Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Epidemiology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
USGS2021

Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses

Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman Flinders Technology Associates (FTA) cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage, and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer ( Odocoileus virginianus ). Tissue samples and nasal swabs acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions.

Pennsylvania↗
USGS2020

A critical review on the potential impacts of neonicotinoid insecticide use: Current knowledge of environmental fate, toxicity, and implications for human health

Neonicotinoid insecticides are widely used in both urban and agricultural settings around the world. Historically, neonicotinoid insecticides have been viewed as ideal replacements for more toxic compounds, like organophosphates, due in part to their perceived limited potential to affect the environment and human health. This critical review investigates the environmental fate and toxicity of neonicotinoids and their metabolites and the potential risks associated with exposure. Neonicotinoids are found to be ubiquitous in the environment, drinking water, and food, with low-level exposure commonly documented below acceptable daily intake standards. Available toxicological data from animal studies indicate possible genotoxicity, cytotoxicity, impaired immune function, and reduced growth and reproductive success at low concentrations, while limited data from ecological or cross-sectional epidemiological studies have identified acute and chronic health effects ranging from acute respiratory, cardiovascular, and neurological symptoms to oxidative genetic damage and birth defects. Due to the heavy use of neonicotinoids and potential for cumulative chronic exposure, these insecticides represent novel risks and necessitate further study to fully understand their risks to humans.

Environmental Science: Processes and Impacts↗
USGS2009

Prey choice and habitat use drive sea otter pathogen exposure in a resource-limited coastal system

The processes promoting disease in wild animal populations are highly complex, yet identifying these processes is critically important for conservation when disease is limiting a population. By combining field studies with epidemiologic tools, we evaluated the relationship between key factors impeding southern sea otter ( Enhydra lutris nereis ) population growth: disease and resource limitation. This threatened population has struggled to recover despite protection, so we followed radio-tagged sea otters and evaluated infection with 2 disease-causing protozoal pathogens, Toxoplasma gondii and Sarcocystis neurona , to reveal risks that increased the likelihood of pathogen exposure. We identified patterns of pathogen infection that are linked to individual animal behavior, prey choice, and habitat use. We detected a high-risk spatial cluster of S. neurona infections in otters with home ranges in southern Monterey Bay and a coastal segment near San Simeon and Cambria where otters had high levels of infection with T. gondii . We found that otters feeding on abalone, which is the preferred prey in a resource-abundant marine ecosystem, had a very low risk of infection with either pathogen, whereas otters consuming small marine snails were more likely to be infected with T. gondii . Individual dietary specialization in sea otters is an adaptive mechanism for coping with limited food resources along central coastal California. High levels of infection with protozoal pathogens may be an adverse consequence of dietary specialization in this threatened species, with both depleted resources and disease working synergistically to limit recovery.

California↗
USGS2017

Unraveling the disease consequences and mechanisms of modular structure in animal social networks

Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living.

PNAS↗
USGS2012

Synchronous cycling of Ichthyophoniasis with Chinook salmon density revealed during the annual Yukon River spawning migration

Populations of Chinook salmon Oncorhynchus tshawytscha in the Yukon River declined by more than 57% between 2003 and 2010, probably the result of a combination of anthropogenic and environmental factors. One possible contributor to this decline is Ichthyophonus , a mesomycetozoan parasite that has previously been implicated in significant losses of fish, including Chinook salmon. A multiyear epidemiological study of ichthyophoniasis in the Yukon River revealed that disease prevalence and Chinook salmon population abundance increased and decreased simultaneously (i.e., were concordant) from 1999 to 2010. The two values rose and fell synchronously 91% of the time for female Chinook salmon and 82% of the time for males; however, there was no significant correlation between Ichthyophonus prevalence and population abundance. This synchronicity might be explained by a single factor, such as a prey item that is critical to Chinook salmon survival as well as a source of Ichthyophonus infection. The host–parasite relationship between Ichthyophonus and migrating Chinook salmon from 2004 to 2010 was similar to that reported for the previous 5 years. During 2004–2010, overall disease prevalence was significantly higher among females (21%) than among males (8%), increased linearly with fish length for both males and females, and increased in both sexes as the fish progressed upriver. These regularly occurring features of host–parasite dynamics confirm a stable base of transmission for Ichthyophonus . However, from 2003 to 2010, disease prevalence decreased from 30% to just 8% in males and from 45% to 9% in females, paralleling a similar decline in Chinook salmon abundance during the same period. These findings may help clarify questions regarding the complex host–parasite dynamics that occur in marine species such as herrings Clupea spp., which have less well-defined population structures.

Alaska↗
USGS2025

A community-based research approach to develop Chronic Wasting Disease outreach with Tribal communities

Chronic Wasting Disease (CWD) is a fatal and contagious neurological disease of cervid populations across North America. Collaborative efforts between government agencies, researchers, policymakers, and stakeholders are necessary to minimize CWD prevalence, spread, and impacts on animal and human health and well-being. However, critical information related to CWD epidemiology, management, and animal and human health risks was not effectively reaching Tribal Nations and their members. To understand these gaps and specific information needs and ensure meaningful participation in CWD management and control efforts, university researchers and Tribal members partnered to conduct semi-structured interviews that focused on deer hunting and the perceived impacts of CWD on Tribal communities. Interviews provided insights into information preferences, knowledge gaps, and perspectives on CWD, revealing a strong sense of responsibility toward deer and the environment. From this collaborative approach, we can create culturally tailored educational resources that address CWD concerns and align with Tribal values.

Michigan, Minnesota, Wisconsin↗
USGS2011

Applying definitions of “asbestos” to environmental and “low-dose” exposure Levels and health effects, particularly malignant mesothelioma

Although asbestos research has been ongoing for decades, this increased knowledge has not led to consensus in many areas of the field. Two such areas of controversy include the specific definitions of asbestos, and limitations in understanding exposure-response relationships for various asbestos types and exposure levels and disease. This document reviews the current regulatory and mineralogical definitions and how variability in these definitions has led to difficulties in the discussion and comparison of both experimental laboratory and human epidemiological studies for asbestos. This review also examines the issues of exposure measurement in both animal and human studies, and discusses the impact of these issues on determination of cause for asbestos-related diseases. Limitations include the lack of detailed characterization and limited quantification of the fibers in most studies. Associated data gaps and research needs are also enumerated in this review.

Journal of Toxicology and Environmental Health, Pa↗
USGS2009

Use of predictive models and rapid methods to nowcast bacteria levels at coastal beaches

The need for rapid assessments of recreational water quality to better protect public health is well accepted throughout the research and regulatory communities. Rapid analytical methods, such as quantitative polymerase chain reaction (qPCR) and immunomagnetic separation/adenosine triphosphate (ATP) analysis, are being tested but are not yet ready for widespread use. Another solution is the use of predictive models, wherein variable(s) that are easily and quickly measured are surrogates for concentrations of fecal-indicator bacteria. Rainfall-based alerts, the simplest type of model, have been used by several communities for a number of years. Deterministic models use mathematical representations of the processes that affect bacteria concentrations; this type of model is being used for beach-closure decisions at one location in the USA. Multivariable statistical models are being developed and tested in many areas of the USA; however, they are only used in three areas of the Great Lakes to aid in notifications of beach advisories or closings. These “operational” statistical models can result in more accurate assessments of recreational water quality than use of the previous day's Escherichia coli (E. coli) concentration as determined by traditional culture methods. The Ohio Nowcast, at Huntington Beach, Bay Village, Ohio, is described in this paper as an example of an operational statistical model. Because predictive modeling is a dynamic process, water-resource managers continue to collect additional data to improve the predictive ability of the nowcast and expand the nowcast to other Ohio beaches and a recreational river. Although predictive models have been shown to work well at some beaches and are becoming more widely accepted, implementation in many areas is limited by funding, lack of coordinated technical leadership, and lack of supporting epidemiological data.

Aquatic Ecosystem Health & Management↗
USGS2026

Moving toward a more human-oriented analysis of urban heat: Examining differences of heat exposure intensity at busy commuting locations

Examining urban thermal environments has become a critical area of research spanning epidemiology, urban planning, and ecology. While traditional metrics like air temperature ( T air ) and satellite-derived surface temperature dominate urban heat studies, these measures often fail to reflect how people actually experience thermal exposure intensity. More human-oriented metrics, such as mean radiant temperature (MRT), and the wet bulb globe temperature (WBGT), better capture this lived experience, particularly at locations where people are likely to encounter outdoor heat, such as bus stops. Human demographics further complicate heat exposure, as access to cooling resources like trees and greenspaces can vary by neighborhood income. Our study addresses these complications by collecting thermal data across 60 commuting locations in Denver, Colorado in the summer. We evaluate (1) the extent to which more human-oriented metrics capture thermal exposure compared to T air and LST, and (2) how heat exposure varies by neighborhood income levels. We observed that bus stops in low-income neighborhoods had an MRT increase 2.8 °C compared wealthier neighborhoods, and that income-driven differences in MRT and WBGT strongly depended on bus stop aspect. After accounting for solar orientation, differences in MRT increased to as much as 6.3 °C at north-facing stops. Our results suggest tree canopy shade explains some observed heat exposure patterns, with south facing bus stops seeing a MRT and WBGT decrease of 0.42 °C and 0.11 °C from a percent increase in tree canopy. Interestingly, depending on bus stop aspect, nearby buildings can increase MRT and WBGT (facing east), or decrease MRT and WBGT (facing south) If planners aim to address this issue, consideration of bus stops, and land covers configuration may help.

Colorado↗
USGS2005

Genetic divergence of rabies viruses from bat species of Colorado, USA

Molecular epidemiological studies have linked many cryptic human rabies cases in the United States with exposure to rabies virus (RV) variants associated with insectivorous bats. In Colorado, bats accounted for 98% of all reported animal rabies cases between 1977 and 1996. The genetic divergence of RV was investigated in bat and terrestrial animal specimens that were submitted for rabies diagnosis to the Colorado Department of Public Health and Environment (CDPHE), Colorado, USA. RV isolates from animal specimens across the United States were also included in the analysis. Phylogenetic analyses were performed on partial nucleoprotein (N) gene sequences, which revealed seven principal clades. RV associated with the colonial big brown bat, Eptesicus fuscus , an bats of the genus Myotis were found to segregate into two distinct clades (I and IV). Clade I was harbored by E. fuscus and Myotis species, but was also identified in terrestrial animals such as domestic cats and striped skunks ( Mephitis mephitis ). Clade IV was divided into subclades IVA, IVB, and IVC; IVA was identified in E. fuscus, and Myotis species bats, and also in a fox; subclades IVB and IVC circulated predominantly in E. fuscus . Clade II was formed by big free-tailed bat ( Nyctinomops macrotis ) and striped skunk ( Mephitis mephitis ) samples. Clade III included RVs that are maintained by generally solitary, migratory bats such as the silver-haired bat ( Lasionycteris noctivagans ) and bats of the genus Lasiurus . Big brown bats were found to harbor this RV variant. None of the Colorado specimens segregated with clades V and VII that harbor RVs associated with terrestrial animals. Different species of bats had the same RV variant, indicating active inter-species rabies transmission. In Colorado, animal rabies occurs principally in bats, and the identification of bat RVs in cat, gray fox Urocyon cinereoargenteus ), and striped skunks demonstrated the importance of rabies spillover from bats to domestic and terrestrial wildlife species.

Vector-Borne and Zoonotic Diseases↗
USGS2021

Sustaining transmission in different host species: The emblematic case of Sarcoptes scabiei

Some pathogens sustain transmission in multiple different host species, but how this epidemiologically important feat is achieved remains enigmatic. Sarcoptes scabiei is among the most host generalist and successful of mammalian parasites. We synthesize pathogen and host traits that mediate sustained transmission and present cases illustrating three transmission mechanisms (direct, indirect, and combined). The pathogen traits that explain the success of S. scabiei include immune response modulation, on-host movement capacity, off-host seeking behaviors, and environmental persistence. Sociality and host density appear to be key for hosts in which direct transmission dominates, whereas in solitary hosts, the use of shared environments is important for indirect transmission. In social den-using species, combined direct and indirect transmission appears likely. Empirical research rarely considers the mechanisms enabling S. scabiei to become endemic in host species—more often focusing on outbreaks. Our review may illuminate parasites’ adaptation strategies to sustain transmission through varied mechanisms across host species.

BioScience↗
USGS2023

Temporal, environmental, and demographic correlates of Ichthyophonus sp. infections in mature Pacific herring populations

Causes of population collapse and failed recovery often remain enigmatic in marine forage fish like Pacific herring ( Clupea pallasii ) that experience dramatic population oscillations. Diseases such as ichthyophoniasis are hypothesized to contribute to these declines, but lack of long-term datasets frequently prevents inference. Analysis of pathogen surveillance and population assessment datasets spanning 2007–2019 indicate that the age-based prevalence estimate of Ichthyophonus infection was, on average, 54% greater among a collapsed population of Pacific herring (Prince William Sound, Alaska, USA) as compared to a nearby population (Sitka Sound, Alaska, USA) that is relatively robust. During the study years, the age-based infection prevalence ranged from 14 to 44% in Prince William Sound and 5 to 33% in Sitka Sound. At both sites, the age-based infection prevalence declined over time, with an average decrease of 7% per year. Statistical analyses indicated that infection prevalence between the two populations was reduced by regional factors affecting both sites, and that these factors were independent of herring density. Infection prevalence in both populations was positively correlated with herring age and negatively correlated with the Pacific Decadal Oscillation. This study demonstrates how synthesis of environmental, stock assessment, and disease assessment data can be leveraged to elucidate epidemiological trends in diseases of wild fish.

ICES Journal of Marine Science↗
USGS2025

Beak deformities in Buteo jamaicensis (Red-tailed Hawk) signal possible emergence of avian keratin disorder among raptors

Beginning in the late 1990s, an unusual cluster of beak deformities was observed among Buteo jamaicensis (Red-tailed Hawk) in the Pacific coastal region of North America. However, information was not available to determine the scope of this problem nor to assess a potential link between beak deformities in hawks and avian keratin disorder (AKD), an emerging disease primarily among passerines that causes overgrowth of the keratinized layer of the beak. To help address these knowledge gaps, we compiled capture records, citizen science reports, and other available data from across North America. As part of a long-term raptor monitoring program in Washington, we detected anomalously high rates of beak deformities in 29% and other keratin abnormalities in an additional 19% of B. jamaicensis between 2014 and 2021. We also identified more than 100 other AKD-like cases in B. jamaicensis , largely clustered in the Pacific coastal region, with most reports from 2000 to present. Pathologic examination of affected hawks revealed gross and microscopic features consistent with AKD in passerines, while shared epidemiological patterns, including timing of emergence, provided further evidence that this disease may impact an ecologically diverse suite of species. We detected poecivirus, a novel avian virus implicated as a likely cause of AKD in Poecile atricapillus (Black-capped Chickadee), in 1 out of 10 swabs collected from live B. jamaicensis , with gross beak deformities, suggesting the possibility of a shared viral etiology across species. However, additional work would be needed to determine the underlying cause of beak deformities in and their potential impacts on B. jamaicensis . By documenting this cluster of beak deformities, we hope to raise awareness among the ornithological community, including raptor researchers, to better track current and future outbreaks of beak deformities and related conditions.

Ornithology↗
USGS2021

Causes of delayed outbreak responses and their impacts on epidemic spread

Livestock diseases have devastating consequences economically, socially and politically across the globe. In certain systems, pathogens remain viable after host death, which enables residual transmissions from infected carcasses. Rapid culling and carcass disposal are well-established strategies for stamping out an outbreak and limiting its impact; however, wait-times for these procedures, i.e. response delays, are typically farm-specific and time-varying due to logistical constraints. Failing to incorporate variable response delays in epidemiological models may understate outbreak projections and mislead management decisions. We revisited the 2001 foot-and-mouth epidemic in the United Kingdom and sought to understand how misrepresented response delays can influence model predictions. Survival analysis identified farm size and control demand as key factors that impeded timely culling and disposal activities on individual farms. Using these factors in the context of an existing policy to predict local variation in response times significantly affected predictions at the national scale. Models that assumed fixed, timely responses grossly underestimated epidemic severity and its long-term consequences. As a result, this study demonstrates how general inclusion of response dynamics and recognition of partial controllability of interventions can help inform management priorities during epidemics of livestock diseases.

Journal of the Royal Society Interface↗
USGS2024

Season of death, pathogen persistence and wildlife behaviour alter number of anthrax secondary infections from environmental reservoirs

An important part of infectious disease management is predicting factors that influence disease outbreaks, such as R , the number of secondary infections arising from an infected individual. Estimating R is particularly challenging for environmentally transmitted pathogens given time lags between cases and subsequent infections. Here, we calculated R for Bacillus anthracis infections arising from anthrax carcass sites in Etosha National Park, Namibia. Combining host behavioural data, pathogen concentrations and simulation models, we show that R is spatially and temporally variable, driven by spore concentrations at death, host visitation rates and early preference for foraging at infectious sites. While spores were detected up to a decade after death, most secondary infections occurred within 2 years. Transmission simulations under scenarios combining site infectiousness and host exposure risk under different environmental conditions led to dramatically different outbreak dynamics, from pathogen extinction ( R < 1) to explosive outbreaks ( R > 10). These transmission heterogeneities may explain variation in anthrax outbreak dynamics observed globally, and more generally, the critical importance of environmental variation underlying host–pathogen interactions. Notably, our approach allowed us to estimate the lethal dose of a highly virulent pathogen non-invasively from observational studies and epidemiological data, useful when experiments on wildlife are undesirable or impractical.

Etosha National Park↗
USGS1979

Geochemical surveys in the United States in relation to health.

Geochemical surveys in relation to health may be classified as having one, two or three dimensions. One-dimensional surveys examine relations between concentrations of elements such as Pb in soils and other media and burdens of the same elements in humans, at a given time. The spatial distributions of element concentrations are not investigated. The primary objective of two-dimensional surveys is to map the distributions of element concentrations, commonly according to stratified random sampling designs based on either conceptual landscape units or artificial sampling strata, but systematic sampling intervals have also been used. Political units have defined sample areas that coincide with the units used to accumulate epidemiological data. Element concentrations affected by point sources have also been mapped. Background values, location of natural or technological anomalies and the geographic scale of variation for several elements often are determined. Three-dimensional surveys result when two-dimensional surveys are repeated to detect environmental changes. -Author

Philosophical Transactions of the Royal Society B:↗
USGS2017

Lyme disease ecology in a changing world: Consensus, uncertainty and critical gaps for improving control

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats, (iv) reservoir competence of host species, and (v) pathogenicity for humans of different genotypes of Borrelia burgdorferi . Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host–vector-borne zoonotic disease.

Philosophical Transactions of the Royal Society B:↗
USGS2026

From understanding to action: Integrating new and old methodologies to manage marine infectious disease

Marine diseases can have far-reaching effects on population, community and ecosystem health; however, our ability to track, predict and manage these diseases has, historically, been poor. As a result, the fields of disease ecology and epidemiology have developed at a slower pace for marine than terrestrial systems [ 1 ]. New methodologies, including genomic tools for diagnostics [ 2 , 3 ], transcriptomic tools for measuring host and pathogen responses to infection (e.g. [ 4 , 5 ]), regional oceanic modelling systems that estimate environmental conditions influencing pathogen dispersal and disease progression [ 6 ], artificial intelligence methods for quantifying pathology from images (e.g. [ 7 ]) and advanced disease modelling techniques [ 8 , 9 ] are precipitating a rapid increase in our understanding of marine pathosystems. In 2016, these efforts led to the first special issue of Philosophical Transactions of the Royal Society B ( Marine diseases, volume 371, issue 1689) focused entirely on marine disease ecology and evolution, and in 2020, the first book, Marine disease ecology, was devoted to this topic [ 10 ]. This special issue, focused on marine disease management , is being published a decade after the first Philosophical Transactions special issue on marine diseases. The shift to a management focus reflects an urgent need for management strategies to address high-impact diseases and the rapid methodological advances that have resulted. The papers included in this issue demonstrate the value of combining classical approaches (e.g. routine disease surveillance, reductionistic pathogen challenge trials, rapid throughput diagnostics) with cutting-edge technologies (e.g. high-resolution oceanographic models, Bayesian models, replicated transcriptomic studies) to identify drivers of disease, quantify impacts and suggest management strategies.

Philosophical Transactions of the Royal Society, S↗