangdong/1/1996 (Gs/GD) clade 2.3.4.4b have made wild birds a focal point for HPAIV wildlife monitoring worldwide (Ramey et al. 2022; Harvey et al. 2023).

Increased detection of HPAIV-attributable morbidity and mortality in poultry, wild birds, free-living mesocarnivores, and marine mammals in recent years has sparked global concern (Verhagen et al. 2021; Alkie et al. 2022, 2023; Banyard et al. 2022; Caliendo et al. 2022). In Eurasia, HPAIVs are considered to be enzootic, circulating endemically in wild birds (Verhagen et al. 2021; Ramey et al. 2022). The recent changes in HPAIV dynamics in wildlife are due to the emergence of HPAIV H5 clade 2.3.4.4b, which appeared in 2014, and now dominates HPAI disease burden globally with sustained transmission in wild birds (Verhagen et al. 2021). Mass mortality events attributed to 2.3.4.4b have been reported in great skuas (Stercorarius skua) in Scotland (Banyard et al. 2022), South American sea lions (Otaria flavescens) in Peru (Gamarra-Toledo et al. 2023), and harbour seals (Phoca vitulina) in North America, among many species (NOAA 2022). Notably, in 2022, seabirds (e.g., auks, sulids, larids) were particularly affected by 2.3.4.4b, which led to unusual mass mortality events in both North America and Europe (USGS 2022; WHISPers, 2023). Despite global efforts to track and understand the H5 2.3.4.4b clade, it is unclear how common HPAIV infection is among migratory seabirds (Lang et al. 2016).

Murres are a genus of seabirds—also known as guillemots in Europe, turrs in Newfoundland and Labrador, Canada, and as akpa (⊲^b∠) in Nunavut, Canada—that includes common murre (COMU; Uria aalge) and thick-billed murre (TBMU; Uria lomvia). They are abundant, migrate across ocean basins (Frederiksen et al. 2016), and congregate at high-density breeding sites, with potential for high levels of fecal-oral and respiratory transmission of viruses at their colonies (Huang et al. 2014). Murres have been identified as reservoir hosts of low pathogenic AIV (LPAIV) throughout their range in the northern hemisphere (Granter et al. 2010; Huang et al. 2014; Wille et al. 2014; Lang et al. 2016), and have now also been found to be infected by HPAIV in the Netherlands (Caliendo et al. 2022) and Scotland (Falchieri et al. 2022). In Canada, AIV data from murres are available from 2007–2022, before and since 2021 HPAIV incursion(s) in wild birds of North America.

Most wildlife monitoring programs in Canada in 2022 were risk-based, with planning based on known information on AIV in some species. However, this study explores the use of AIV monitoring data at a species-level and how its findings can inform hunters on harvest limits and provide them with guidance regarding risk mitigation and education campaigns. Ideally, disease monitoring is a component of broader population models of mortality and morbidity from multiple sources, which feed into conservation and management priorities and guided actions (Fig. 1). Ongoing monitoring in wild birds and commercial poultry will help identify deviations from normal disease circulation and burden.

Given this context, this analysis is a case study of monitoring viral prevalence in wildlife within a regional outbreak with elevated urgency in a species with conservation, management, and public health implications (Stephen et al. 2018). Prevalence of HPAIV and LPAIV infection were calculated in murres sampled across Canada in 2022, and compared to 2007–2021, where monitoring was episodic as part of long-term population monitoring and research priorities. Our objectives were to: (i) report the detection of HPAIV in murres in Canada in 2022 since the HPAIV incursions into North America; (ii) evaluate differences in LPAIV and HPAIV prevalence in murres in 2022 across regions and sampling months; (iii) investigate how AIV prevalence has changed in murres in Canada in 2022 compared to previous years; and (iv) apply power analyses to inform sampling plans for future viral monitoring in relation to the wildlife health policy needs for murres. Further, we discuss the successes and areas for improvement in the monitoring of pathogens in wildlife generally.

HPAIV H5 clade 2.3.4.4b viruses were widely detected in Canada in 2022 in live and dead murres sampled in the Atlantic and a single live murre from the southeastern Arctic. AIV and HPAIV prevalence in live birds were significantly higher in the Atlantic than Arctic, and were significantly higher during summer months than the rest of the year. HPAIV has not yet been detected in murres in the Pacific, but sampling has been sparse. In comparison with 2007–2021, a period during which HPAIV was not detected in murres, HPAIV and AIV prevalence were significantly elevated in 2022 in the Atlantic and the Arctic.

HPAIV prevalence was low in the Arctic in 2022, but LPAIV prevalence had increased. It is unclear to what extent the relatively higher frequency of LPAIV versus HPAIV in the Arctic is affected by sampling gaps, geographic isolation from affected flyways (lack of opportunity), or other ecological factors. Sampling efforts for AIV monitoring in murres from 2007 to 2022 were highly variable and not comprehensive across breeding colonies, therefore it is possible that HPAIV circulated below detection levels in 2021 in particular; however, there was also a lack of detected excess morbidity or mortality at breeding colonies in 2021. The absence of HPAIV detections in Arctic murres in 2021 corroborates a phylogeographic study that found northern seabird colonies were not implicated among wild birds importing HPAIV in 2021 from Europe to North America via the Atlantic (Caliendo et al. 2022). The patterns of AIV geographic diffusion and interspecies transmission must also take into consideration both virus and host diversity, host behavior, summer temperatures, and geographic distance (Hicks et al. 2022).

We recommend that in future monitoring years 100 samples be collected per site where possible, or per province, to be sufficiently powered to detect moderate increases in HPAIV or AIV prevalence. Additionally, sampling at the same time of year and at the same breeding colonies over time would reduce spatial and temporal (seasonal) bias in sampling, thereby providing more informative data for long term trends assessment. We also recommend recording population parameters, especially annual survival (Frederiksen et al. 2021), alongside disease monitoring to provide more robust information for potential population-level effects.

All the H5 sequences from murres in 2022 fell within clade 2.3.4.4b, and this clade accounted for nearly all the AIV detected in the Atlantic, which is not unexpected based on its preponderance in Canada and the United States (US) since 2021. H5 clade 2.3.4.4b was first detected in Canada in November 2021 in a great black-backed gull (Larus marinus) in St. John’s, NL and then on an exhibition farm amid mass mortality in December 2021 (Caliendo et al. 2022). Phylogenetic analysis of samples from a bald eagle (Haliaeetus leucocephalus) and broiler chickens in BC from February and April 2022 suggested H5 2.3.4.4b was likely first introduced to North America in 2021 via migratory birds through both the Pacific and North Atlantic flyways (Alkie et al. 2022). Prior to the 2021 2.3.4.4b sub-epidemic, high pathogenicity H5 had not been detected since 2015, when H5 clade 2.3.4.4 was identified in BC within small flock chickens and a Cooper’s hawk (Accipiter cooperii; Berhane et al. 2016). From 2014–2015 in the Pacific region of the US, clade 2.3.4.4 (originated from H5N8 then reassorted into H5N1, H5N2) was detected in 2.4% of hunter-harvested birds (Bevins et al. 2016). By June 2015, H5 2.3.4.4 had disappeared in poultry due to interventions such as culling and quarantine, and enigmatically, the clade also appeared to have disappeared in waterfowl (Krauss et al. 2016). However, Ramey et al. responded that this constituted weak evidence of disappearance since the majority of negative samples were collected before the outbreak, in states and provinces where large outbreaks were not reported, and from seabirds, shorebirds, and gulls, as opposed to waterfowl from the order Anseriformes (Ramey et al. 2016); therefore, it is unclear whether H5 2.3.4.4 circulated below detection levels or outside of well-sampled areas, or was indeed eradicated in North America after 2015. Possible mechanisms for this apparent disappearance include existing immunity, antigenic determinants in wild aquatic bird populations, and the cyclic nature of subtype dominance (Krauss et al. 2016). It remains to be seen whether accrual of population-level immunity to H5 2.3.4.4b in wild birds will result in a shift to another subtype or clade, or whether something intrinsic to this clade permits long-term establishment in the wild bird reservoir.

Sampling bias and observational gaps limit the generalizability of our findings. The limitations of small sample sizes and the occurrence of rare events have been considered regularly in ecology (Dixon et al. 2005; Sequeira et al. 2019). When pathogens circulate in wildlife at low prevalence, sample size can influence case ascertainment. The idea that “if you look hard enough you will detect something” (e.g., Mallory et al. 2004) is important to consider when evaluating how prevalence may change over time. While AIV monitoring in murres has not been consistent across the study period, sampling in 2022 did not greatly outpace 2021 in the Atlantic and Arctic; approximately 100 murres in NU were tested annually for AIV prior to 2022. Spurred on by the global concerns around HPAIV, murres were tested in the summer of 2021 as part of an anticipatory effort to increase surveillance (Fig. 3A). Given that sampling effort has not significantly changed, but we see differences in AIV and HPAIV prevalence, this suggests that these are likely reflecting population-level changes. Other sampling biases that may have affected the results are ease of access for live and dead birds, spatially clustered sampling, survival bias among live birds, and pathogenicity bias in birds found dead.

By aggregating data into regions, this analysis was subject to bias due to the modifiable aerial unit problem, whereby summaries are affected by the size and shape of the aggregation unit (Dark and Bram, 2007). Pairwise site-level differences in AIV prevalence were significantly lower within- than between-region, suggesting that regional delineations reflected to some extent meaningful ecological, migratory, and geographic groupings. In a related point, we detected differences in AIV prevalence between breeding colonies and further sampling is required over time to understand if this is a reproducible occurrence. This is consistent with the spatiotemporal variation in AIV prevalence that has been described in wild migratory birds of North America (Munster et al. 2007).

There is an increased need to have up-to-date estimates of prevalence, disease burden, and mortality attributable to HPAIV to inform seabird management and public health risk assessments. At the population level, monitoring viral prevalence and disease burden to determine background and AIV-associated mortality is critical. Disease burden estimates can be incorporated into population status models that consider multiple sources of mortality, where mortality exceeding a threshold can be used as a criterion to warrant taking action with wildlife management tools such as harvest limits and education (Fig. 1B).

Gaps in viral monitoring make it challenging to detect outbreaks and understand whether they are increasing in frequency or severity. Improving viral monitoring systems for data collection, curation, and analysis in wildlife will improve our ability to rapidly detect, respond to, and learn from outbreaks (Verhagen et al. 2021; USGS 2022; WHISPers 2023). There is a critical need to develop evidence-based, wildlife viral monitoring tools by collaborating across agencies to analyze existing data, design programs that are cost-effective, and produce high quality data (Stephen et al. 2004; Giacinti et al. 2022). In Canada, some of the challenges faced by wildlife health surveillance programs include a lack of a regulatory framework surrounding cooperation and coordination across government levels and agencies, as well as complex sampling biases and competing priorities (Giacinti et al. 2022). This results in waves of interest, and the monitoring taking place is resource-dependent and often triggered by some event, such as mass mortalities in wild birds or domestic culling, accompanied by economic losses and public impetus. Resources wane with weakening public interest and eventually are diverted to the next emerging issue. This can be seen in the patterns of AIV monitoring in murres in Canada as described above.

Reactive outbreak mobilization within wildlife viral monitoring programs has also been exemplified for coronaviruses (Ntumvi et al. 2022; Ruiz-Avarena et al. 2022), paramyxoviruses (Drexler et al. 2012), Nipah virus (Epstein et al. 2020), Zika virus (Metsky et al. 2017), Ebola virus (Leroy et al. 2004), and influenza viruses (Bevins et al. 2014; Alkie et al. 2022). There are exceptions to this globally, such as for West Nile virus (Kilpatrick 2011). Although Canada is widely seen to have quite robust wildlife health monitoring programs, this is largely driven by the dedication of regional personnel, and there are clear deficiencies for an ongoing monitoring program. Again, this is demonstrated in the murre dataset as regions differed in their ability to mobilize to increase AIV surveillance at different levels.

From a murre management and conservation perspective, combining viral monitoring with other data, such as presence of other microbes, contaminants, and immune function (Mallory et al. 2010), that affect birds’ survival can reveal cumulative and pleiotropic effects on acute survival and reproduction. In birds, for example, higher prevalence of parasites has been linked to reduced reproductive fecundity (Hudson and Dobson, 1991), and high contaminant levels of mercury may be correlated with more frequently severe viral infections (Teitelbaum et al. 2022). Human activities resulting in environmental and climate changes, as well as habitat loss could alter viral persistence in the environment and provide additional opportunities for viral reassortment and cross-species transmission (Morin et al. 2018; Carlson et al. 2022). Pathogen monitoring is only one aspect of a more comprehensive understanding of wild birds’ population dynamics.

Murre populations experience mortality for a variety of reasons outside of HPAIV, including as bycatch in fisheries gear, oil spill events, poor nutrition, extreme weather, and harvest (Gaston et al. 2002; Wiese et al. 2004; Wiese and Robertson 2004; Clairbaux et al. 2019; Frederiksen et al. 2019). Although tracking banded individuals and birds with logging devices has clarified murre wintering strategies and site fidelity (McFarlane Tranquilla et al. 2014), as well as size and composition of wintering populations (Frederiksen et al. 2016), tracking survival of birds across their range could add a finer resolution of when, where, and possibly how birds are dying. Serological samples paired with swabs from live birds would clarify the role of prior exposure and immunity towards estimated incidence and survival rates. Continued monitoring for HPAIV in birds found dead, including beached bird surveillance, is an additional important surveillance tool to quantify changes in HPAIV diversity and associated mortality.

The population-level impacts of HPAIV are relevant for the sustainability and availability of murres as a food source for subsistence and sociocultural value. The results presented here suggest that during this harvest season, typically 3.5 months between September to March in Atlantic Canada, murres experience low to negligible levels of active infections. The hunter health risk of AIV is low if harvested birds are handled and cooked properly (Canadian Food Inspection Agency 2022). Nonetheless, this information is important to be able to share with harvesters as it relates to bird handling and food security questions. Thus, even though AIV prevalence during the winter murre harvest is likely low, continued winter screening of murres to inform public health advice, and detect any changes in winter prevalence of AIV is advisable, again at the same sample size targets (∼100 individuals per region).

With continuous measurements and predefined action plans, HPAIV monitoring could evolve into HPAIV surveillance (Hoinville et al. 2013). There are often no predefined conservation and management policies or actions for surveillance, but they can include adjusting hunter permitting and safety guidance, education campaigns to reduce exposure, or wildlife vaccination for targeted species of conservation concern, based upon estimates of disease prevalence to counterbalance excess bird mortality (Fig. 1). For the case of murres in Canada, surveillance of AIV is important for both tracking the virus and pathology in murre populations as part of a conservation program, and to inform public health discussions around hunter safety and guidelines related to human ingestion. Within a One Health monitoring framework, which emphasizes the connections between the health of humans, wild and domestic animals, and environments, interdisciplinary collaboration is key to understand, control and prevent zoonoses, and more broadly to enhance ecosystem health (Gibbs 2014).

This analysis of spatiotemporal trends in the prevalence of AIV in murres across Canada serves as a case study of wildlife viral epidemiological monitoring, which could be generalized more broadly for additional species. We are best equipped to understand and mitigate the cumulative impacts of pathogenic threats by quantifying the microbial burden on bird health and survival in the context of the complexity of other health-determining factors.

We gratefully acknowledge all the agencies, laboratories, field crews, individuals, communities, hunters, and laboratory staff who participated in sample collection, transport, molecular analyses, and data curation. Special thanks to Trevor Thompson and Cynthia Pekarik for supporting and enabling this work. We also thank the British Columbia Ministry of Agriculture and Food Animal Health Centre staff and pathologists, wildlife rehabilitation centres, Birds Studies Canada, Fisheries and Oceans Canada, Ecotrust Canada, and Parks Canada. Funding for this study was provided by Environment and Climate Change Canada. We thank the referees for providing comments on our manuscript.