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USGS2011

A novel member of the family Hepeviridae from cutthroat trout ( Oncorhynchus clarkii )

Beginning in 1988, the Chinook salmon embryo (CHSE-214) cell line was used to isolate a novel virus from spawning adult trout in the state of California, USA. Termed the cutthroat trout ( Oncorhynchus clarkii ) virus (CTV), the small, round virus was not associated with disease, but was subsequently found to be present in an increasing number of trout populations in the western USA, likely by a combination of improved surveillance activities and the shipment of infected eggs to new locations. Here, we report that the full length genome of the 1988 Heenan Lake isolate of CTV consisted of 7269 nucleotides of positive-sense, single-stranded RNA beginning with a 5' untranslated region (UTR), followed by three open reading frames (ORFs), a 3' UTR and ending in a polyA tail. The genome of CTV was similar in size and organization to that of Hepatitis E virus (HEV) with which it shared the highest nucleotide and amino acid sequence identities. Similar to the genomes of human, rodent or avian hepeviruses, ORF 1 encoded a large, non-structural polyprotein that included conserved methyltransferase, protease, helicase and polymerase domains, while ORF 2 encoded the structural capsid protein and ORF 3 the phosphoprotein. Together, our data indicated that CTV was clearly a member of the family Hepeviridae , although the level of amino acid sequence identity with the ORFs of mammalian or avian hepeviruses (13-27%) may be sufficiently low to warrant the creation of a novel genus. We also performed a phylogenetic analysis using a 262. nt region within ORF 1 for 63 isolates of CTV obtained from seven species of trout reared in various geographic locations in the western USA. While the sequences fell into two genetic clades, the overall nucleotide diversity was low (less than 8.4%) and many isolates differed by only 1-2 nucleotides, suggesting an epidemiological link. Finally, we showed that CTV was able to form persistently infected cultures of the CHSE-214 cell line that may have use in research on the biology or treatment of hepevirus infections of humans or other animals.

Virus Research↗

USGS2017

Molecular testing of adult Pacific salmon and trout (Oncorhynchus spp.) for several RNA viruses demonstrates widespread distribution of piscine orthoreovirus in Alaska and Washington

This research was initiated in conjunction with a systematic, multiagency surveillance effort in the United States (U.S.) in response to reported findings of infectious salmon anaemia virus (ISAV) RNA in British Columbia, Canada. In the systematic surveillance study reported in a companion paper, tissues from various salmonids taken from Washington and Alaska were surveyed for ISAV RNA using the U.S.-approved diagnostic method, and samples were released for use in this present study only after testing negative. Here, we tested a subset of these samples for ISAV RNA with three additional published molecular assays, as well as for RNA from salmonid alphavirus (SAV), piscine myocarditis virus (PMCV) and piscine orthoreovirus (PRV). All samples ( n = 2,252; 121 stock cohorts) tested negative for RNA from ISAV, PMCV, and SAV. In contrast, there were 25 stock cohorts from Washington and Alaska that had one or more individuals test positive for PRV RNA; prevalence within stocks varied and ranged from 2% to 73%. The overall prevalence of PRV RNA-positive individuals across the study was 3.4% (77 of 2,252 fish tested). Findings of PRV RNA were most common in coho ( Oncorhynchus kisutch Walbaum) and Chinook ( O. tshawytscha Walbaum) salmon.

Alaska, Washington↗

USGS2024

A meta-analysis highlights the idiosyncratic nature of tradeoffs in laboratory models of virus evolution

Different theoretical frameworks have been invoked to guide the study of virus evolution. Three of the more prominent ones are (i) the evolution of virulence, (ii) life history theory, and (iii) the generalism–specialism dichotomy. All involve purported tradeoffs between traits that define the evolvability and constraint of virus-associated phenotypes. However, as popular as these frameworks are, there is a surprising paucity of direct laboratory tests of the frameworks that support their utility as broadly applicable theoretical pillars that can guide our understanding of disease evolution. In this study, we conduct a meta-analysis of direct experimental evidence for these three frameworks across several widely studied virus–host systems: plant viruses, fungal viruses, animal viruses, and bacteriophages. We extracted 60 datasets from 28 studies and found a range of relationships between traits in different analysis categories (e.g., frameworks, virus–host systems). Our work demonstrates that direct evidence for relationships between traits is highly idiosyncratic and specific to the host–virus system and theoretical framework. Consequently, scientists researching viral pathogens from different taxonomic groups might reconsider their allegiance to these canons as the basis for expectation, explanation, or prediction. Future efforts could benefit from consistent definitions, and from developing frameworks that are compatible with the evidence and apply to particular biological and ecological contexts.

Virus Evolution↗

USGS2017

The pathogenesis of clade 2.3.4.4 H5 highly pathogenic avian influenza viruses in Ruddy Duck (Oxyura jamaicensis) and Lesser Scaup (Aythya affinis)

Waterfowl are the natural hosts of avian influenza virus (AIV) and disseminate the virus worldwide through migration. Historically, surveillance and research efforts for AIV in waterfowl have focused on dabbling ducks. The role of diving ducks in AIV ecology has not been well characterized. In this study, we examined the relative susceptibility and pathogenicity of clade 2.3.4.4 H5 highly pathogenic AIV (HPAIV) in two species of diving ducks. Juvenile and adult Ruddy Duck ( Oxyura jamaicensis ) and juvenile Lesser Scaup ( Aythya affinis ) were intranasally inoculated with A/Northern Pintail/WA/40964/2014 H5N2 HPAIV. Additional groups of juvenile Lesser Scaups were inoculated with A/Gyrfalcon/WA/41088/2014 H5N8 HPAIV. The approximate 50% bird infectious doses (BID 50 ) of the H5N2 isolate for adult Ruddy Ducks was <10 2 50% egg infectious doses (EID 50 ) and for the juvenile Lesser Scaups it was <10 4 EID 50 . There were insufficient juvenile Ruddy Ducks to calculate the BID 50 . The BID 50 for the juvenile Lesser Scaups inoculated with the H5N8 isolate was 10 3 EID 50 . Clinical disease was not observed in any group; however, mortality occurred in the juvenile Ruddy Ducks inoculated with the H5N2 virus (three of five ducks), and staining for AIV antigen was observed in numerous tissues from these ducks. One adult Ruddy Duck also died and although it was infected with AIV (the duck was positive for virus shedding and AIV antigen was detected in tissues), it was also infected with coccidiosis. The proportion of ducks shedding virus was related to the dose administered, but the titers were similar among dose groups. The group with the fewest ducks shedding virus was the adult Ruddy Ducks. There was a trend for the Lesser Scaups to shed higher titers of virus than the Ruddy Ducks. No virus shedding was detected after 7 d postinoculation in any group. Similar to dabbling ducks, Lesser Scaups and Ruddy Ducks are susceptible to infection with this H5 HPAIV lineage, although they excrete lower titers of virus.

Journal of Wildlife Diseases↗

USGS2020

Assessing the risks posed by SARS-CoV-2 in and via North American bats — Decision framing and rapid risk assessment

The novel β-coronavirus, SARS-CoV-2, may pose a threat to North American bat populations if bats are exposed to the virus through interaction with humans, if the virus can subsequently infect bats and be transmitted among them, and if the virus causes morbidity or mortality in bats. Further, if SARS-CoV-2 became established in bat populations, it could possibly serve as a source for new infection in humans, domesticated animals, or other wild animals. Wildlife management agencies in the United States are concerned about these potential risks and have begun to issue guidance regarding work that brings humans into contact with bats, but decision making is difficult because of the high degree of uncertainty about many of the relevant processes that could lead to virus transmission and establishment. The risk assessment described in this report was undertaken to provide management agencies with an understanding of the likelihood that the various steps in the causal pathways would lead to SARS-CoV-2 infection of North American bats from people. This assessment focused on the active season for bats in the temperate zone of North America (April 15 through November 15), and used Myotis lucifugus (little brown bats) as a surrogate species. At the time of this work (April 2020), no empirical data about the effects of SARS-CoV-2 on North American bats were available, so a formal process of expert judgment was used to elicit estimates of the underlying parameters. Twelve experts in bat ecology, epidemiology, virology, and wildlife disease from the United States, United Kingdom, and Australia participated in the elicitation. A Monte Carlo simulation model was used to integrate the parameter estimates elicited from the experts and to predict the likelihood of exposure and infection in bats through a series of transmission pathways, with particular attention to capturing uncertainty in the predictions. Given the current state of knowledge as expressed by the expert panel, the results of this assessment indicate that there is a non-negligible risk of transmission of SARS-CoV-2 from humans to bats. For example, if a research scientist were shedding SARS-CoV-2 virus while handling bats under the field protocols used in North America prior to the COVID-19 pandemic, the risk model indicates that 50 percent (uncertainty, 15–84 percent) of those bats could be exposed to virus, and 17 percent (uncertainty, 3–51 percent) could become infected. Use of personal protective equipment, especially a respirator, is expected to reduce the exposure risk. The expert panel estimated that exposure risk from research scientists could be reduced 94–96 percent (uncertainty, 86–99 percent) through proper use of appropriate N95 respirators (a type of mechanical filter worn over the nose and mouth), dedicated clothing (such as Tyvek coveralls), and gloves. Should any North American bats become infected with SARS-CoV-2, the expert panel estimated that there is an approximately 33-percent chance the virus could spread within a bat population. This study, conducted by the U.S. Geological Survey in cooperation with the U.S. Fish and Wildlife Service, identified several critical uncertainties that could affect the estimate of risks associated with SARS-CoV-2 entering bat populations—notably, the underlying probability that a human would be shedding virus while working with bats, the likelihood of the virus replicating in bat tissue, and the likelihood of transmission of the virus within bat populations. Ongoing empirical work during May–October 2020 may shed light on these issues. Follow-up work is needed to better understand the probability of transmission of SARS-CoV-2 to bats from the general public; the manner in which the probabilities of exposure, infection, and transmission would differ during hibernation compared to the breeding season; and the likelihood of important effects, like morbidity and mortality in bats, the possibility of zoonosis from a North American bat reservoir, and effects of and on other wildlife.

North America↗

USGS2025

U.S. Geological Survey science strategy to address highly pathogenic avian influenza and its effects on wildlife health 2025–29

Executive Summary Highly pathogenic avian influenza (HPAI) is an ecologically and economically important animal disease that can also directly affect humans (a “zoonotic” disease). HPAI was once limited almost exclusively to domestic poultry but has rapidly adapted to diverse animal hosts. Viruses causing HPAI now appear to be maintained and dispersed by wild birds largely independent of poultry, though HPAI continues to cause considerable economic losses and supply chain disruptions in the domestic poultry trade. Coincident with the adaptation of HPAI viruses to wild birds, particularly waterfowl and gulls, increasingly diverse wild bird hosts are becoming exposed to HPAI, often resulting in disease and death. More sporadically, HPAI has caused mass mortality events, particularly among seabirds. Furthermore, viral spillover to wild and domestic mammals has become more common. Spillover to wild mammals has resulted in mortality among diverse terrestrial and marine taxa, including episodic losses of such scale as to represent potential conservation challenges. Since approximately March 2024, HPAI has also affected dairy cows, which represents a new threat to the agricultural economy. Lastly, HPAI has increasingly affected humans through domestic animal exposures, exemplifying the considerable implications of this disease beyond animal health. Rapid changes in the ecology of HPAI are currently outpacing research efforts. For example, it is not entirely clear which newly established hosts may become reservoirs for HPAI viruses (in other words, capable of maintaining HPAI viruses within a broad population indefinitely) and how this may influence viral evolution and dissemination. As a result, there are considerable information gaps regarding HPAI in wildlife that, if filled, would improve the ability of scientists, managers, agricultural industry representatives, and healthcare professionals to understand and to anticipate the effects of HPAI on wild animal, domestic animal, environmental, and human health (“One Health”). The U.S. Geological Survey (USGS) is the lead Federal agency providing scientific research on avian influenza viruses (AIVs), including HPAI viruses, that affect wildlife for which the Department of the Interior (DOI) has management authority. States have jurisdiction over wildlife on Federal lands within their borders (43 CFR § 24.3), so the USGS Ecosystems Mission Area (EMA) coordinates with State natural resource management agencies. The EMA focuses its research on HPAI through priorities identified by the USGS Avian Influenza Science Team ( app. 1 ). Priorities identified by the USGS Avian Influenza Science Team are based on Administration priorities, Congressional direction, and discussions with State, Federal, and Tribal natural resource management agencies that identify specific scientific gaps that need to be filled to inform sound wildlife management decisions. Notable non-DOI Federal partners include the U.S. Department of Agriculture, the lead for the HPAI regulatory response in poultry and livestock, and the Centers for Disease Control and Prevention (CDC), the lead agency for the HPAI response pertaining to human health. The USGS offers unique expertise and capacity pertaining to research on diseases affecting free-ranging wildlife populations. This expertise has been critical to interjurisdictional surveillance and capacity-building efforts, including programs administered by the U.S. Department of Agriculture and the CDC. The USGS also provides resources, guidance, and tools to inform surveillance and interventions conducted by natural resource management agencies. More specifically, the USGS EMA provides objective and rigorous scientific data for inferring (1) the utility of new methods to detect and characterize AIVs, including those maintained in wildlife and the environment; (2) effects of HPAI on wildlife; (3) spatiotemporal patterns of wildlife host and AIV dispersal; (4) the presence and persistence of AIVs in the environment; (5) how HPAI in wildlife influences consumptive and nonconsumptive utilization of wildlife; (6) how new tools and scientific methods may promote sound management decisions for HPAI-affected wildlife, particularly species of conservation concern; and (7) the combined effects of HPAI and other stressors on ecosystem health and resiliency. This science strategy builds upon research outlined in a previous USGS science strategy for HPAI (2016–20) by Harris and others (2016) . This strategy also details research priorities identified by the Administration (for example, U.S. Department of Agriculture, 2025 ) and others based on USGS Avian Influenza Science Team discussions with natural resource management agencies to address HPAI and wildlife health over the next 5 years (2025–29). This strategy presents 7 goals and 26 objectives that focus USGS and partner efforts on priorities that will fill data gaps regarding the effects of HPAI on wildlife managed by or co-managed with the U.S. Department of the Interior such that agencies and partners might anticipate or limit adverse effects on public resources. This strategy also identifies research priorities intended to address HPAI in wildlife and wildlife habitat that are anticipated to support interjurisdictional One Health efforts.

Circular↗

USGS1976

Fatal vaccine-induced canine distemper virus infection in black-footed ferrets

Four black-footed ferrets that were live-trapped in South Dakota and transported to the Patuxent Wildlife Research Center died within 21 days after vaccination with modified live canine distemper virus. Immunofluorescence, European ferret inoculation, virus isolation attempts, and serum-neutralization tests indicated insufficient attenuation of the vaccine for this species.

Journal of the American Veterinary Medical Associa↗

USGS2025

Laboratory transmission of adult salmon enteritis and associated pathogens in juvenile Chinook salmon ( Oncorhynchus tshawytscha )

Adult salmon enteritis (ASE), characterised by severe ulcerative enteritis, has been linked to prespawn mortality (PSM) in spring Chinook salmon ( Oncorhynchus tshawytscha ) in certain rivers in Oregon, USA. Catastrophic losses of spring Chinook salmon have resulted from PSM, a significant threat to their population stability. Understanding the causes of ASE is therefore critical for mitigating PSM and supporting conservation. This study investigates the potential infectious aetiology of ASE using a juvenile Chinook salmon model. Fish were immunocompromised with dexamethasone implants, fasted, and exposed to intestinal tissues from ASE-affected adult Chinook. Histopathology of recipient fish revealed mid-intestinal lesions consistent with ASE. The microsporidium Enterocytozoon schreckii , which is observed in ASE-affected adults from rivers, was transmitted for the first time to juvenile Chinook Salmon, making E. schreckii a potential new pathogen of juvenile salmon. Additionally, intranuclear inclusions were identified in enterocytes by histopathology and viral particles were detected by electron microscopy in recipient fish. The study demonstrates that intestinal lesions consistent with ASE can be experimentally induced in juvenile Chinook salmon through oral exposure to infected tissues, supporting an infectious aetiology. Further research is needed to isolate specific pathogens, including viruses and E. schreckii , and to elucidate their roles in ASE development.

Oregon↗

USGS2019

Isolation, characterization and molecular identification of a novel aquareovirus that infects the endangered fountain darter, Etheostoma fonticola

The fountain darter Etheostoma fonticola (FOD) is a federally endangered fish listed under the US Endangered Species Act. Here, we identified and characterized a novel aquareovirus isolated from wild fountain darters inhabiting the San Marcos River. This virus was propagated in Chinook salmon embryo (CHSE)-214, rainbow trout gonad-2 and fathead minnow cells at 15°C. The epithelioma papulosum cyprini cell line was refractory at all temperatures evaluated. High throughput sequencing technologies facilitated the complete genome sequencing of this virus utilizing ribosomal RNA-depleted RNA extracted from infected CHSE-214 cells. Conventional PCR primer sets were developed for the detection and confirmation of this virus to assist diagnostic screening methods. Phylogenetic analysis suggests this virus belongs to the Aquareovirus A genus. This research provides requisite initial data critical to support hatchery and refugia biosecurity measures for this endangered species.

Diseases of Aquatic Organisms↗

USGS2025

Identification of novel hepaciviruses and Sylvilagus-associated viruses via metatranscriptomics in North American lagomorphs

Cottontails ( Sylvilagus spp.) and jackrabbits ( Lepus spp.) within the Leporidae family are native to North America and are found in a wide range of habitats, including deserts, forests, and grasslands. Although there is a growing body of research describing the arrival of the highly virulent rabbit haemorrhagic disease virus 2 (RHDV2, GI.2) on this continent, and its impact on native lagomorphs, information about the natural virome and microbiome of healthy and deceased American lagomorphs is relatively limited. In this study, we used a meta-transcriptomics approach to conduct whole pathogen profiling on healthy and deceased animals in the USA. We analysed 48 matched liver and lung sample pools from apparently healthy cottontails and jackrabbits in Texas and an additional 48 liver samples from deceased animals from nine other US states. This approach enabled the discovery of three distinct new viruses and revealed additional new insights into the lung and liver microbiomes of North American lagomorphs. Of the three new viruses, a tetnovirus and a novel picorna-like virus were likely of insect origin and therefore considered environmental contaminants. Of particular interest was a new species of hepacivirus, with around 50% sequence identity to a known hepacivirus from a xeric four-striped grass rat ( Rhabdomys pumilio ). Phylogenetic analysis from 41 individual hepacivirus genomes recovered from our lagomorph samples revealed two distinct clades, corresponding with different cottontail species. No hepaciviruses were detected in any of the jackrabbit samples. This is the first description of a hepacivirus in lagomorphs. Our findings extend the Hepacivirus genus, provide new insights into its evolution, and describe the first baseline on microbial diversity in North American lagomorphs, an important step towards understanding the role of potential pathogens for population management and conservation.

Arizona, California, Iowa, Massachusetts, Montana,↗

USGS2010

Prevalence of antibodies to type A influenza virus in wild avian species using two serologic assays

Serologic testing to detect antibodies to avian influenza (AI) virus has been an underused tool for the study of these viruses in wild bird populations, which traditionally has relied on virus isolation and reverse transcriptase-polymerase chain reaction (RT-PCR). In a preliminary study, a recently developed commercial blocking enzyme-linked immunosorbent assay (bELISA) had sensitivity and specificity estimates of 82% and 100%, respectively, for detection of antibodies to AI virus in multiple wild bird species after experimental infection. To further evaluate the efficacy of this commercial bELISA and the agar gel immunodiffusion (AGID) test for AI virus antibody detection in wild birds, we tested 2,249 serum samples collected from 62 wild bird species, representing 10 taxonomic orders. Overall, the bELISA detected 25.4% positive samples, whereas the AGID test detected 14.8%. At the species level, the bELISA detected as many or more positive serum samples than the AGID in all 62 avian species. The majority of positive samples, detected by both assays, were from species that use aquatic habitats, with the highest prevalence from species in the orders Anseriformes and Charadriiformes. Conversely, antibodies to AI virus were rarely detected in the terrestrial species. The serologic data yielded by both assays are consistent with the known epidemiology of AI virus in wild birds and published reports of host range based on virus isolation and RT-PCR. The results of this research are also consistent with the aforementioned study, which evaluated the performance of the bELISA and AGID test on experimental samples. Collectively, the data from these two studies indicate that the bELISA is a more sensitive serologic assay than the AGID test for detecting prior exposure to AI virus in wild birds. Based on these results, the bELISA is a reliable species-independent assay with potentially valuable applications for wild bird AI surveillance.

Alaska, California, Delaware, Georgia, Michigan, M↗

USGS2005

Overview of recent DNA vaccine development for fish

Since the first description of DNA vaccines for fish in 1996, numerous studies of genetic immunisation against the rhabdovirus pathogens infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV) have established their potential as both highly efficacious biologicals and useful basic research tools. Single small doses of rhabdovirus DNA constructs provide extremely strong protection against severe viral challenge under a variety of conditions. DNA vaccines for several other important fish viruses, bacteria, and parasites are under investigation, but they have not yet shown high efficacy. Therefore, current research is focussed on mechanistic studies to understand the basis of protection, and on improvement of the nucleic acid vaccine applications against a wider range of fish pathogens.

Conference Paper↗

USGS2006

The fitting of general force-of-infection models to wildlife disease prevalence data

Researchers and wildlife managers increasingly find themselves in situations where they must deal with infectious wildlife diseases such as chronic wasting disease, brucellosis, tuberculosis, and West Nile virus. Managers are often charged with designing and implementing control strategies, and researchers often seek to determine factors that influence and control the disease process. All of these activities require the ability to measure some indication of a disease's foothold in a population and evaluate factors affecting that foothold. The most common type of data available to managers and researchers is apparent prevalence data. Apparent disease prevalence, the proportion of animals in a sample that are positive for the disease, might seem like a natural measure of disease's foothold, but several properties, in particular, its dependency on age structure and the biasing effects of disease-associated mortality, make it less than ideal. In quantitative epidemiology, the a??force of infection,a?? or infection hazard, is generally the preferred parameter for measuring a disease's foothold, and it can be viewed as the most appropriate way to a??adjusta?? apparent prevalence for age structure. The typical ecology curriculum includes little exposure to quantitative epidemiological concepts such as cumulative incidence, apparent prevalence, and the force of infection. The goal of this paper is to present these basic epidemiological concepts and resulting models in an ecological context and to illustrate how they can be applied to understand and address basic epidemiological questions. We demonstrate a practical approach to solving the heretofore intractable problem of fitting general force-of-infection models to wildlife prevalence data using a generalized regression approach. We apply the procedures to Mycobacterium bovis (bovine tuberculosis) prevalence in bison (Bison bison) in Wood Buffalo National Park, Canada, and demonstrate strong age dependency in the force of infection as well as an increased mortality hazard in positive animals.

Ecology↗

USGS2014

Optimizing surveillance for South American origin influenza A viruses along the United States Gulf Coast through genomic characterization of isolates from blue-winged teal (Anas discors)

Relative to research focused on intercontinental viral exchange between Eurasia and North America, less attention has been directed towards understanding the redistribution of influenza A viruses (IAVs) by wild birds between North America and South America. In this study, we genomically characterized 45 viruses isolated from blue-winged teal (Anas discors) along the Texas and Louisiana Gulf Coast during March of 2012 and 2013, coincident with northward migration of this species from Neotropical wintering areas to breeding grounds in the United States and Canada. No evidence of South American lineage genes were detected in IAVs isolated from blue-winged teal supporting restricted viral gene flow between the United States and southern South America. However, it is plausible that blue-winged teal redistribute IAVs between North American breeding grounds and wintering areas throughout the Neotropics, including northern South America, and that viral gene flow is limited by geographical barriers further south (e.g. the Amazon Basin). Surveillance for the introduction of IAVs from Central America and northern South America into the United States may be further optimized through genomic characterization of viruses resulting from coordinated, concurrent sampling efforts targeting blue-winged teal and sympatric species throughout the Neotropics and along the United States Gulf Coast.

Transboundary and Emerging Diseases↗

USGS2020

Hyperpigmented melanistic skin lesions of smallmouth bass Micropterus dolomieu from the Chesapeake Bay watershed

Hyperpigmented melanistic skin lesions (HPMLs) of smallmouth bass Micropterus dolomieu are observed in the Potomac and Susquehanna rivers, Chesapeake Bay watershed, USA. Routine, nonlethal population surveys were conducted at 8 sites on the mainstem Susquehanna River and 9 on the Juniata River, a tributary of the Susquehanna River, between 2012 and 2018, and the prevalence of HPMLs was documented. A total of 4078 smallmouth bass were collected from the mainstem Susquehanna River and 6478 from the Juniata River. Lesions were primarily seen in bass greater than 200 mm, and prevalence in the Susquehanna River (8%) was higher (p < 0.001) than in the Juniata River (2%). As part of ongoing fish health monitoring projects, smallmouth bass were collected at additional sites, primarily tributaries of the Susquehanna (n = 758) and Potomac (n = 545) rivers between 2013 and 2018. Prevalence in the Susquehanna River (13%) was higher (p < 0.001) than the Potomac (3%). Microscopically, HPMLs were characterized by an increased number of melanocytes in the epidermis or within the dermis and epidermis. RNAseq analyses of normal and melanistic skin identified 3 unique sequences in HPMLs. Two were unidentified and the third was a viral helicase (E1). Transcript abundance in 16 normal skin samples and 16 HPMLs showed upregulation of genes associated with melanogenesis and cell proliferation in HPMLs. The E1 transcript was detected in 12 of the 16 melanistic areas but in no samples from normal skin. Further research will be necessary to identify the putative new virus and determine its role in melanocyte proliferation.

Delaware, Maryland, Pennsylvania, Virginia, West V↗

USGS1987

A prospective field evaluation of an enzyme immunoassay: Detection of eastern equine encephalomyelitis virus antigen in pools of Culiseta melanura

A prospective field study was conducted to determine the sensitivity and specificity of an enzyme immunoassay (EIA) compared to virus isolation in cell culture for the detection of eastern equine encephalomyelitis (EEE) virus in naturally infected mosquitoes. A total of 10,811 adult female Culiseta melanura were collected in light traps during 1985 from four locations in Maryland. Eastern equine encephalomyelitis virus was isolated from 5 of 495 mosquito pools in African green monkey kidney and baby hamster kidney cell cultures. All five virus-infected pools were detected by the EIA, and all 490 uninfected pools were correctly scored as not containing virus. The EIA did not produce false positive or false negative results. Results support the assertion of previous researchers that the antigen detection EIA is a rapid, sensitive, specific, and simple alternative to traditional bioassays for the detection of EEE virus in mosquitoes.

Journal of the American Mosquito Control Associati↗

USGS2004

West Nile Virus and wildlife

West Nile virus (WNV) has spread rapidly across North America, resulting in human deaths and in the deaths of untold numbers of birds, mammals, and reptiles. The virus has reached Central America and the Caribbean and may spread to Hawaii and South America. Although tens of thousands of birds have died, and studies of some bird species show local declines, few regionwide declines can be attributed to WNV. Predicting future impacts of WNV on wildlife, and pinpointing what drives epidemics, will require substantial additional research into host susceptibility, reservoir competency, and linkages between climate, mosquitoes, and disease. Such work will entail a collaborative effort between scientists in governmental research groups, in surveillance and control programs, and in nongovernmental organizations. West Nile virus was not the first, and it will not be the last, exotic disease to be introduced to the New World. Its spread in North America highlights the need to strengthen animal monitoring programs and to integrate them with research on disease ecology.

BioScience↗

USGS2024

A systematic review of laboratory investigations into the pathogenesis of avian influenza viruses in wild avifauna of North America

The lack of consolidated information regarding the response of wild bird species to infection with avian influenza virus (AIV) is a challenge to both conservation managers and researchers alike, with related sectors also impacted, such as public health and commercial poultry. Using two independent searches, we reviewed published literature for studies describing wild bird species experimentally infected with avian influenza to assess host species’ relative susceptibility to AIVs. Additionally, we summarize broad-scale parameters for elements such as shedding duration and minimum infectious dose that can be used in transmission modelling efforts. Our synthesis shows that waterfowl (i.e. Anatidae) compose the vast majority of published AIV pathobiology studies, whereas gulls and passerines are less represented in research despite evidence that they also are susceptible and contribute to highly pathogenic avian influenza disease dynamics. This study represents the first comprehensive effort to compile available literature regarding the pathobiology of AIVs in all wild birds in over a decade. This database can now serve as a tool to all researchers, providing generalized estimates of pathobiology parameters for a variety of wild avian families and an opportunity to critically examine and assess what is known and identify where further insight is needed.

Proceeding of the Royal Society B↗