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USGS2022

Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse

Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse ( Tympanuchus phasianellus : 9 exposed, 18 unexposed and greater prairie chickens ( T. cupido ; 11, 11). Exposure to crop production had greater effect on microbiota richness ( t = 6.675, P < 0.001) and composition (PERMANOVA r 2 = 0.212, P = 0.001) than did the host species ( t = 4.762, P < 0.001; r 2 = 0.070, P = 0.001) or their interaction ( t = 3.449; r 2 = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed ( T. cupido chao1 = 152.8 ± 20.5; T. phasianellus 115.3 ± 17.1) than in unexposed (102.9 ± 15.1 and 101.1 ± 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean ± standard deviation; T. cupido 24.8 ± 10.0 and 10.1 ± 5.5, respectively; T. phasianellus 13.4 ± 6.8/4.9 ± 2.8) and resistome ( T. cupido 46.8 ± 11.7/28.9 ± 10.2, T. phasianellus 38.3 ± 16.7/18.9 ± 14.2) than unexposed birds ( T. cupido virulome: 14.2 ± 13.5, 4.5 ± 4.2; T. cupido resistome: 31.6 ± 20.2 and 13.1 ± 12.0; T. phasianellus virulome: 5.2 ± 4.7 and 1.4 ± 1.5; T. phasianellus resistome: 13.7 ± 16.1 and 4.0 ± 6.4).

Nebraska↗

USGS2017

Highlighting the complexities of a groundwater pilot study during an avian influenza outbreak: Methods, lessons learned, and select contaminant results

The highly pathogenic avian influenza (H5N2) outbreak in the Midwestern United States (US) in 2015 was historic due to the number of birds and poultry operations impacted and the corresponding economic loss to the poultry industry and was the largest animal health emergency in US history. The U.S. Geological Survey (USGS), with the assistance of several state and federal agencies, aided the response to the outbreak by developing a study to determine the extent of virus transport in the environment. The study goals were to: develop the appropriate sampling methods and protocols for measuring avian influenza virus (AIV) in groundwater, provide the first baseline data on AIV and outbreak- and poultry-related contaminant occurrence and movement into groundwater, and document climatological factors that may have affected both survival and transport of AIV to groundwater during the months of the 2015 outbreak. While site selection was expedient, there were often delays in sample response times due to both relationship building between agencies, groups, and producers and logistical time constraints. This study's design and sampling process highlights the unpredictable nature of disease outbreaks and the corresponding difficulty in environmental sampling of such events. The lessons learned, including field protocols and approaches, can be used to improve future research on AIV in the environment.

Iowa↗

USGS2017

The effect of aluminium and sodium impurities on the in vitro toxicity and pro-inflammatory potential of cristobalite

Background Exposure to crystalline silica (SiO 2 ), in the form of quartz, tridymite or cristobalite, can cause respiratory diseases, such as silicosis. However, the observed toxicity and pathogenicity of crystalline silica is highly variable. This has been attributed to a number of inherent and external factors, including the presence of impurities. In cristobalite-rich dusts, substitutions of aluminium (Al) for silicon (Si) in the cristobalite structure, and impurities occluding the silica surface, have been hypothesised to decrease its toxicity. This hypothesis is tested here through the characterisation and in vitro toxicological study of synthesised cristobalite with incremental amounts of Al and sodium (Na) dopants. Methods Samples of synthetic cristobalite with incremental amounts of Al and Na impurities, and tridymite, were produced through heating of a silica sol-gel. Samples were characterised for mineralogy, cristobalite purity and abundance, particle size, surface area and surface charge. In vitro assays assessed the ability of the samples to induce cytotoxicity and TNF-α production in J774 macrophages, and haemolysis of red blood cells. Results Al-only doped or Al+Na co-doped cristobalite contained between 1 and 4 oxide wt% Al and Na within its structure. Co-doped samples also contained Al- and Na-rich phases, such as albite. Doping reduced cytotoxicity to J774 macrophages and haemolytic capacity compared to non-doped samples. Al-only doping was more effective at decreasing cristobalite reactivity than Al+Na co-doping. The reduction in the reactivity of cristobalite is attributed to both structural impurities and a lower abundance of crystalline silica in doped samples. Neither non-doped nor doped crystalline silica induced production of the pro-inflammatory cytokine TNF-α in J774 macrophages. Conclusions Impurities can reduce the toxic potential of cristobalite and may help explain the low reactivity of some cristobalite-rich dusts. Whilst further work is required to determine if these effects translate to altered pathogenesis, the results have potential implications for the regulation of crystalline silica exposures.

Environmental Research↗

USGS2025

Detection of Giardia and Cryptosporidium in surface water of a subarctic city

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

Alaska↗

USGS2020

Increased prespawning mortality threatens an integrated natural- and hatchery-origin sockeye salmon population in the Lake Washington Basin

The life cycle of diadromous fishes such as salmonids involves natural mortality in a series of distinct life history stages, occurring sequentially in different habitats. Decades of research have emphasized mortality at the embryo, juvenile, and sub-adult stages but it is increasingly clear that some adults that survive and return to freshwater habitats die during the final homeward migration or after they reach the spawning grounds, prior to breeding. These are termed “en route” and “prespawning” mortality, respectively, and can threaten populations depleted by mortality at previous stages. In this study, we present evidence that the sockeye salmon, Oncorhynchus nerka, population that returns to the Lake Washington Basin, in Washington State, USA, is experiencing both forms of adult mortality. Counts of the salmon entering the basin on their return migration in June and July were compared to counts in the major spawning grounds in September through November for 1995–2018. The disparity has increased markedly in recent years. The counts on the spawning grounds have decreased as a proportion of the number entering the system with an average 49 % of sockeye unaccounted for, consistent with increased en route mortality. In addition, prespawning mortality rates have increased in salmon that reach the Cedar River, the main spawning tributary, both at a hatchery holding adult fish in 1995–2018, and in the naturally spawning populations when monitored in the last five years. Hatchery records indicated <10 % prespawning mortality for 1995–2010, increasing to an average 43 % for 2014 – 2018. Recent carcass surveys in the Cedar River documented that 33.6% (2014), 22.3% (2015), 30.3% (2016) and 50.0% (2018) of female sockeye died before completing spawning. These recent increases in prespawning mortality have been associated with warm water during entry to freshwater, but comparably warm water in past decades had no such effect. Steady warming of river temperatures around the median run completion date from < 8.0 °C to > 13.0 °C was correlated with increased prespawning mortality rates at the hatchery from 1995–2018. We conclude that warming conditions during migration and spawning, in concert with other factors such as infections with pathogens, are responsible for the increased prespawning mortality of adult sockeye salmon that are high enough to threaten the population’s viability.

Washington↗

USGS2022

Scope of the cortisol stress response in Chinook salmon during maturation

In semelparous Pacific salmon, increased cortisol levels accompany sexual maturation and may be related to the rapid senescence and death that occur after spawning. In fish with extremely high cortisol, pre-spawning mortality is more likely. This may be because elevated cortisol is accompanied by energy depletion and reduces the immune capacity of sexually maturing individuals, thus increasing their susceptibility to parasites and pathogens. Several studies have measured cortisol levels in Pacific salmon during the last few weeks prior to spawning, but there is a lack of information regarding longer-term changes in resting and stressed cortisol levels of migrating adult Pacific salmon. A better understanding of the scope of the cortisol response during sexual maturation could contribute to understanding the extremely high pre-spawning mortality experienced by some threatened populations of Pacific salmon. The objective of this study was to determine the scope of the cortisol stress response in spring Chinook salmon as well as the dynamics of resting cortisol during maturation. We conducted a laboratory experiment in which plasma cortisol in adult Chinook salmon was measured before and after application of a standardized stressor applied at monthly intervals during the last three months prior to spawning. We found that resting and stressed cortisol levels increased during the last three months prior to spawning. We also found that sexually maturing Chinook salmon are able to mount a cortisol response to acute stressors when resting levels are elevated during maturation. Additionally, the effects of stress and time on cortisol dynamics differed between males and females as well as between individuals, which has implications for population resilience to anthropogenic stressors in wild populations.

Oregon↗

USGS2017

Characterizing interactions between fire and other disturbances and their impacts on tree mortality in western U.S. Forests

Increasing evidence that pervasive warming trends are altering disturbance regimes and their interactions with fire has generated substantial interest and debate over the implications of these changes. Previous work has primarily focused on conditions that promote non-additive interactions of linked and compounded disturbances, but the spectrum of potential interaction patterns has not been fully considered. Here we develop and define terminology, expand on the existing conceptual framework and review the patterns and mechanisms of disturbance interactions with a focus on interactions between fire and other forest disturbances and a specific emphasis on resulting tree mortality. The types of interactions reflect the positive, negative, or neutral responses to the incidence, intensity, and effects of the interaction. These types of interactions are not always mutually exclusive, but can be distinct. The collective effect of the interactions will determine the longer-term ecosystem response that can result in a resistant, resilient, or compounded interaction. Our review indicates that the interactions of drought, bark beetles , or pathogens with fire often result in neutral or maintained interactions that do not negatively or positively influence the incidence or intensity following fire. The effect of these disturbance interactions on tree mortality ranged from antagonistic (reduced mortality compared to individual disturbances) to synergistic (greater mortality compared to individual disturbances) within and among disturbance interaction types but often resulted in additive effects (mortality is consistent with the summation of the two disturbances). Synergistic effects on tree mortality have been observed when the severity of the initial disturbance is moderate to high and time between disturbances is relatively short. When the sequence of disturbance interaction is reversed (e.g., fire precedes other disturbances) the conditions can generally promote impeded interactions (lower incidence of interaction), reduced interactions (lower intensity of interaction), and antagonistic interactions (lower tree mortality). While recent research on fire-disturbance interactions has increased over the last decade and provided important insights, more research that identifies the specific thresholds of incidence, intensity, and effects of interaction by region and forest type are needed to better assist management solutions that promote desired outcomes in rapidly changing ecosystems.

Forest Ecology and Management↗

USGS2018

Identifying management-relevant research priorities for responding to disease-associated amphibian declines

A research priority can be defined as a knowledge gap that, if resolved, identifies the optimal course of conservation action. We (a group of geographically distributed and multidisciplinary research scientists) used tools from nominal group theory and decision analysis to collaboratively identify and prioritize information needs within the context of disease-associated amphibian decline , in order to develop a strategy that would support US management agency needs. We developed iterated influence diagrams to create and assess a unified research strategy. We illustrated a transparent process for identifying specific knowledge gaps in amphibian disease ecology relevant to environmental management, and then constructed a research plan to address these uncertainties. The resulting priorities include a need to: (1) understand the drivers of the community-disease relationship, (2) determine the mechanisms by which exposure to contaminants influence disease outcomes, (3) identify elements of terrestrial and aquatic habitats that stabilize host-pathogen dynamics, (4) discuss how metapopulations may be managed to reduce the speed and intensity of disease outbreaks, and (5) define the relationship between habitat management and the environmental and host microbiomes. Along with identifying research priorities for disease management, we present the details of the process used to develop a consensus plan for addressing disease-related declines in amphibians on federally managed lands of the United States.

Global Ecology and Conservation↗

USGS2026

Status assessment of peregrine falcons in North America using integrated population models

Species status assessments require an understanding of underlying population dynamics and important drivers of species demography. Large-scale assessments can be difficult due to challenges collating data obtained through different methods and different sources at multiple scales. Integrated population models (IPMs) provide a unified framework to combine multiple data sources and jointly estimate population parameters over a large spatiotemporal scale. We developed separate IPMs to estimate abundance and demographic rates for a northern (NMP) and southern (SMP) management population of peregrine falcons ( Falco peregrinus ) in North America from 2008 through 2019 (SMP) and 2020 (NMP). An outbreak of highly pathogenic avian influenza (HPAI) starting in 2021 led us to extend our modeling effort to assess its impact on these management populations by updating both IPMs using index data of population size through 2024 in a predictive framework. Survival probabilities differed drastically between first-year and after-first-year individuals in both management populations. After-first-year survival was nearly identical between the NMP and SMP, but first-year survival was lower in the SMP. Mean productivity was significantly lower in the NMP compared to the SMP, whereas the probability of breeding was similar in both management populations. Estimated total abundance for the NMP was substantially larger than the SMP, representing most of the North American peregrine population. Population growth was positive for both management populations, albeit at a slower rate for the NMP. The NMP declined from 2017 to 2018 coinciding with a drop in 2018 estimated productivity. When we extended the IPMs with updated count data through 2024, the NMP slightly declined but estimated abundance remained above levels at the start of the time series analyzed. The SMP grew at a similar rate to that predicted during the period informed by demographic data. We did not detect a continental-scale change in population size or trajectory in either management population associated with the arrival of HPAI in 2021. Further monitoring can support determination of whether the declines in the NMP were temporary, can enhance understanding of the underlying mechanisms, and can be used to guide the conservation and management of the peregrine falcon population in North America.

North America↗

USGS2021

Plague transforms positive effects of precipitation on prairie dogs to negative effects

Rodents characteristically benefit from increased precipitation, especially in typically dry habitats; “good years” of high precipitation improve their forage and water balance. However, Yersinia pestis (plague), a flea-borne pathogen of mammals that was introduced to western North America, has the greatest negative impact on at least some species of rodents during years of above-average precipitation. In the absence of plague mitigation, negative effects of plague in wet years might overwhelm the otherwise beneficial effects of increased moisture. In Montana and Utah, USA, where plague now occurs enzootically, we investigated the influence of precipitation on finite rates of annual population change (2000–2005) for 3 species of prairie dogs ( Cynomys spp.) in replicated plots treated with deltamethrin dust and in non-treated plots for paired comparisons. There was a significant interaction between precipitation and treatment. When we reduced plague vector fleas, prairie dog visual counts tended to increase with increasing precipitation. Simultaneously, there was a negative relationship between counts and precipitation on paired plots where plague was not managed, suggesting that plague transformed and reversed the otherwise beneficial effect of increased precipitation. Are the good years gone for prairie dogs? Even if the good years are not gone, they are perhaps relatively scarce compared to historic times prior to the invasion of plague. This scenario might apply to other ecosystems and may pose broad conservation challenges in western North America.

Montana, Utah↗

USGS2007

Protozoal meningoencephalitis in sea otters (Enhydra lutris): A histopathological and immunohistochemical study of naturally occurring cases

Protozoal meningoencephalitis is considered to be an important cause of mortality in the California sea otter ( Enhydra lutris ). Thirty nine of 344 (11.3%) California (CA) and Washington state (WA) sea otters examined from 1985 to 2004 had histopathological evidence of significant protozoal meningoencephalitis. The aetiological agents and histopathological changes associated with these protozoal infections are described. The morphology of the actively multiplicative life stages of the organisms (tachyzoites for Toxoplasma gondii and merozoites for Sarcocystis neurona ) and immunohistochemical labelling were used to identify infection with S. neurona ( n =22, 56.4%), T. gondii ( n =5, 12.8%) or dual infection with both organisms ( n =12, 30.8%). Active S. neurona was present in all dual infections, while most had only the latent form of T. gondii . In S. neurona meningoencephalitis, multifocal to diffuse gliosis was widespread in grey matter and consistently present in the molecular layer of the cerebellum. In T. gondii meningoencephalitis, discrete foci of gliosis and malacia were more widely separated, sometimes incorporated pigment-laden macrophages and mineral, and were found predominantly in the cerebral cortex. Quiescent tissue cysts of T. gondii were considered to be incidental and not a cause of clinical disease and mortality. Protozoal meningoencephalitis was diagnosed more frequently in the expanding population of WA sea otters (10 of 31, 32.3%) than in the declining CA population (29 of 313, 9.3%). Among sea otters with protozoal meningoencephalitis, those that had displayed neurological signs prior to death had active S. neurona encephalitis, supporting the conclusion that S. neurona is the most significant protozoal pathogen in the central nervous system of sea otters.

California, Washington↗

USGS2013

Influence of temperature on viral hemorrhagic septicemia (Genogroup IVa) in Pacific herring, Clupea pallasii Valenciennes

An inverse relationship between water temperature and susceptibility of Pacific herring ( Clupea pallasii ) to viral hemorrhagic septicemia, genogroup IVa (VHS) was indicated by controlled exposure studies where cumulative mortalities, viral shedding rates, and viral persistence in survivors were greatest at the coolest exposure temperatures. Among groups of specific pathogen-free (SPF) Pacific herring maintained at 8, 11, and 15 °C, cumulative mortalities after waterborne exposure to viral hemorrhagic septicemia virus (VHSV) were 78%, 40%, and 13%, respectively. The prevalence of survivors with VHSV-positive tissues 25 d post-exposure was 64%, 16%, and 0% (at 8, 11 and 15 °C, respectively) with viral prevalence typically higher in brain tissues than in kidney/spleen tissue pools at each temperature. Similarly, geometric mean viral titers in brain tissues and kidney/spleen tissue pools decreased at higher temperatures, and kidney/spleen titers were generally 10-fold lower than those in brain tissues at each temperature. This inverse relationship between temperature and VHS severity was likely mediated by an enhanced immune response at the warmer temperatures, where a robust type I interferon response was indicated by rapid and significant upregulation of the herring Mx gene. The effect of relatively small temperature differences on the susceptibility of a natural host to VHS provides insights into conditions that preface periodic VHSV epizootics in wild populations throughout the NE Pacific.

Journal of Experimental Marine Biology and Ecology↗

USGS2013

Partial least squares for efficient models of fecal indicator bacteria on Great Lakes beaches

At public beaches, it is now common to mitigate the impact of water-borne pathogens by posting a swimmer's advisory when the concentration of fecal indicator bacteria (FIB) exceeds an action threshold. Since culturing the bacteria delays public notification when dangerous conditions exist, regression models are sometimes used to predict the FIB concentration based on readily-available environmental measurements. It is hard to know which environmental parameters are relevant to predicting FIB concentration, and the parameters are usually correlated, which can hurt the predictive power of a regression model. Here the method of partial least squares (PLS) is introduced to automate the regression modeling process. Model selection is reduced to the process of setting a tuning parameter to control the decision threshold that separates predicted exceedances of the standard from predicted non-exceedances. The method is validated by application to four Great Lakes beaches during the summer of 2010. Performance of the PLS models compares favorably to that of the existing state-of-the-art regression models at these four sites.

Journal of Environmental Management↗

USGS2023

Estrogenic activity response to best management practice implementation in agricultural watersheds in the Chesapeake Bay watershed

Best management practices (BMPs) have been predominantly used throughout the Chesapeake Bay watershed (CBW) to reduce nutrients and sediments entering streams, rivers, and the bay. These practices have been successful in reducing loads entering the estuary and have shown the potential to reduce other contaminants (pesticides, hormonally active compounds, pathogens) in localized studies and modeled load estimates. However, further understanding of relationships between BMPs and non-nutrient contaminant reductions at regional scales using sampled data would be beneficial. Total estrogenic activity was measured in surface water samples collected over a decade (2008–2018) in 211 undeveloped NHDPlus V2.1 watersheds within the CBW. Bayesian hierarchical modeling between total estrogenic activity and landscape predictors including landcover, runoff, BMP intensity, and a BMP*agriculture intensity interaction term indicates a 96% posterior probability that BMP intensity on agricultural land is reducing total estrogenic activity. Additionally, watersheds with high agriculture and low BMPs had a 49% posterior probability of exceeding an effects-based threshold in aquatic organisms of 1 ng/L but only a 1% posterior probability of exceeding this threshold in high-agriculture, high-BMP watersheds.

Chesapeake Bay watershed↗

USGS2010

Spatial and temporal dynamics of lake whitefish (Coregonus clupeaformis) health indicators: linking individual-based indicators to a management-relevant endpoint

We examined the spatial and temporal dynamics of health indicators in four lake whitefish ( Coregonus clupeaformis ) stocks located in northern lakes Michigan and Huron from 2003 to 2006. The specific objectives were to (1) quantify spatial and temporal variability in health indicators; (2) examine relationships among nutritional indicators and stock-specific spatial and temporal dynamics of pathogen prevalence and intensity of infection; and (3) examine relationships between indicators measured on individual fish and stock-specific estimates of natural mortality. The percent of the total variation attributed to spatial and temporal sources varied greatly depending on the health indicator examined. The most notable pattern was a downward trend in the concentration of highly unsaturated fatty acids (HUFAs), observed in all stocks, in the polar lipid fraction of lake whitefish dorsal muscle tissue over the three study years. Variation among stocks and years for some indicators were correlated with the prevalence and intensity of the swimbladder nematode Cystidicola farionis , suggesting that our measures of fish health were related, at some level, with disease dynamics. We did not find relationships between spatial patterns in fish health indicators and estimates of natural mortality rates for the stocks. Our research highlights the complexity of the interactions between fish nutritional status, disease dynamics, and natural mortality in wild fish populations. Additional research that identifies thresholds of health indicators, below (or above) which survival may be reduced, will greatly help in understanding the relationship between indicators measured on individual fish and potential population-level effects.

Michigan↗

USGS2014

Enterococcus phages as potential tool for identifying sewage inputs in the Great Lakes region

Bacteriophages are viruses living in bacteria that can be used as a tool to detect fecal contamination in surface waters around the world. However, the lack of a universal host strain makes them unsuitable for tracking fecal sources. We evaluated the suitability of two newly isolated Enterococcus host strains (ENT-49 and ENT-55) capable for identifying sewage contamination in impacted waters by targeting phages specific to these hosts. Both host strains were isolated from wastewater samples and identified as E. faecium by 16S rRNA gene sequencing. Occurrence of Enterococcus phages was evaluated in sewage samples ( n = 15) from five wastewater treatment plants and in fecal samples from twenty-two species of wild and domesticated animals (individual samples; n = 22). Levels of Enterococcus phages, F + coliphages, Escherichia coli and enterococci were examined from four rivers, four beaches, and three harbors. Enterococcus phages enumeration was at similar levels (Mean = 6.72 Log PFU/100 mL) to F + coliphages in all wastewater samples, but were absent from all non-human fecal sources tested. The phages infecting Enterococcus spp. and F + coliphages were not detected in the river samples (detection threshold < 10 PFU/100 mL), but were present in the beach and harbor samples (range = 1.83 to 2.86 Log PFU/100 mL). Slightly higher concentrations (range = 3.22 to 3.69 Log MPN/100 mL) of E. coli and enterococci when compared to F + coliphages and Enterococcus phages, were observed in the river, beach and harbor samples. Our findings suggest that the bacteriophages associated with these particular Enterococcus host strains offer potentially sensitive and human-source specific indicators of enteric pathogen risk.

Journal of Great Lakes Research↗

USGS2012

Histological observations in the Hawaiian reef coral, Porites compressa, affected by Porites bleaching with tissue loss

The scleractinian finger coral Porites compressa is affected by the coral disease Porites bleaching with tissue loss (PBTL). This disease initially manifests as bleaching of the coenenchyme (tissue between polyps) while the polyps remain brown with eventual tissue loss and subsequent algal overgrowth of the bare skeleton. Histopathological investigation showed a loss of symbiont and melanin-containing granular cells which was more pronounced in the coenenchyme than the polyps. Cell counts confirmed a 65% reduction in symbiont density. Tissue loss was due to tissue fragmentation and necrosis in affected areas. In addition, a reduction in putative bacterial aggregate densities was found in diseased samples but no potential pathogens were observed.

Journal of Invertebrate Pathology↗

USGS2017

Relative abundance of deformed wing virus, Varroa destructor virus 1, and their recombinants in honey bees (Apis mellifera) assessed by kmer analysis of public RNA-Seq data

Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids were observed in recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.

Journal of Invertebrate Pathology↗