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USGS2018

Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine ( Pinus ponderosa ), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum ) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

Systematic Biology↗

USGS2018

Decision making for mitigating wildlife diseases: From theory to practice for an emerging fungal pathogen of amphibians

Conservation science can be most effective in its decision‐support role when seeking answers to clearly formulated questions of direct management relevance. Emerging wildlife diseases, a driver of global biodiversity loss, illustrate the challenges of performing this role: in spite of considerable research, successful disease mitigation is uncommon. Decision analysis is increasingly advocated to guide mitigation planning, but its application remains rare. Using an integral projection model, we explored potential mitigation actions for avoiding population declines and the ongoing spatial spread of the fungus Batrachochytrium salamandrivorans ( Bsal ). This fungus has recently caused severe amphibian declines in north‐western Europe and currently threatens Palearctic salamander diversity. Available evidence suggests that a Bsal outbreak in a fire salamander ( Salamandra salamandra ) population will lead to its rapid extirpation. Treatments such as antifungals or probiotics would need to effectively interrupt transmission (reduce probability of infection by nearly 90%) in order to reduce the risk of host extirpation and successfully eradicate the pathogen. Improving the survival of infected hosts is most likely to be detrimental as it increases the potential for pathogen transmission and spread. Active removal of a large proportion of the host population has some potential to locally eradicate Bsal and interrupt its spread, depending on the presence of Bsal reservoirs and on the host's spatial dynamics, which should therefore represent research priorities. Synthesis and applications . Mitigation of Batrachochytrium salamandrivorans epidemics in susceptible host species is highly challenging, requiring effective interruption of transmission and radical removal of host individuals. More generally, our study illustrates the advantages of framing conservation science directly in the management decision context, rather than adapting to it a posteriori .

Journal of Applied Ecology↗

USGS2005

Molecular assays for targeting human and bovine enteric viruses in coastal waters and their application for library-independent source tracking

Rapid population growth and urban development along waterways and coastal areas have led to decreasing water quality. To examine the effects of upstream anthropogenic activities on microbiological water quality, methods for source-specific testing are required. In this study, molecular assays targeting human enteroviruses (HEV), bovine enteroviruses (BEV), and human adenoviruses (HAdV) were developed and used to identify major sources of fecal contamination in the lower Altamaha River, Georgia. Two-liter grab samples were collected monthly from five tidally influenced stations between July and December 2002. Samples were analyzed by reverse transcription- and nested-PCR. PCR results were confirmed by dot blot hybridization. Eleven and 17 of the 30 surface water samples tested positive for HAdV and HEV, respectively. Two-thirds of the samples tested positive for either HEV or HAdV, and the viruses occurred simultaneously in 26% of samples. BEV were detected in 11 of 30 surface water samples. Binary logistic regression analysis showed that the presence of both human and bovine enteric viruses was not significantly related to either fecal coliform or total coliform levels. The presence of these viruses was directly related to dissolved oxygen and streamflow but inversely related to water temperature, rainfall in the 30 days preceding sampling, and chlorophyll-?? concentrations. The stringent host specificity of enteric viruses makes them good library-independent indicators for identification of water pollution sources. Viral pathogen detection by PCR is a highly sensitive and easy-to-use tool for rapid assessment of water quality and fecal contamination when public health risk characterization is not necessary. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.

Applied and Environmental Microbiology↗

USGS2015

Evaluation of aquifer interconnection from aquifer characteristics computed by using specific capacity data within the vicinity of the Tremont Barrel Fill site, Clark County, Ohio

The Tremont Barrel Fill site is immediately north of the Tremont City Landfill near Tremont City, Clark County, Ohio. The site was an unlined pit used as a repository for disposing industrial liquid wastes and sludge from 1976 through 1979. Previous investigations led the U.S. Environmental Protection Agency (USEPA) to conclude that the site poses a contamination risk to nearby residents relying on private supply wells opened to the underlying deep sand and gravel and limestone aquifers. The USEPA also concluded there is a potential risk to the residents of the nearby Tremont City; the city obtains its municipal water supply from the Mad River Valley aquifer, which is recharged by the adjacent limestone aquifer. The U.S. Geological Survey (USGS) assessed the degree of hydraulic interconnection, and thus possible contaminant pathway(s), between the two aquifers (the sand and gravel and the limestone) underlying the Barrel Fill site, with consideration for the impact of an identified interconnection between the limestone and the Mad River Valley aquifer used for municipal supply. Aquifer interconnection between the sand and gravel aquifer overlying the limestone aquifer is assessed by analysis of specific capacity data from well-construction logs for derivation of estimates of transmissivity (T) and horizontal hydraulic conductivity (K h ). Data of this nature is limited in the control or knowledge about how well these data were collected and reported; therefore, the T and K h are estimations. Similar values of T and K h are used to infer the degree of aquifer interconnection based on the USEPA Hazard Ranking System, which states that aquifers are considered interconnected when the hydraulic conductivities are within two orders of magnitude. The results of the hydraulic analysis from 127 wells open to either the sand and gravel or the limestone aquifer indicate that the transmissivity of these aquifers is within one order of magnitude and horizontal hydraulic conductivity is within two orders of magnitude. As such, on the basis of the applied ranking system the two aquifers can be considered hydraulically interconnected.

Ohio↗

USGS2025

Potential risks of vegetation treatments to introduce and increase invasive annual grasses in rangelands of Montana, North Dakota, and South Dakota— A science synthesis to inform National Environmental Policy Act analyses

The U.S. Geological Survey is working with Federal land management agencies to develop a series of planned structured science syntheses to support environmental effects analyses that agencies conduct under the National Environmental Policy Act (NEPA). This report synthesizes science information relevant to environmental effects analyses concerned with potential increases in the distribution and abundance of invasive annual grasses (IAGs) from proposed vegetation treatments for habitat restoration. The focal environments for this synthesis are rangelands in the intermontane valleys of Montana and the northern Great Plains of Montana, North Dakota, and South Dakota. The synthesis is organized to align with the standard elements of NEPA analyses and provides information on relevant scientific studies, data availability, analysis methods, and mitigation measures. We found that the likelihood of increasing IAGs from vegetation treatments depends on treatment type and environmental context. In sagebrush ecosystems of the focal region, prescribed fire often reduces or does not increase IAGs. Treatments that cause soil disturbances, such as mechanical removals of sagebrush or firebreak constructions, are more likely to increase IAGs than other treatments. Herbicides applied to reduce sagebrush cover have not increased the proportion of IAGs in the plant community. Temperature and precipitation have been strong factors in determining IAG responses to vegetation treatments in sagebrush ecosystems of the focal region, where more precipitation in spring and summer likely provides a competitive edge to native, perennial grasses more than winter annual grasses like Bromus tectorum L. (cheatgrass). In grasslands, prescribed fire often reduces IAGs, but effects depend on the abundance of native species and are often short lived. Mowing can increase or decrease IAGs in grassland ecosystems. Grassland site conditions, such as southeast-facing slopes, sandier or rockier sites, or lower native species cover or richness affect the likelihood of invasion by annual grasses. Maintaining adequate cover of perennial vegetation creates rangelands that are resistant and resilient to annual grass invasions. Managers can minimize invasion potential by focusing on treatment type, placement, and seasonal timing. Herbicides also can provide effective mitigation, especially in combination with other controls such as prescribed fire or grazing. This report can be incorporated by reference in NEPA documentation, included in a project record, or provide a general reference for understanding and identifying literature about increases in IAGs associated with vegetation treatments in rangelands in this focal region.

Montana, North Dakota, South Dakota↗

USGS2015

Population and genetic outcomes 20 years after reintroducing bobcats ( Lynx rufus ) to Cumberland Island, Georgia USA

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size ( N e ) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations.

Georgia↗

USGS2021

Numerical analysis of the effect of subgrid variability in a physically based hydrological model on runoff, soil moisture, and slope stability

In coarse resolution hydrological modeling we face the problem of subgrid variability, the effects of which are difficult to express and are often hidden in the parameterization and calibration. We present a numerical experiment with the physically based hydrological model ParFlow‐CLM with which we quantify the effect of subgrid heterogeneities in headwater catchments within the cell size typically used for regional hydrological applications. We simulate homogeneous domains and domains with subgrid heterogeneities in topography or soil thickness for two climates and soil types. The presence of side slope is the main error source, leading to large underestimation of runoff, and marginally also of evapotranspiration. The spatial distribution of soil saturation in the presence of subgrid variability in topography also leads to underestimation of landslide risk. Soil thickness is the second influential subgrid property, affecting soil moisture distribution and surface runoff formation. Results are consistent for the climates and the soil types considered. The topographic wetness index approach is tested as a way to downscale soil moisture simulations within the domain. Although this method is successful in reproducing some spatial variability and patterns, it fails when the coarse grid mean soil saturation is inaccurate or subgrid topography does not represent subsurface flow paths accurately. We conclude that ignoring subgrid variability in topography and soil thickness in coarse‐scale hydrological models may lead locally to underestimation of runoff and slope instability. Users of such models should be aware of these biases and consider ways to include subgrid effects in coarse‐scale hydrological predictions.

Water Resources Research↗

USGS2019

Assessment of operational and structural factors influencing performance of fish collectors in forebays of high-head dams

Providing efficient downstream passage is critical for improving populations of migratory fishes in impounded river systems. High‐head dams, such as those used for water storage or flood‐risk management, pose unique passage challenges requiring unique solutions. Systems to collect fish in dam forebays (“forebay collectors”) for transport to downstream release locations have been used at some high‐head dams in the western United States since the 1950s. Collection efficiency of these facilities has ranged from nearly 0% to 100%, suggesting the need for a better understanding of factors affecting performance in these complex environments if they are to be designed and deployed at new sites. We compiled information on environmental, structural, and performance characteristics of seven existing forebay collectors to quantify factors affecting their performance based on a meta‐analysis using a data set containing 52 separate collection estimates. Covariates included species type (steelhead Oncorhynchus mykiss, Chinook Salmon O. tshawytscha, Coho Salmon O. kisutch, and Sockeye Salmon O. nerka), collector inflow, collector entrance area, relative size of the dam forebay, and whether or not nets were used to enhance collection. We found that inflow, the use of lead nets, the size of the collector entrance area, the relative size of the dam forebay, and the interaction between collector entrance and forebay areas were significant predictors of collection performance. There was also evidence for differences between species. Chinook Salmon exhibited the lowest collection rates among the projects we examined, while steelhead collection rates were highest. These results provide guidance to design more efficient forebay collectors and improve the success of existing systems.

Oregon, Washington↗

USGS2022

Quantifying the relationship between prey density, livestock and illegal killing of leopards

Many large mammalian carnivores are facing population declines due to illegal killing (e.g., shooting) and habitat modification (e.g., livestock farming). Illegal killing occurs cryptically and hence is difficult to detect. However, reducing illegal killing requires a solid understanding of its magnitude and underlying drivers, while accounting for the imperfect detection of illegal killing events. Despite the importance of illegal killing of large carnivores in comparison with other causes of mortality, its relationship with potential drivers such as livestock density and wild prey abundance is rarely described. Using ranger-collected data (2007-2019) of leopard killing events and data on covariates (livestock density, wild prey abundance, road length, protected area size, elevation) across Iran, we applied a single-visit N-mixture model to jointly model variation in detection probability and expected annualized number of leopard killing events. Over the study period, we estimated 428 leopard mortalities (95% CI 184–1014), which was 45% larger than the observed number. Expected intensity of leopard killing was positively related to protected area size, livestock density and wild prey abundance. Detection of leopard killing was higher in areas with more developed road networks. Synthesis and applications: Ranger based monitoring data on poaching of carnivores are cost effective, but traditional analysis does not take into account imperfect detection. We show that innovative statistics (single-visit N-mixture modeling) can reliably quantify poaching events and address their drivers, at large geographical scales. We used the example of the Persian leopard across Iran, but our approach is also applicable to understand killing dynamics of other species. Results suggest that a high frequency of leopard killing is likely to occur in areas with > 100 livestock per km 2 and > 450 individuals of wild prey per km 2 . This highlights the need for improved management of livestock grazing and effective measures around high-risk protected areas to mitigate human-leopard conflict and reduce killing of leopards.

Journal of Applied Ecology↗

USGS2010

High tsunami frequency as a result of combined strike-slip faulting and coastal landslides

Earthquakes on strike-slip faults can produce devastating natural hazards. However, because they consist predominantly of lateral motion, these faults are rarely associated with significant uplift or tsunami generation. And although submarine slides can generate tsunami, only a few per cent of all tsunami are believed to be triggered in this way. The 12 January M w 7.0 Haiti earthquake exhibited primarily strike-slip motion but nevertheless generated a tsunami. Here we present data from a comprehensive field survey that covered the onshore and offshore area around the epicentre to document that modest uplift together with slope failure caused tsunamigenesis. Submarine landslides caused the most severe tsunami locally. Our analysis suggests that slide-generated tsunami occur an order-of-magnitude more frequently along the Gonave microplate than global estimates predict. Uplift was generated because of the earthquake's location, where the Caribbean and Gonave microplates collide obliquely. The earthquake also caused liquefaction at several river deltas that prograde rapidly and are prone to failure. We conclude that coastal strike-slip fault systems such as the Enriquillo-Plantain Garden fault produce relief conducive to rapid sedimentation, erosion and slope failure, so that even modest predominantly strike-slip earthquakes can cause potentially catastrophic slide-generated tsunami - a risk that is underestimated at present.

Nature Geoscience↗

USGS1976

Leasing policies for the extractive resources

Much of the available analysis of policies for the disposal of publicly held resources is based on comparatively straightforward extensions of the neoclassical pricing and allocation theory. As such, these analyses have to a large extent not fully incorporated the fact that firms normally acquire rights to these resources in sealed tender markets. In this paper, a simple bidding model is used to show that the choice of disposal policies can influence the firm's bid and also the public revenues obtained from the sale of the resource. It is additionally shown that the implications of such policy choices are conditioned by the firm's attitudes towards risk. Finally, it is argued that a modification of existing prescriptions may be necessary if a more realistic specification of the disposal problem taking account of the sealed tender market in which rights are obtained, is considered.

The Annals of Regional Science↗

USGS2010

High tsunami frequency as a result of combined strike-slip faulting and coastal landslides

Earthquakes on strike-slip faults can produce devastating natural hazards. However, because they consist predominantly of lateral motion, these faults are rarely associated with significant uplift or tsunami generation. And although submarine slides can generate tsunami, only a few per cent of all tsunami are believed to be triggered in this way. The 12 January Mw 7.0 Haiti earthquake exhibited primarily strike-slip motion but nevertheless generated a tsunami. Here we present data from a comprehensive field survey that covered the onshore and offshore area around the epicentre to document that modest uplift together with slope failure caused tsunamigenesis. Submarine landslides caused the most severe tsunami locally. Our analysis suggests that slide-generated tsunami occur an order-of-magnitude more frequently along the Gonave microplate than global estimates predict. Uplift was generated because of the earthquake?s location, where the Caribbean and Gonave microplates collide obliquely. The earthquake also caused liquefaction at several river deltas that prograde rapidly and are prone to failure. We conclude that coastal strike-slip fault systems such as the Enriquillog-Plantain Garden fault produce relief conducive to rapid sedimentation, erosion and slope failure, so that even modest predominantly strike-slip earthquakes can cause potentially catastrophic slide-generated tsunamig-a risk that is underestimated at present. ?? 2010 Macmillan Publishers Limited. All rights reserved.

Nature Geoscience↗

USGS2012

A climate trend analysis of Ethiopia

This brief report, drawing from a multi-year effort by the U.S. Agency for International Development (USAID) Famine Early Warning Systems Network (FEWS NET), examines recent trends in March-June, June-September, and March-September rainfall and temperature, identifying significant reductions in rainfall and increases in temperature over time in many areas of Ethiopia. Conclusions: * Spring and summer rains in parts of Ethiopia have declined by 15-20 percent since the mid-1970s. * Substantial warming across the entire country has exacerbated the dryness.* An important pattern of observed existing rainfall declines coincides with heavily populated areas of the Rift Valley in south-central Ethiopia, and is likely already adversely affecting crop yields and pasture conditions. * Rapid population growth and the expansion of farming and pastoralism under a drier, warmer climate regime could dramatically increase the number of at-risk people in Ethiopia during the next 20 years.* Many areas of Ethiopia will maintain moist climate conditions, and agricultural development in these areas could help offset rainfall declines and reduced production in other areas.

Fact Sheet↗

USGS2004

Has the conversion of natural wetlands to agricultural land increased the incidence and severity of damaging freezes in south Florida?

On several occasions, winter freezes have wrought severe destruction on Florida agriculture. A series of devastating freezes around the turn of the twentieth century, and again during the 1980s, were related to anomalies in the large-scale flow of the ocean–atmosphere system. During the twentieth century, substantial areas of wetlands in south Florida were drained and converted to agricultural land for winter fresh vegetable and sugarcane production. During this time, much of the citrus industry also was relocated to those areas to escape the risk of freeze farther to the north. The purpose of this paper is to present a modeling study designed to investigate whether the conversion of the wetlands to agriculture itself could have resulted in or exacerbated the severity of recent freezes in those agricultural areas of south Florida. For three recent freeze events, a pair of simulations was undertaken with the Regional Atmospheric Modeling System. One member of each pair employed land surface properties that represent pre-1900s (near natural) land cover, whereas the other member of each pair employed data that represent near-current land-use patterns as derived from analysis of Landsat data valid for 1992/93. These two different land cover datasets capture well the conversion of wetlands to agriculture in south Florida during the twentieth century. Use of current land surface properties resulted in colder simulated minimum temperatures and temperatures that remained below freezing for a longer period at locations of key agricultural production centers in south Florida that were once natural wetlands. Examination of time series of the surface energy budget from one of the cases reveals that when natural land cover is used, a persistent moisture flux from the underlying wetlands during the nighttime hours served to prevent the development of below-freezing temperatures at those same locations. When the model results were subjected to an important sensitivity factor, the depth of standing water in the wetlands, the outcome remained consistent. These results provide another example of the potential for humans to perturb the climate system in ways that can have severe socioeconomic consequences by altering the land surface alone.

Monthly Weather Review↗

USGS2007

Geographic Research in the USGS Western Region

The two geography research programs of the U.S. Geological Survey (USGS), Land Remote Sensing and Geographic Analysis and Monitoring, have very strong relevance to the USGS mission and science strategy. In the western United States, the particular niche of these geography programs is in connecting USGS science to people and communities. Reports from the National Academy of Sciences and other organizations invariably encourage the U.S. Geological Survey (USGS) to ensure the quality of its science while finding ways to make it more relevant to important societal issues. Much of the geography research conducted in the USGS Western Region does exactly that. In Menlo Park, California, the geography research team is focused on developing tools and techniques to help people assess risk from natural hazards and environmental impacts. In Flagstaff and Tucson, Arizona, geography scientists explore new ways to use remote sensing to help communities deal with environmental issues.

Fact Sheet↗

USGS2021

Exposure of predatory and scavenging birds to anticoagulant rodenticides in France: Exploration of data from French surveillance programs

Wild raptors are widely used to assess exposure to different environmental contaminants, including anticoagulant rodenticides (ARs). ARs are used on a global scale for rodent control, and act by disruption of the vitamin K cycle that results in haemorrhage usually accompanied by death within days. Some ARs are highly persistent and bioaccumulative, which can cause significant exposure of non-target species. We characterized AR exposure in a heterogeneous sample of dead raptors collected over 12 years (2008–2019) in south-eastern France. Residue analysis of 156 liver samples through LC-MS/MS revealed that 50% (78/156) were positive for ARs, with 13.5% (21/156) having summed second-generation AR (SGAR) concentrations >100 ng/g ww. While SGARs were commonly detected (97.4% of positive samples), first-generation ARs were rarely found (7.7% of positive samples). ARs were more frequently detected and at greater concentration in predators (prevalence: 82.5%) than in scavengers (38.8%). Exposure to multiple ARs was common (64.1% of positive samples). While chlorophacinone exposure decreased over time, an increasing exposure trend was observed for the SGAR brodifacoum, suggesting that public policies may not be efficient at mitigating risk of exposure for non-target species. Haemorrhage was observed in 88 birds, but AR toxicosis was suspected in only 2 of these individuals, and no difference in frequency of haemorrhage was apparent in birds displaying summed SGAR levels above or below 100 ng/g ww. As for other contaminants, 17.2% of liver samples (11/64) exhibited Pb levels compatible with sub-clinical poisoning (>6 μg/g dw), with 6.3% (4/64) above the threshold for severe/lethal poisoning (>30 μg/g dw). Nine individuals with Pb levels >6 μg/g dw also had AR residues, demonstrating exposure to multiple contaminants. Broad toxicological screening for other contaminants was positive for 18 of 126 individuals, with carbofuran and mevinphos exposure being the suspected cause of death of 17 birds. Our findings demonstrate lower but still substantial AR exposure of scavenging birds compared to predatory birds, and also illustrate the complexity of diagnosing AR toxicosis through forensic investigations.

Science of the Total Environment↗

USGS2020

Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia

Highly pathogenic avian influenza (HPAI) viruses of the H5 A/goose/Guangdong/1/96 lineage can cause severe disease in poultry and wild birds, and occasionally in humans. In recent years, H5 HPAI viruses of this lineage infecting poultry in Asia have spilled over into wild birds and spread via bird migration to countries in Europe, Africa, and North America. In 2016/2017, this spillover resulted in the largest HPAI epidemic on record in Europe and was associated with an unusually high frequency of reassortments between H5 HPAI viruses and cocirculating low-pathogenic avian influenza viruses. Here, we show that the seven main H5 reassortant viruses had various combinations of gene segments 1, 2, 3, 5, and 6. Using detailed time-resolved phylogenetic analysis, most of these gene segments likely originated from wild birds and at dates and locations that corresponded to their hosts’ migratory cycles. However, some gene segments in two reassortant viruses likely originated from domestic anseriforms, either in spring 2016 in east China or in autumn 2016 in central Europe. Our results demonstrate that, in addition to domestic anseriforms in Asia, both migratory wild birds and domestic anseriforms in Europe are relevant sources of gene segments for recent reassortant H5 HPAI viruses. The ease with which these H5 HPAI viruses reassort, in combination with repeated spillovers of H5 HPAI viruses into wild birds, increases the risk of emergence of a reassortant virus that persists in wild bird populations yet remains highly pathogenic for poultry.

PNAS↗

USGS2022

A lesser scaup (Aythya affinis ) naturally infected with Eurasian 2.3.4.4 highly pathogenic H5N1 avian influenza virus – Movement ecology and host factors

Despite the recognized role of wild waterfowl in the potential dispersal and transmission of highly pathogenic avian influenza (HPAI) virus, little is known about how infection affects these birds. This lack of information limits our ability to estimate viral spread in the event of an HPAI outbreak, thereby limiting our abilities to estimate and communicate risk. Here we present telemetry data from a wild Lesser Scaup ( Aythya affinis ), captured during a separate ecology study in the Chesapeake Bay, Maryland. This bird tested positive for infection with clade 2.3.4.4 HPAI virus of the A/goose/Guangdong/1/1996 (Gs/GD) H5N1 lineage (results received post-release) during the 2021–22 ongoing outbreaks in North America. While the infected bird was somewhat lighter than other adult males surgically implanted with transmitters (790g, ߂ = 868g, n = 11), it showed no clinical signs of infection at capture, during surgery, nor upon release. The bird died 3d later, pathology undetermined as the specimen was not able to be recovered. Analysis of movement data within the 3d window showed that the infected individual's maximum and average hourly movements (3894.3m, 428.8m respectively) were noticeably lower than noninfected conspecifics tagged and released the same day (߂ = 21594.5m, ߂ = 1097.9m, respectively; n = 4). We identified four instances where the infected bird had close contact (fixes located within 25m and 15 min) with another marked bird during this time. Collectively, these data suggest that the HPAI positive bird observed in this study may have been shedding virus for some period prior to death, with opportunities for direct bird to bird or environmental transmission. Although limited by low sample size and proximity to the time of tagging, we hope that these data will provide useful information as managers continue to respond to this ongoing outbreak event.

Transboundary and Emerging Diseases↗