Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Viruses”

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 937 records · Page 52Linked to original sources

Weak support for disappearance and restricted emergence/persistence of highly pathogenic influenza A in North American waterfowl

Krauss et al. (1) use lack of detection of highly pathogenic (HP) H5 clade 2.3.4.4 (henceforth "H5") influenza A viruses (IAVs) from >22,000 wild bird samples collected in North America in 2014–2015 to argue that HP H5 IAVs disappeared from waterfowl and that unresolved mechanisms restrict emergence and perpetuation of HP IAVs in natural reservoir species. Here we offer an alternative interpretation.

Proceedings of the National Academy of Sciences↗

Potentials and limits for the use of ozone as a fish disease control agent

Ozone and chlorine inactivation curves were determined in three types of freshwater at 20 C for the destruction of the fish pathogens Aeromonas salmonicida the etiologic agent of furunculosis, and Yersinia ruckeri the enteric redmouth bacterium (ERM). Ozone and chlorine inactivation curves were also obtained in the same water types at 10 C for the fish pathogenic viruses infectious hematopoietic necrosis (IHNV), and infectious pancreatic necrosis (IPNV). Acute toxicity tests using the rainbow trout as a representative salmonid revealed that ozone was highly toxic at the dose levels used. Partial chronic (3. mo.) testing revealed that ozone exposure at 2 μg/L causes only minimal physiological changes, none of which would be expected to compromise biological function.

Ozone: Science and Engineering↗

Infectious diseases of fishes in the Salish Sea

As in marine regions throughout other areas of the world, fishes in the Salish Sea serve as hosts for many pathogens, including nematodes, trematodes, protozoans, protists, bacteria, viruses, and crustaceans. Here, we review some of the better-documented infectious diseases that likely contribute to significant losses among free-ranging fishes in the Salish Sea and discuss the environmental and ecological factors that may affect the population-level impacts of disease. Demonstration of these diseases and their impacts to critical and endangered resources provides justification to expand pathogen surveillance efforts and to incorporate disease forecasting and mitigation tools into ecosystem restoration efforts.

Washington↗

Passive immunization of Pacific herring against viral hemorrhagic septicemia.

The plasma of Pacific herring Clupea pallasii that survived laboratory-induced viral hemorrhagic septicemia (VHS) epizootics contained humoral substances that, when injected into naive animals, conferred passive immunity against the disease. Among groups exposed to viral hemorrhagic septicemia virus (VHSV), injection of donor plasma from VHS survivors resulted in significantly greater survival (50%) and significantly lower tissue titers (1.5 x 10(5) plaque-forming units [PFU]/g) than the injection of plasma from VHSV-naive donors (6% survival; 3.7 x 10(6) PFU/g). Additionally, the magnitude of the protective immune response increased during the postexposure period; plasma that was collected from survivors at 123 d postexposure (931 degree-days) provided greater protection than plasma collected from survivors at 60 d postexposure (409 degree-days). These results provide proof of concept that the VHSV exposure history of Pacific herring populations can be determined post hoc; furthermore, the results can be used as the foundation for developing additional high-throughput diagnostic techniques that may be effective at quantifying herd immunity and forecasting the potential for future VHS epizootics in populations of wild Pacific herring.

Journal of Aquatic Animal Health↗

Movement analysis of free-grazing domestic ducks in Poyang Lake, China: A disease connection

Previous work suggests domestic poultry are important contributors to the emergence and transmission of highly pathogenic avian influenza throughout Asia. In Poyang Lake, China, domestic duck production cycles are synchronized with arrival and departure of thousands of migratory wild birds in the area. During these periods, high densities of juvenile domestic ducks are in close proximity to migratory wild ducks, increasing the potential for the virus to be transmitted and subsequently disseminated via migration. In this paper, we use GPS dataloggers and dynamic Brownian bridge models to describe movements and habitat use of free-grazing domestic ducks in the Poyang Lake basin and identify specific areas that may have the highest risk of H5N1 transmission between domestic and wild birds. Specifically, we determine relative use by free-grazing domestic ducks of natural wetlands, which are the most heavily used areas by migratory wild ducks, and of rice paddies, which provide habitat for resident wild ducks and lower densities of migratory wild ducks. To our knowledge, this is the first movement study on domestic ducks, and our data show potential for free-grazing domestic ducks from farms located near natural wetlands to come in contact with wild waterfowl, thereby increasing the risk for disease transmission. This study provides an example of the importance of movement ecology studies in understanding dynamics such as disease transmission on a complicated landscape.

Poyang Lake↗

Biosafety practices when working with bats: A guide to field research considerations

Introduction: Field work with bats is an important contribution to many areas of research in environmental biology and ecology, as well as microbiology. Work with bats poses hazards such as bites and scratches, and the potential for exposure to infectious pathogens such as rabies virus. It also exposes researchers to many other potential hazards inherent to field work, such as environmental conditions, delayed emergency responses, or challenging work conditions. Methods: This article discusses the considerations for a thorough risk assessment process around field work with bats, pre- and post-occupational health considerations, and delves into specific considerations for areas related to biosafety concerns—training, personal protective equipment, safety consideration in field methods, decontamination, and waste. It also touches on related legal and ethical issues that sit outside the realm of biosafety, but which must be addressed during the planning process. Discussion: Although the focal point of this article is bat field work located in northern and central America, the principles and practices discussed here are applicable to bat work elsewhere, as well as to field work with other animal species, and should promote careful considerations of how to safely conduct field work to protect both researchers and animals.

Applied Biosafety↗

Disease emergence in birds: Challenges for the twenty-first century

The paper by Hartup et al. (2001) on House Finch ( Carpodacus mexicanus ) conjunctivitis is an example of the rapid geographic spread that can result from disease emergence in naïve populations. That event was neither novel nor transient relative to its occurrence or effects. Disease emergence and reemergence are hallmarks of the latter part of the twentieth century (Center for Disease Control 1994, Levins et al. 1994, DaSilva and Laccarino 1999, Gratz 1999). Current examples involving domestic animals include the problems in Europe with bovine spongiform encephalopathy (BSE, or “mad cow disease”) (Brown 2001) and foot-and-mouth disease (FMD) (Kitching 1999). Human health has been affected by diseases caused by an array of viruses (Morse 1993, Nichol et al. 1993, Murphy and Nathanson 1994), bacteria (Dennis 1998, DaSilva and Laccarino 1999), rickettsia (Walker and Dumier 1996, Azad et al. 1997), protozoans (Tuerrant 1997, Saini et al. 2000), and metazoan parasites (Hildreth et al. 1991, Gubler 1998), as well as other causes. Acquired immune deficiency syndrome (AIDS) has received the most notoriety of those diseases (Hahn et al. 2000, Schwartlander et al. 2000). A similar pattern exists on a global scale for free-ranging wildlife populations (Table 1) (Friend 1994, 1995; Epstein et al. 1998, Daszak et al. 2000). However, in comparison to disease emergence affecting humans and domestic animals, response to emerging diseases of wildlife is generally superficial. We present concepts and data to support our contention that failure to adequately address disease emergence in free-ranging wildlife is resulting in a diminished capability to achieve and sustain desired geographic distributions and population abundance for species of wild birds, including some threatened and endangered avifauna. For clarity, we define disease and disease emergence in the context of our use of those terms because they are the focus of our comments. Disease is any departure from health (Guralnik 1982); that is, dysfunction contributing to physiological, physical, reproductive, behavioral, or other impairment that reduces the probability of survival of individuals. If enough individuals are affected, the collective effects can reduce the sustainability of the population. Although disease can result from exposure to a wide variety of physical, chemical, and biological agents and other conditions, we focus this paper on microbes and parasites and to overt mortality caused by them. Thus, disease effects presented only represent the proverbial “tip of the iceberg” relative to the challenges wild avifauna face from disease. Our perspective of disease emergence expands the earlier definitions of emerging diseases by others (Centers for Disease Control and Prevention 1994, Morse 1995) to include all species. Our comments are defined by the context of disease occurrences that have increased within the past three decades, or threaten to increase in the near future relative to populations affected, geographic distribution, or magnitude of effects.

The Auk↗

Prevalence of pox-like lesions and malaria in forest bird communitites on leeward Mauna Loa volcano, Hawaii

Introduced avian pox virus and malaria have had devastating impacts on native Hawaiian forest birds, yet little has been published about their prevalence and distribution in forest bird communities outside of windward Hawaii Island. We surveyed native and non-native forest birds for these two diseases at three different elevations on leeward Mauna Loa Volcano at the Kona Forest Unit of Hakalau Forest National Wildlife Refuge. Prevalence of malaria by both serology and microscopy varied by elevation and ranged from 28% at 710 m to 13% at 1830 m. Prevalence of pox-like lesions also varied by altitude, ranging in native species from 10% at 710 m to 2% at 1830 m. Native species at all elevations had the highest prevalence of malarial antibody and pox-like lesions. By contrast, pox-like lesions were not detected in individuals of four non-native species and only 5% of Japanese White-eye ( Zosterops japonicus ) was positive for malaria. A significantly high proportion of birds with pox-like lesions also had serological evidence of concurrent, chronic malarial infections, suggesting an interaction between these diseases, dual transmission of both diseases by the primary mosquito vector ( Culex quinquefasciatus ) or complete recovery of some pox-infected birds without loss of toes. Results from this study document high prevalence of malaria and pox at this refuge. Development of effective disease control strategies will be important for restoration of remnant populations of the endangered ‘Akiapola‘au ( Hemignathus munroi ), Hawaii Creeper ( Oreomystis mana ), and Hawaii ‘Akepa ( Loxops coccineus coccineus ) that still occur on the refuge.

Hawai'i↗

Serum virome of southern Beaufort Sea polar bears (Ursus maritimus) during a period of rapid climate change

Climate change affects the behavior, physiology and life history of many Arctic wildlife species. It can also influence the distribution and ecology of infectious agents. The southern Beaufort Sea (SB) subpopulation of polar bears ( Ursus maritimus ) has experienced dramatic behavioral changes due to retreating sea ice and other climate-related factors, but the effects of these changes on physiology and infection remain poorly understood. Using serum from polar bears sampled between 2004 and 2015 and metagenomic DNA sequencing, we identified 48 viruses, all of the family Anelloviridae . Anelloviruses are small, ubiquitous infectious agents with circular single-stranded DNA genomes that are not known to cause disease but, in humans, covary in diversity and load with immunological compromise. We therefore examined the usefulness of anelloviruses as biomarkers of polar bear physiological stress related to climate and habitat use. Polar bear anelloviruses sorted into two distinct clades on a phylogenetic tree, both of which also contained anelloviruses of giant pandas ( Ailuropoda melanoleuca ), another ursid. Neither anellovirus diversity nor load were associated with any demographic variables, behavioral factors or direct physiological measures. However, pairwise genetic distances between anelloviruses were positively correlated with pairwise differences in sampling date, suggesting that the polar bear “anellome”is evolving over time. These findings suggest that anelloviruses are not a sensitive indicator of polar physiological stress, but they do provide a baseline for evaluating future changes to polar bear viromes.

Alaska↗

The future of fungi: Threats and opportunities

The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.

G3 Genes, Genomes, Genetics↗

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↗

Manipulating wild and tamed phytobiomes: Challenges and opportunities

This white paper presents a series of perspectives on current and future phytobiome management, discussed at the Wild and Tamed Phytobiomes Symposium in University Park, PA, USA, in June 2018. To enhance plant productivity and health, and to translate lab- and greenhouse-based phytobiome research to field applications, the academic community and end-users need to address a variety of scientific, practical, and social challenges. Prior discussion of phytobiomes has focused heavily on plant-associated bacterial and fungal assemblages, but the phytobiomes concept covers all factors that influence plant function. Here we discuss various management considerations, including abiotic conditions (e.g. soil, nutrient applications), microorganisms (e.g. bacterial and fungal assemblages, bacterial and fungal inoculants, viruses), macroorganisms (e.g. arthropods, plant genetics), and societal factors (e.g. communication approaches, technology diffusion). An important near-term goal for this field should be to estimate the potential relative contribution of different components of the phytobiome to plant health, as well as the potential and risk of modifying each in the near-future.

Phytobiomes Journal↗

Social effects of rabies infection in male vampire bats (Desmodus rotundus)

Rabies virus (RABV) transmitted by the common vampire bat ( Desmodus rotundus ) poses a threat to agricultural development and public health throughout the Neotropics. The ecology and evolution of rabies host-pathogen dynamics are influenced by two infection-induced behavioral changes. RABV-infected hosts often exhibit increased aggression which facilitates transmission, and rabies also leads to reduced activity and paralysis prior to death. Although several studies document rabies-induced behavioral changes in rodents and other dead-end hosts, surprisingly few studies have measured these changes in vampire bats, the key natural reservoir throughout Latin America. Here, we take advantage of an experiment designed to test the safety and efficacy of an oral rabies vaccine in captive male vampire bats to quantify for the first time how rabies affects allogrooming and aggressive behaviors in the vampire bat. Compared to non-rabid vampire bats, rabid individuals reduced their allogrooming prior to death, but we did not detect increases in aggression among bats. To put our results in context, we review what is known and what remains unclear about behavioral changes of rabid vampire bats.

Biology Letters↗

The impacts of co-circulating pathogens in Pacific herring depend on interactions between viral life-cycle traits and transmission parameters, highlighting interdependencies between pathogen epizootics

The average host susceptibility decreases as the epizootic progresses because easily infected hosts are first removed from the population. While host susceptibility is pathogen-specific, it is likely that host susceptibility is correlated between different pathogens, so that co-circulating pathogens may have reciprocal impacts on their epidemics. However, despite well-documented examples of concomitant infections in marine hosts, reciprocal epizootic effects have not been documented in wild marine organisms. We quantify reciprocal impacts between viral haemorrhagic septicaemia and viral erythrocytic necrosis in Pacific herring ( Clupea pallasii ) using field and laboratory work. We show that the causative viruses for both diseases circulate through herring populations and that infection with one pathogen has negative impacts on the epizootic and infection characteristics of the other pathogen, suggesting positive correlations in the susceptibility to infection between pathogens. We then use simulations of a two-strain pathogen model to show that the impact of the correlation is modulated by transmission parameters, such as the incubation period and the initial transmission rate. Our work shows that co-occurring epizootics pose a management challenge because single-pathogen management actions may amplify the epizootics of the non-targeted pathogen. This study provides a framework to evaluate the consequences of reciprocal epizootic impacts through field, experimental and modelling work.

Washington↗

Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)

With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer ( Odocoileus virginianus ) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants ( Mycoplasma ovipneumoniae , Trueperella pyogenes , Pasteurella multocida , Anaplasma phagocytophilum , Fusobacterium necrophorum ); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.

Microbial Genomics↗

A multi-state occupancy modelling framework for robust estimation of disease prevalence in multi-tissue disease systems

Given the public health, economic and conservation implications of zoonotic diseases, their effective surveillance is of paramount importance. The traditional approach to estimating pathogen prevalence as the proportion of infected individuals in the population is biased because it fails to account for imperfect detection. A statistically robust way to reduce bias in prevalence estimates is to obtain repeated samples (or sample many tissues in multi‐tissue disease systems) and to apply statistical methods that account for imperfect detection and permit the interdependence of the infection process across multiple tissues. We developed a multi‐state occupancy modelling framework which considers two scenarios about the infection process, one where no assumptions about the dependencies among the tissues are made (general), and another where dependence among tissues is not permitted (constrained). We applied this framework to pseudorabies virus (PrV) DNA detection data obtained from whole blood; and oral, nasal and genital mucosa of 510 feral swine Sus scrofa during the years 2014–2016 in Florida, USA. The constrained model was better supported by data. PrV prevalence estimates varied among tissues and were higher than the naïve estimates, ranging from to 0.06 (CI: 0.02–0.14) in genital to 0.54 (CI: 0.14 ‐ 0.82) in nasal tissue. Probability of PrV detection ranged from 0.11 (CI: 0.06–0.18) in nasal to 0.51 (CI: 0.21–0.81) in genital tissue. PrV prevalence was not affected by the age or sex of the animal or the year of sampling, but prevalence increased as drought severity increased. The conditional probability of detecting PrV given infection in at least one tissue type within an individual was highest for nasal tissue, suggesting that nasal is the best tissue to sample for PrV surveillance if only one tissue can be sampled, at least for systems with tissue‐specific prevalence and detection probabilities similar to ours. Synthesis and applications . We focused on inferences about pathogen prevalence in multi‐tissue disease systems, dealing with both nondetection and potential dependencies among tissues in infection status. We found strong evidence of variation in both prevalence and detection probabilities among tissues. Our results emphasize the importance of sampling multiple tissues and of applying inference methods that account for imperfect detection in the surveillance of systemic diseases. The multi‐state modelling framework is broadly applicable to the surveillance of pathogens that infect multiple tissues and can be used even when the infection status of the pathogen in one tissue may depend on the infection status of the pathogen in other tissue(s).

Journal of Applied Ecology↗

A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats

The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field-applicable and user-friendly CRISPR/Cas-based biosensor for the detection of Pseudogymnoascus destructans ( Pd ), the causative fungal agent of white-nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect Pd DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing Pd- positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of Pd- positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease-associated pathogen detection and monitoring applications.

Molecular Ecology Resources↗

Modeling the response of an endangered rabbit population to RHDV2 and vaccination

Rabbit hemorrhagic disease virus 2 (RHDV2), recently detected in the western United States, has the potential to cause mass mortality events in wild rabbit and hare populations. Currently, few management strategies exist other than vaccination. We developed a spatially explicit model of RHDV2 for a population of riparian brush rabbits ( Sylvilagus bachmani riparius ), a subspecies of brush rabbit classified as endangered in the United States, on a subsection of the San Joaquin River National Wildlife Refuge. The goal of our model was to provide guidance regarding vaccination strategies for an endangered rabbit species. Our model predicts that increased interactions between rabbits (a proxy for landscape connectivity) and disease transmission rates among susceptible hosts (individual brush rabbits and conspecifics) have the greatest influence on the outcome of a potential vaccination campaign. Our model projects that across a range of parameter estimates (given an RHDV2 incursion), the median estimated population size with a 0%–10% vaccination rate after 1 year is 538 rabbits (95% Confidence Interval [C.I.] 69–1235), approximately 36% of the expected size of the study population of 1470 rabbits without an RHDV2 introduction. With a 10%–20%, 20%–30%, or 30%–40% vaccination rate, the median estimated population size increased to 628 rabbits (95% C.I. 130–1298), 723 rabbits (95% C.I. 198–1317), and 774 rabbits (95% C.I. 228–1410), respectively. These estimates represent 43%, 49%, and 53% of the expected population size without an RHDV2 introduction. Overall, a 1% increase in vaccination rate was associated with a six rabbit (95% C.I. 5–7) increase in total remaining population size. This result is dependent on assumptions regarding environmental transmission, home range size (and contact rates of rabbits). Given the relatively short lifespan of rabbits and the potential need for boosters, vaccination programs are most likely to be successful for small target populations where relatively high vaccination rates can be maintained.

California↗