The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as 'genotyping-in-thousands-by sequencing' (GT-seq), now enable the efficient and cost-effective genotyping of hundreds of loci and individuals in the same sequencing run. Here, we develop a GT-seq panel for individual identification and kinship inference in Alaska black bears. Using genomic data from restriction site-associated DNA sequencing of hunter-harvested bears from Southcentral Alaska (n = 85), we identified 170 microhaplotype and single nucleotide polymorphism (SNP) loci that were highly heterozygous in local populations. To enable sexing of individuals, we also included a previously published sex-linked locus in the GT-seq panel. We empirically validated the GT-seq panel using samples collected at different spatial scales. These samples included tissues (n = 82) obtained from bears within a small geographic area in Anchorage, Alaska, which were likely to be relatives as well as the hunter-harvested samples collected from geographically widespread locations throughout Southcentral Alaska. Empirical validation indicated high genotyping success and genotype reproducibility across replicate subsamples. Computer simulations demonstrated that the GT-seq panel had ample statistical power for distinguishing distinct individuals and first-order relatives (parent-offspring and full-sibling pairs) from unrelated individuals. As a final proof of concept, the panel was used to identify individual bears and close kin sampled from urban and wild habitats in Anchorage, Alaska. We anticipate that the GT-seq panel will be a useful genomic resource for the monitoring and management of Alaska black bear populations.

Highly pathogenic avian influenza virus (HPAIV) H5Nx clade 2.3.4.4b has circulated in North America since late 2021, resulting in higher rates of morbidity and mortality in wild birds than observed in this region before. The objective of this study was to determine whether baiting, which is widely conducted in Canada and the United States as part of waterfowl management practices (e.g., duck banding), influences the occurrence of avian influenza virus (AIV) in wetlands. We used a quasi-experimental design, collecting superficial sediment samples (n = 336) and fecal samples (n = 242) from paired baited (treatment) and non-baited (control) sites at 2 wetlands in Saskatchewan, Canada, between August and September 2022. We visited sampling sites 3 times during the sampling period: prior to the commencement of baiting activities (t0), approximately 14 days after t0 (t1), and 24 days after t0 (t2). We screened samples for AIV using real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) targeting the matrix gene and subjected the PCR-positive samples to next-generation sequencing. We used a mixed-effects logistic regression model to estimate the effect of baiting on the odds of AIV positivity in sediment samples, while controlling for clustering by wetland. At control sites, we did not detect evidence for a difference in the odds of AIV detection in sediment at t1 or t2 versus t0; however, at baited sites, the odds of AIV detection at t1 were 5.43 (95% CI = 1.99, 14.79) times the odds at t0 and at t2 the odds of AIV detection were 8.73 (95% CI = 3.29, 23.18) times the odds at t0. We detected HPAIV clade 2.3.4.4b H5N1 in sediment at 1 treatment site following baiting. There was also a trend towards increased fecal AIV positivity and increased fecal and sediment AIV diversity in baited versus non-baited sites; however, there was insufficient power to determine if these findings were statistically significant. Overall, our results indicate that baiting is associated with localized increases in AIV environmental contamination, with baiting potentially creating concentrated areas of AIV accumulation. As such, wetland baiting activities may pose a risk to wildlife population health through the propagation of AIV in wetlands and the waterfowl using those environments and efforts to replace, refine, or reduce this activity may be warranted depending on local ecosystem contexts and cost-benefit analyses.

Giardia and Cryptosporidium spp. are globally distributed protozoan parasites that can cause gastrointestinal disease in humans and animals. These zoonotic parasites and their ecological relationships have been understudied in Alaska and elsewhere, despite being identified as priority zoonotic pathogens. We aimed to detect and characterize Giardia and Cryptosporidium spp. in waterbodies within Anchorage, Alaska, USA using two methods, including the Environmental Protection Agency (EPA) Method 1623 that relies on microscopy and a molecular detection approach. The molecular approach was ultimately unsuccessful and therefore only data obtained using Method 1623 are presented. Giardia or Cryptosporidium spp. was detected from nine of 15 urban streams and lakes sampled (60 %), six of which were positive for both parasites (40 %). Fewer than 10 cysts or oocysts were detected in 10 L of surface water. Further research to characterize Giardia and Cryptosporidium beyond the genus level would help elucidate the zoonotic potential and ecology of these parasites within the region and more broadly in Alaska.

Climate change is inducing wide-scale permafrost thaw in the Arctic and subarctic, triggering concerns that long-dormant pathogens could reemerge from the thawing ground and initiate epidemics or pandemics. Viruses, as opposed to bacterial pathogens, garner particular interest because outbreaks cannot be controlled with antibiotics, though the effects can be mitigated by vaccines and newer antiviral drugs. To evaluate the potential hazards posed by viral pathogens emerging from thawing permafrost, we review information from a diverse range of disciplines. This includes efforts to recover infectious virus from human remains, studies on disease occurrence in polar animal populations, investigations into viral persistence and infectivity in permafrost, and assessments of human exposure to the enormous viral diversity present in the environment. Based on currently available knowledge, we conclude that the risk posed by viruses from thawing permafrost is no greater than viruses in other environments such as temperate soils and aquatic systems.

Understanding migratory waterfowl spatiotemporal distributions is important because, in addition to their economic and cultural value, wild waterfowl can be infectious reservoirs of highly pathogenic avian influenza virus (HPAIV). Waterfowl migration has been implicated in regional and intercontinental HPAIV dispersal, and predictive capabilities of where and when HPAIV may be introduced to susceptible spillover hosts would facilitate biosecurity and mitigation efforts. To develop forecasts for HPAIV dispersal, an improved understanding of how individual birds interact with their environment and move on a landscape scale is required. Using an agent-based modeling approach, we integrated individual-scale energetics, species-specific morphology and behavior, and landscape-scale weather and habitat data in a mechanistic stochastic framework to simulate Mallard (Anas platyrhynchos) and Northern Pintail (Anas acuta) annual migration across the Northern Hemisphere. Our model recreated biologically realistic migratory patterns using a first principles approach to waterfowl ecology, behavior, and physiology. Conducting a limited structural sensitivity analysis comparing reduced models to eBird Status and Trends in reference to the full model, we identified density dependence as the main factor influencing spring migration and breeding distributions, and wind as the main factor influencing fall migration and overwintering distributions. We show evidence of weather patterns in Northeast Asia causing significant intercontinental pintail migration to North America. By linking individual energetics to landscape-scale processes, we identify key drivers of waterfowl migration while developing a predictive model responsive to daily weather patterns. This model paves the way for future waterfowl migration research predicting HPAIV transmission, climate change impacts, and oil spill effects.

In 2021-22, clade 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses were introduced by wild birds into North America, leading to geographically widespread disease. In response to HPAI outbreaks throughout late 2021 and early 2022, we recorded observations of sick and dead birds, estimated abundance of carcasses, collected swab and sera samples to detect viruses, and monitored bird nesting on the Yukon-Kuskokwim Delta region of Alaska to document potential effects of disease. Thirty-six reports of sick and dead birds were registered across the region. Nineteen carcasses were opportunistically collected for diagnostic testing, of which 12 were confirmed to be infected with clade 2.3.4.4b HPAI viruses. Carcass abundance estimates from line-distance sampling provided evidence that the most common species of dead birds from the western Yukon-Kuskokwim Delta region were Cackling Goose (Branta hutchinsii minima), Glaucous Gull (Larus hyperboreus), and Black Brant (Branta bernicla nigricans). Only one paired cloacal and oropharyngeal swab sample from a Northern Pintail (Anas acuta) tested positive for clade 2.3.4.4b HPAI virus, out of 464 live-captured duck and goose samples. Of 195 sera samples from waterfowl screened for antibodies reactive to influenza A viruses, antibodies were found in 41-98% of samples collected from Emperor Goose (Anser canagicus), Cackling Goose, Black Brant, and Spectacled Eider (Somateria fischeri). In addition, 15-98% of the same sera samples were reactive to a clade 2.3.4.4b H5 antigen. Fewer Black Brant and Emperor Goose nests were found on long-term study plots during 2022 than in previous years. Collectively, we found that HPAI viruses affected at least seven species of wild birds inhabiting the region during 2022. The full scope of impacts of HPAI at this location during 2022 is unknown, but our data indicate that acute effects to avian population health on the Yukon-Kuskokwim Delta region were likely modest.

Serum samples from wild mammals inhabiting Alaska, USA, showed that 4 species, including Ursus arctos bears and Vulpes vulpes foxes, were exposed to influenza A(H5N1) viruses. Results indicated some mammals in Alaska survived H5N1 virus infection. Surveillance efforts may be improved by incorporating information on susceptibility and detectable immune responses among wild mammals.

The environmental tenacity of influenza A viruses (IAVs) in the environment likely plays a role in their transmission; IAVs are able to remain infectious in aquatic habitats and may have the capacity to seed outbreaks when susceptible wild bird hosts utilize these same environments months or even seasons later. Here, we aimed to assess the persistence of low-pathogenicity IAVs from naturally infected ducks in Northwestern Minnesota through a field experiment. Viral infectivity was measured using replicate samples maintained in distilled water in a laboratory setting as well as in filtered water from four natural water bodies maintained in steel perforated drums (hereafter, mesocosms) within the field from autumn 2020 to spring 2021. There was limited evidence for the extended persistence of IAVs held in mesocosms; from 65 initial IAV-positive samples, only six IAVs persisted to at least 202 days in the mesocosms compared to 17 viruses persisting at least this long when held under temperature-controlled laboratory settings in distilled water. When accounting for the initial titer of samples, viruses detected at a higher concentration at the initiation of the experiment persisted longer than those with a lower starting titer. A parallel experimental laboratory model was used to further explore the effects of water type on viral persistence, and the results supported the finding of reduced tenacity of IAVs held in mesocosms compared to distilled water. The results of this investigation provide evidence that many factors, including temperature and physicochemical properties, impact the duration of viral infectivity in natural settings, further extending our understanding of the potential and limitations of environmental-based methodologies to recover infectious IAVs.

The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR (qPCR) data. First, we quantified distributions of gene copy numbers at a set of six sex-linked genes, including the sex-determining gene DMRT1, for individuals across 17 species and seven orders of birds (n = 150). Using these data, we built predictive logistic models for sex identification and tested their performance with independent samples from 51 species and 13 orders (n = 209). Models using the two loci most highly correlated with sex had greater accuracy than models using the full set of sex-linked loci, across all taxonomic levels of analysis. Sex identification was highly accurate when individuals to be assigned were of species used in model building. Our analytical approach was widely applicable across diverse neognath bird lineages spanning millions of years of evolutionary divergence. Unlike previous methods, our probabilistic framework incorporates uncertainty around qPCR measurements as well as biological variation within species into decision-making rules. We anticipate that this method will be useful for sexing birds, including those of high conservation concern and/or subsistence value, that have proven difficult to sex using traditional approaches. Additionally, the general analytical framework presented in this paper may also be applicable to other organisms with sex chromosomes.

The ongoing panzootic of highly pathogenic H5 clade 2.3.4.4b avian influenza (HPAI) spread to North America in late 2021, with detections of HPAI viruses in Alaska beginning in April 2022. HPAI viruses have since spread across the state, affecting many species of wild birds as well as domestic poultry and wild mammals. To better understand the dissemination of HPAI viruses spatiotemporally and among hosts in Alaska and adjacent regions, we compared the genomes of 177 confirmed HPAI viruses detected in Alaska during April-December 2022. Results suggest multiple viral introductions into Alaska between November 2021 and August or September 2022, as well as dissemination to areas within and outside of the state. Viral genotypes differed in their spatiotemporal spread, likely influenced by timing of introductions relative to population immunity. We found evidence for dissemination of HPAI viruses between wild bird species, wild birds and domestic poultry, as well as wild birds and wild mammals. Continued monitoring for and genomic characterization of HPAI viruses in Alaska can improve our understanding of the evolution and dispersal of these economically costly and ecologically relevant pathogens.

Background: The geographic expansion and evolution of A/Goose/Guangdong/1/1996(H5N1) (Gs/GD) lineage H5Nx highly pathogenic avian influenza (HPAI) viruses since 1996 have raised awareness of enzootic circulation among migratory birds and the potential for intercontinental transport and spread. Recent Pacific- and Atlantic-route introductions of HPAI to North America were facilitated by avian migration through subarctic zones, specifically Alaska and Iceland. This study aimed to identify recent historical patterns of exposure to HPAI viruses among birds within and migrating through both regions and evaluate how geographic, demographic, and taxonomic differences contribute to exposure risk at two intercontinental staging locations. Methods: During 2010-2019, blood samples were obtained from captured wild migratory seabirds and waterfowl in Alaska and Iceland. All live birds were released following completion of sampling. Sampling date, species, sampling location, and age class was documented for each bird, and sex was documented when possible. Lentiviral pseudoviruses that express the influenza hemagglutinin surface glycoprotein for H5Nx HPAI and H5 low-pathogenicity avian influenza (LPAI) were constructed for use in serological assays to screen for and quantify titers of antibodies against the latter viruses. Data were analyzed to compare (a) categorical baseline ecological traits between Iceland and Alaska, and (b) ecological traits between birds identified to be seropositive and suggestive/seronegative/fully cross-reactive birds to H5Nx HPAI in Iceland and Alaska. Factors associated with seroreactivity to H5Nx HPAI and H5 LPAI were assessed. Results:The seroprevalence of HPAI among birds in both locations was 7.3% (112/1526). Findings reveal variability in seroprevalence by year, higher rates of exposure to H5 LPAI than H5Nx HPAI overall, and significantly more seropositive and suggestive exposure of birds to H5Nx HPAI in Alaska as compared to Iceland. Geographic, demographic, and taxonomic differences contribute to exposure risk between Alaska and Iceland. Most tested birds were immuno-naïve to HPAI in both locations, which indicates many migratory birds in the subarctic are susceptible to HPAI infection, demonstrating substantial risk for intercontinental transmission between Asia, Europe, and North America. Conclusions: Our findings provide further justification for increased viral and serosurveillance in Alaska and Iceland to monitor subarctic movements of migratory birds and intercontinental transmission dynamics of currently circulating and new strains of HPAI globally.

We detected and characterized highly pathogenic avian influenza viruses among hunter-harvested wild water-fowl inhabiting western Alaska during September-October 2022 using a molecular sequencing pipeline applied to RNA extracts derived directly from original swab samples. Genomic characterization of 10 H5 clade 2.3.4.4b avian influenza viruses detected with high confidence provided evidence for three independent viral in-troductions into Alaska. Our results highlight the utility and some potential limits of applying molecular pro-cessing approaches directly to RNA extracts from original swab samples for viral research and monitoring.

The development and application of approaches to detect and quantify environmental DNA (eDNA) have potential to improve our understanding of the distribution, abundance, and health of Atlantic Salmon Salmo salar and Pacific salmon Oncorhynchus spp. Here, we review 61 articles focusing on eDNA applications pertaining to salmon occupying natural habitat and aquaculture facilities in the context of advances, opportunities, and challenges. Given recent advances, eDNA now serves as a useful tool for detecting Atlantic Salmon and Pacific salmon and understanding threats to the health of fish and their habitats. Opportunities exist to apply sensitive and minimally invasive eDNA approaches to detect fish and assess fish habitat, assess range expansions of salmon and salmon pathogens, and detect invasive species that may threaten salmon health and abundance. Near real-time eDNA detection and quantification approaches to inform fisheries management may be on the horizon. Challenges limiting the widespread application of eDNA approaches for informing salmon management include accounting for the many factors affecting detection and quantification of eDNA, limits of data for deriving inference, and expense. Through continued development and refinement, eDNA approaches are anticipated to become increasingly available to, and utilized by, managers of Atlantic Salmon and Pacific salmon fisheries.

Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted. IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene blaOXA-48. This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.

Understanding relationships between infection and wildlife movement patterns is important for predicting pathogen spread, especially for multispecies pathogens and those that can spread to humans and domestic animals, such as avian influenza viruses (AIVs). Although infection with low pathogenic AIVs is generally considered asymptomatic in wild birds, prior work has shown that influenza-infected birds occasionally delay migration and/or reduce local movements relative to their uninfected counterparts. However, most observational research to date has focused on a few species in northern Europe; given that influenza viruses are widespread globally and outbreaks of highly pathogenic strains are increasingly common, it is important to explore influenza-movement relationships across more species and regions. Here, we used telemetry data to investigate relationships between influenza infection and movement behavior in 165 individuals from four species of North American waterfowl that overwinter in California, USA. We studied both large-scale migratory and local overwintering movements and found that relationships between influenza infection and movement patterns varied among species. Northern pintails (Anas acuta) with antibodies to avian influenza, indicating prior infection, made migratory stopovers that averaged 12 days longer than those with no influenza antibodies. In contrast, greater white-fronted geese (Anser albifrons) with antibodies to avian influenza made migratory stopovers that averaged 15 days shorter than those with no antibodies. Canvasbacks (Aythya valisineria) that were actively infected with influenza upon capture in the winter delayed spring migration by an average of 28 days relative to birds that were uninfected at the time of capture. At the local scale, northern pintails and canvasbacks that were actively infected with influenza used areas that were 7.6 and 4.9 times smaller than those of uninfected ducks, respectively, during the period of presumed active influenza infection. We found no evidence for an influence of active influenza infection on local movements of mallards (Anas platyrhynchos). These results suggest that avian influenza can influence waterfowl movements and illustrate that the relationships between avian influenza infection and wild bird movements are context- and species-dependent. More generally, understanding and predicting the spread of multihost pathogens requires studying multiple taxa across space and time.

A Eurasian lineage highly pathogenic avian influenza virus (HPAIV) of the clade 2.3.4.4b (Goose/Guangdong lineage) was detected in migratory bird populations in North America in December 2021, and it, along with its reassortants, have since caused wild and domestic bird outbreaks across the continent. Relative to previous outbreaks, HPAIV cases among wild birds in 2022 exhibited wider geographic extent within North America and higher levels of mortality, suggesting the potential for population-level impacts. Given the possible conservation implications of HPAIV in wild birds, natural resource managers have sought guidance on actions that may mitigate negative effects of disease among North American bird populations, including modification of existing management practices. Banding of waterfowl is a critical tool for population management for several harvested species in North America, but some banding techniques, such as bait trapping, can lead to increased congregation of waterfowl, potentially altering HPAIV transmission. We used an expert opinion exercise to assess how bait trapping of dabbling ducks in Canada may influence HPAIV transmission and wild bird health. The expert group found that it is moderately likely that bait trapping of dabbling ducks in wetlands will significantly increase the transmission of HPAIV among individual ducks, but there is a low probability that this will result in significant population-level effects on North American dabbling ducks. Considering the lack of empirical work studying how capture and handling methods may change transmission of HPAIV among waterfowl, as well as the importance of bait trapping for waterfowl management in North America, future work should focus on filling knowledge gaps pertaining to the influence of baiting on HPAIV occurrence to better inform banding procedures and management decision making.

Objectives: A variety of methods have been developed to detect antimicrobial resistance (AMR) in differ-ent environments to better understand the evolution and dissemination of this public health threat. Com-parisons of results generated using different AMR detection methods, such as quantitative PCR (qPCR) and whole-genome sequencing (WGS), are often imperfect, and few studies have analysed samples in parallel to evaluate differences. In this study, we compared bacterial culture and WGS to a culture-independent commercially available qPCR assay to evaluate the concordance between methods and the utility of each in answering research questions regarding the presence and epidemiology of AMR in wild bird habitats.Methods: We first assessed AMR gene detection using qPCR in 45 bacterial isolates from which we had existing WGS data. We then analysed 52 wild bird faecal samples and 9 spatiotemporally collected water samples using culture-independent qPCR and WGS of phenotypically resistant indicator bacterial isolates.Results: Overall concordance was strong between qPCR and WGS of bacterial isolates, although concor-dance differed among antibiotic classes. Analysis of wild bird faecal and water samples revealed that more samples were determined to be positive for AMR via qPCR than via culture and WGS of bacterial isolates, although qPCR did not detect AMR genes in two samples from which phenotypically resistant isolates were found.Conclusions: Both qPCR and culture followed by sequencing may be effective approaches for characteris-ing AMR genes harboured by wild birds, although data streams produced using these different tools may have advantages and disadvantages that should be considered given the application and sample matrix.Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

To assess infection with or exposure to endo- and ectoparasites in Alaska brown bears (Ursus arctos), blood and fecal samples were collected during 2013-17 from five locations: Gates of the Arctic National Park and Preserve; Katmai National Park; Lake Clark National Park and Preserve; Yakutat Forelands; and Kodiak Island. Standard fecal centrifugal flotation was used to screen for gastrointestinal parasites, molecular techniques were used to test blood for the presence of Bartonella and Babesia spp., and an ELISA was used to detect antibodies reactive to Sarcoptes scabiei, a species of mite recently associated with mange in American black bears (Ursus americanus). From fecal flotations (n=160), we identified the following helminth eggs: Uncinaria sp. (n=16, 10.0%), Baylisascaris sp. (n=5, 3.1%), Dibothriocephalus sp. (n=2, 1.2%), and taeniid-type eggs (n=1, 0.6%). Molecular screening for intraerythrocytic parasites (Babesia spp.) and intracellular bacteria (Bartonella spp.) was negative for all bears tested. We detected antibodies to S. scabiei in six of 59 (10.2%) individuals. The relatively low level of parasite detection in this study meets expectations for brown bear populations living in large, relatively undisturbed habitats near the northern edge of the range. These results provide a contemporary understanding of parasites in Alaska brown bears and establish baseline levels of parasite presence to monitor for changes over time and relative to ecologic alterations.