Highly Pathogenic Avian Influenza virus in endangered whooping cranes

Whooping cranes are an iconic species. North America’s tallest bird, they stand 1.5m tall and are easily recognizable to many Canadians by their wingspan of up to 2.5m, snowy-white body with black-tipped wings, large red head patch, and bugling call (Figure 1).

Figure 1. Adult whooping cranes on a wetland in central Saskatchewan, October 2025. Photo © Michael Forsberg.

Brought to the brink of extinction by overhunting and habitat loss, the species that once likely exceeded 10,000 individuals was reduced to only 15 cranes by 1941. Those birds belonged to the Aransas-Wood Buffalo population. This single flock over-winters in the Aransas National Wildlife Refuge on the Texas Gulf Coast and migrates north in the spring to breed near the northeast corner of Wood Buffalo National Park (which spans the Alberta-Northwest Territories border) and adjacent areas of the Northwest Territories. Through herculean efforts in both Canada and the United States the species was saved from the fate of the passenger pigeon to where they now number approximately 830 total individuals in North America with about 560 birds in the Aransas-Wood Buffalo Population. With their distinctive appearance and rarity, the sighting of whooping cranes during their spring and fall migrations is a highlight of many people’s outdoor experience.

Classified as endangered in Canada and the US, the whooping crane is collaboratively managed by wildlife specialists in both countries. Counts are made annually on the breeding and wintering grounds, and in some years, individuals are fitted with leg-mounted satellite trackers to track their movements and survival.

Figure 2. The first whooping crane, found severely scavenged on October 9th, 2025. Photo courtesy of Mark Bidwell, CWS

This fall, Mark Bidwell and John Conkin, wildlife biologists with the Canadian Wildlife Service (CWS) based in Saskatoon, were tracking 49 whooping cranes as they migrated south through Saskatchewan when, in early October, they received a message that one of the transmitters had been immobile for several days approximately 90 km east of Saskatoon, suggesting the animal had died. When Mark and John investigated on October 9th, they found the partially scavenged carcass of an adult whooping crane. They immediately contacted the Western/Northern Regional Centre of the Canadian Wildlife Health Cooperative (W/N CWHC) based out of the Western College of Veterinary Medicine in Saskatoon to arrange an autopsy. When the carcass was submitted, Mark warned us that not much remained due to scavenging (Figure 2). We were suspicious that highly pathogenic avian influenza (HPAIV) might be the cause of death as we had been diagnosing this disease in geese, ducks, raptors, and in other avian and mammalian species beginning in September as fall migration increased throughout the province. Additionally, even more observations of sick and dead birds were submitted to us by members of the public through our wildlife reporting website (http://cwhc.wildlifesubmissions.org/) and Wildlife Health Tracker app, and reports were also made to the Saskatchewan Ministry of Environment via their telephone hotline.

Once the carcass arrived at our diagnostic laboratory, Dr. Shelagh Copeland and team went to work, firstly to diagnose the cause of death, but also to radiograph, collect, and test samples following the autopsy protocol established by the joint US and Canadian Whooping Crane Health Advisory Committee. The W/N CWHC operates their diagnostic lab out of a facility managed by Prairie Diagnostic Services (PDS), the provincial veterinary diagnostic laboratory, which allows us ready access to a range of diagnostic tests and expertise. Within a couple of days, PDS was able to confirm that tissues were positive for H5 avian influenza virus consistent with HPAIV. The limited tissues that could be collected from the scavenged carcass were processed for histology and examined with light microscopy by W/N CWHC pathologists to determine that the crane had indeed died of avian influenza.

Figure 3. The second whooping crane, found scavenged on October 22nd, 2025. Photo courtesy of Mark Bidwell, CWS.

We were just finalizing these autopsy findings when a member of the public reported a second dead whooping crane to CWS, this time on a wetland about 95 km NW of Saskatoon. When first reported on October 21 this crane had recently died, but when retrieved by CWS biologists the following day it was being scavenged by a bald eagle with gulls in close proximity (these species are also susceptible to HPAIV; Figure 3). Surveys and public reports indicated this wetland had been used by up to 85 whooping cranes during the previous three weeks, and two adult whooping cranes and their chick were present when the carcass was recovered. Within a few days of its arrival to the W/N CWHC lab, we were able to confirm that this crane had also died of H5 positive avian influenza virus. Tissue samples from these cranes were collected for genetic biobanking, a collaboration with the Toronto Zoo, but these samples unfortunately had to be discarded because of the H5 AIV diagnosis.

Samples from the two cranes were submitted to the National Centre for Foreign Animal Disease (NCFAD), Canadian Food Inspection Agency Laboratory in Winnipeg, Manitoba, for confirmatory testing. Despite advanced decomposition of the carcasses, HPAI H5N1 virus was successfully isolated from both specimens. Whole‑genome sequencing revealed that the viruses belonged to the D1.1 genotype of clade 2.3.4.4b H5N1, and were genetically closely related to other D1.1 viruses currently circulating in North America. The D1.1 genotype emerged in late 2024 following reassortment events between Eurasian H5N1 clade 2.3.4.4b viruses and North American low‑pathogenic avian influenza strains. First detected in British Columbia poultry in October 2024, D1.1 rapidly spread during autumn migration, becoming the dominant HPAI genotype across the Pacific, Central, and Mississippi flyways. Since its emergence, D1.1 has been confirmed in wild birds, commercial poultry, and backyard flocks across Canada and the United States, with over 80 poultry premises affected in Canada alone. Importantly, D1.1 has demonstrated an expanded host range. In January 2025, the USDA confirmed the first detection of D1.1 in dairy cattle in Nevada, marking a novel spillover into livestock. Human infections associated with D1.1 have also been reported, including a critical case in a teenager in British Columbia in November 2024 and a dairy worker in Nevada in February 2025. While human‑to‑human transmission has not been documented, these zoonotic cases underscore the public health risk. The complete genome sequences of the viruses isolated from both cranes have been deposited in the Global Initiative on Sharing All Influenza Data (GISAID) under accession numbers EPI_ISL_20249109 and EPI_ISL_20249110.

The deaths of these two endangered whooping cranes highlight several important points about wildlife health and conservation. First, endangered species, due to their critically low population numbers, are particularly vulnerable to the effects of disease. Diseases that are maintained in species that are widespread and relatively abundant can often withstand losses, whereas these same diseases can have a significant impact on rare species due to a higher proportion of the population being affected. Additionally, when a population is reduced to very low numbers, such as when whooping cranes were reduced to 15 individuals, the species can lose genetic diversity, called a “genetic bottleneck”, which can make them more vulnerable to disease. These endangered species often have low reproductive rates which can also slow or prevent recovery.

Secondly, infectious diseases are constant and evolving threats, especially for endangered species. Early attempts at captive rearing of whooping cranes revealed the species was particularly susceptible to Eastern Equine Encephalitis virus, a mosquito borne virus endemic to eastern North America, prompting a vaccination program to protect these birds in captivity. Fortunately, they did not appear to be particularly susceptible to West Nile virus (https://healthywildlife.ca/west-nile-virus-wnv-things-you-should-know/), another mosquito borne virus introduced into New York City in 1999 that had spread to most of North America by 2009, causing mortalities in other avian species and, in some cases, population declines.

The current Eurasian HPAIV was first detected in North America in late 2021, introduced across the Atlantic via migratory birds. Susceptibility of whooping cranes to the strain is unknown, but testing by Environment and Climate Change Canada of live whooping cranes suggests a history of low exposure to avian influenza viruses, and potentially high susceptibility given the lack of pre-existing immunity. These two mortalities are the only confirmed cases of HPAIV in wild whooping cranes, but in September a captive juvenile crane that was about to be released died of avian influenza in Wisconsin. Crane species worldwide have fallen victim to HPAIV, with the global H5N1 outbreak causing mass mortalities of cranes in the Middle East, Asia, Europe and North America. Wildlife biologists report that cranes’ social behavior and use of wetlands shared with waterfowl probably increases the risk of virus transmission.

Outcomes are hard to predict as the virus is mutating and evolving, affecting its virulence, transmission characteristics, and range of susceptible species. The lesions in these cranes were dramatic, involving primarily the brain and in one bird the heart; lesions may have been present in other tissues, but they were not available for evaluation due to scavenging. The lesions indicate the birds were sick for days. This pattern is typical of what we see in some other species of wild birds that die of highly pathogenic avian influenza virus.

Finally, wildlife health surveillance and wildlife conservation programs are highly collaborative, requiring expertise in a range of disciplines such as wildlife biologists, ecologists, molecular biologists, veterinary pathologists and diagnosticians to name a few. Laboratory facilities that can respond quickly to these events are also key requirements. Participation by members of the public is also important – in this case, the second crane did not have a radio-transmitter that could have alerted CWS to the death – and includes reporting mortalities and the presence of sick wildlife to further the understanding of the geographic distribution and relative risk of disease. Furthermore, confirmation of what disease is involved in die-offs is essential as wildlife can die for several reasons and some diseases, such as HPAIV, are more significant than others and have broader implications for domestic animal and human health. This requires people who can collect carcasses or sick wildlife and bring them to the lab for diagnosis. These people need to act quickly as predators and scavengers can quickly render carcasses unusable.

Satellite-tracked whooping cranes continue to be closely monitored as they migrate south from Canada through the US Great Plains to overwinter in coastal Texas. Highly pathogenic avian influenza virus continues to cause mortality in waterbirds all along their migratory route. The population’s resilience will be tested as they navigate the high likelihood of contact with waterfowl shedding the virus and contaminated wetlands. Having been brought back from the brink of extinction due to the efforts of many, whooping cranes have proven they can overcome considerable threats, but their recovery depends on continued support.

Written by: Dr. Trent Bollinger, Dr. Shelagh Copeland, Sabine Kirsch, and Dr. Beatriz Garcia De Sousa (the Western/Northern CWHC team)

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