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 451 records · Page 25Linked to original sources
USGS2017

Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore

Urban expansion has widespread impacts on wildlife species globally, including the transmission and emergence of infectious diseases. However, there is almost no information about how urban landscapes shape transmission dynamics in wildlife. Using an innovative phylodynamic approach combining host and pathogen molecular data with landscape characteristics and host traits, we untangle the complex factors that drive transmission networks of Feline Immunodeficiency Virus (FIV) in bobcats ( Lynx rufus ). We found that the urban landscape played a significant role in shaping FIV transmission. Even though bobcats were often trapped within the urban matrix, FIV transmission events were more likely to occur in areas with more natural habitat elements. Urban fragmentation also resulted in lower rates of pathogen evolution, possibly owing to a narrower range of host genotypes in the fragmented area. Combined, our findings show that urban landscapes can have impacts on a pathogen and its evolution in a carnivore living in one of the most fragmented and urban systems in North America. The analytical approach used here can be broadly applied to other host-pathogen systems, including humans.

Molecular Ecology↗
USGS2017

Potential for water borne and invertebrate transmission of West Nile virus in the Great Salt Lake, Utah

In November and December of 2013, a large mortality event involving 15,000 - 20,000 eared grebes ( Podiceps nigricollis ) occurred at the Great Salt Lake (GSL), UT. The onset of the outbreak in grebes was followed by a mortality event in > 86 bald eagles ( Haliaeetus leucocephalus ). During the die-off, West Nile virus (WNV) was detected by RT-PCR or viral culture in carcasses of grebes and eagles submitted to the National Wildlife Health Center. However, no mosquito activity, the primary vector of WNV, was detected by the State of Utah's WNV monitoring program. Transmission of WNV has rarely been reported during the winter in North America in the absence of known mosquito activity; however, the size of this die-off, the habitat in which it occurred, and the species involved are unique. We experimentally investigated whether WNV could survive in water with a high saline content, as found at the GSL, and whether brine shrimp, the primary food of migrating eared grebes on the GSL, could have played a role in transmission of WNV to feeding birds. We found that WNV can survive up to 72 h at 4°C in water containing 30 — 150 ppt NaCl and brine shrimp, incubated with WNV in 30 ppt NaCl, may adsorb WNV to their cuticle and, through feeding, may infect epithelial cells of their gut. Both mechanisms may have potentiated the WNV die-off in migrating eared grebes on the GSL.

Utah↗
USGS1969

Infectious pancreatic necrosis virus: Lyophilization and subsequent stability in storage at 4 C

Infectious pancreatic necrosis virus (ATCC strain VR # 299) was lyophilized with different additives and stored at 4 C. Ampoules were assayed at 2 days, at 1, 3, and 6 months, and at 1, 3, and 4 years. Processing losses were least and subsequent maintenance of infectivity was best in skim milk, lactalbumin hydrolysate, and lactose. Quantitative data are given in tabular form.

Applied Microbiology↗
USGS2015

Novel H5 clade 2.3.4.4 reassortant (H5N1) virus from a green-winged teal in Washington, USA

Eurasian (EA)-origin H5N8 clade 2.3.4.4 avian influenza viruses were first detected in North America during December 2014. Subsequent reassortment with North American (AM) low-pathogenic wild-bird-origin avian influenza has generated at least two reassortants, including an EA/AM H5N1 from an apparently healthy wild green-winged teal, suggesting continued ongoing reassortment.

Washington↗
USGS2019

The nucleoprotein and phosphoprotein are major determinants of the virulence of viral hemorrhagic septicemia virus in rainbow trout

Viral hemorrhagic septicemia virus (VHSV), a fish rhabdovirus, infects several marine and freshwater fish species. There are many strains of VHSV that affect different fish, but some strains of one genetic subgroup have gained high virulence in rainbow trout ( Oncorhynchus mykiss ). To define the genetic basis of high virulence in trout, we used reverse genetics to create chimeric VHSVs in which viral nucleoprotein (N), P (phosphoprotein), or M (matrix protein) genes, or the N and P genes, were exchanged between a trout-virulent European VHSV strain (DK-3592B) and a trout-avirulent North American VHSV strain (MI03). Testing of the chimeric recombinant VHSV (rVHSV) by intraperitoneal injection in juvenile rainbow trout showed that exchanges of the viral P or M genes had no effect on the trout virulence phenotype of either parental strain. However, reciprocal exchanges of the viral N gene resulted in a partial gain of function in the chimeric trout-avirulent strain (22% mortality) and complete loss of virulence for the chimeric trout-virulent strain (2% mortality). Reciprocal exchanges of both the N and P genes together resulted in complete gain of function in the chimeric avirulent strain (82% mortality), again with complete loss of virulence in the chimeric trout-virulent strain (0% mortality). Thus, the VHSV N gene contains an essential determinant of trout virulence that is strongly enhanced by the viral P gene. We hypothesize that the host-specific virulence mechanism may involve increased efficiency of the viral polymerase complex when the N and P proteins have adapted to more efficient interaction with a host component from rainbow trout.

Journal of Virology↗
USGS2020

Differences in antibody responses against Chelonid Alphaherpesvirus 5 (ChHV5) suggest differences in virus biology in ChHV5-seropositive green turtles from Hawaii and ChHV5-seropositive green turtles from Florida

Fibropapillomatosis (FP) is a tumor disease associated with a herpesvirus (chelonid herpesvirus 5 [ChHV5]) that affects mainly green turtles globally. Understanding the epidemiology of FP has been hampered by a lack of robust serological assays to monitor exposure to ChHV5. This is due in part to an inability to efficiently culture the virus in vitro for neutralization assays. Here, we expressed two glycoproteins (FUS4 and FUS8) from ChHV5 using baculovirus. These proteins were immobilized on enzyme-linked immunosorbent assay plates in their native form and assayed for reactivity to two types of antibodies, full-length 7S IgY and 5.7S IgY, which has a truncated Fc region. Turtles from Florida were uniformly seropositive to ChHV5 regardless of tumor status. In contrast, in turtles from Hawaii, we detected strong antibody reactivity mainly in tumored animals, with a lower antibody response being seen in nontumored animals, including those from areas where FP is enzootic. Turtles from Hawaii actively shedding ChHV5 were more seropositive than nonshedders. In trying to account for differences in the serological responses to ChHV5 between green turtles from Hawaii and green turtles from Florida, we rejected the cross-reactivity of antibodies to other herpesviruses, differences in viral epitopes, or differences in procedure as likely explanations. Rather, behavioral or other differences between green turtles from Hawaii and green turtles from Florida might have led to the emergence of biologically different viral strains. While the strains from turtles in Florida apparently spread independently of tumors, the transmission of the Hawaiian subtype relies heavily on tumor formation.

Florida, Hawaii↗
USGS2015

Discovery of a novel hepatovirus (Phopivirus of seals) related to human hepatitis A virus

Describing the viral diversity of wildlife can provide interesting and useful insights into the natural history of established human pathogens. In this study, we describe a previously unknown picornavirus in harbor seals (tentatively named phopivirus) that is related to human hepatitis A virus (HAV). We show that phopivirus shares several genetic and phenotypic characteristics with HAV, including phylogenetic relatedness across the genome, a specific and seemingly quiescent tropism for hepatocytes, structural conservation in a key functional region of the type III internal ribosomal entry site (IRES), and a codon usage bias consistent with that of HAV.

mBio↗
USGS2025

Rapid increase in antibodies to influenza A virus H5 and N1 in Lesser Scaup (Aythya affinis) following the introduction of 2.3.4.4B H5N1 into North America

Clade 2.3.4.4b Eurasian-origin H5N1 entered North America in late 2021 and spread across the continent. While studies have characterized the antibody response mounted by dabbling ducks following exposure, little data are available for diving ducks. This study sought to identify influenza A virus (IAV) infection and antibodies in Lesser and Greater Scaup captured in Maryland, Illinois, and Rhode Island. In Maryland, IAV seroprevalence increased from the 2021/2022 to 2022/2023 sampling season, with IAV antibody prevalence increasing for juvenile (38% to 80%) and adult (82% to 90%) Lesser Scaup. While adult Lesser Scaup sampled in Illinois in 2021/2022 had IAV antibody prevalence comparable to those sampled in Maryland (76% and 82%, respectively), they had higher antibody prevalence to both H5 (48% and 18%) and N1 (68% and 35%), potentially due to being sampled in March versus December and January. Our data suggest that Lesser Scaup had limited antibodies to highly pathogenic H5 IAV prior to the introduction of clade 2.3.4.4b H5N1 to North America, but relevant antibodies were widely observed in the months and year following. Our more limited data suggest similar trends may have occurred in Greater Scaup as well.

Canadian Journal of Microbiology↗
USGS1970

Control of infectious Hematopoietic Necrosis virus disease by elevating the water temperature

Studies were performed to determine if increasing water temperatures could control infectious hematopoietic necrosis virus (IHN) disease in sockeye salmon ( Oncorhynchus nerka ). Mortalities could be prevented if the water temperature was raised to at least 18 C within the first 24 hr after infection of the fish and if the fish were maintained at this temperature for 4–6 days. The disease did not recur after the elevated temperature treatment, but the fish would still contract the disease if they were reinfected. Reasons for the protecting action are discussed.

Journal of the Fisheries Research Board of Canada↗
USGS2016

Identification of the major capsid protein of erythrocytic necrosis virus (ENV) and development of quantitative real-time PCR assays for quantification of ENV DNA

Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fish that is caused by the erythrocytic necrosis virus (ENV), which was recently identified as a novel member of family Iridoviridae by next-generation sequencing. Phylogenetic analysis of the ENV DNA polymerase grouped ENV with other erythrocytic iridoviruses from snakes and lizards. In the present study, we identified the gene encoding the ENV major capsid protein (MCP) and developed a quantitative real-time PCR (qPCR) assay targeting this gene. Phylogenetic analysis of the MCP gene sequence supported the conclusion that ENV does not group with any of the currently described iridovirus genera. Because there is no information regarding genetic variation of the MCP gene across the reported host and geographic range for ENV, we also developed a second qPCR assay for a more conserved ATPase-like gene region. The MCP and ATPase qPCR assays demonstrated good analytical and diagnostic sensitivity and specificity based on samples from laboratory challenges of Pacific herring Clupea pallasii . The qPCR assays had similar diagnostic sensitivity and specificity as light microscopy of stained blood smears for the presence of intraerythrocytic inclusion bodies. However, the qPCR assays may detect viral DNA early in infection prior to the formation of inclusion bodies. Both qPCR assays appear suitable for viral surveillance or as a confirmatory test for ENV in Pacific herring from the Salish Sea.

Journal of Veterinary Diagnostic Investigation↗
USGS2024

Antibody response of endangered riparian brush rabbits to vaccination against rabbit hemorrhagic disease virus 2

Rabbit hemorrhagic disease virus 2 (RHDV2; Caliciviridae , Lagovirus europaeus ), the cause of a highly transmissible and fatal lagomorph disease, has spread rapidly through the western United States and Mexico, resulting in substantial mortality in domestic and wild rabbits. The disease was first detected in California in May 2020, prompting an interagency/zoo/academia/nonprofit team to implement emergency conservation actions to protect endangered riparian brush rabbits ( Sylvilagus bachmani riparius ) from RHDV2. Prior to vaccinating wild rabbits, we conducted a vaccine safety trial by giving a single SC dose of Filavac VHD K C+V (Filavie) vaccine to 19 adult wild riparian brush rabbits captured and temporarily held in captivity. Rabbits were monitored for adverse effects, and serum was collected before vaccination, and at 7–10, 14–20, and 60 d post-vaccination. Sera were tested using an ELISA to determine antibody response and timing of seroconversion. Reverse-transcription quantitative real-time PCR (RT-qPCR) was performed on rectal swabs to evaluate infection status. No adverse effects from the vaccine were observed. Before vaccination, 18 of 19 rabbits were seronegative, and RHDV2 was not detected by RT-qPCR on any rectal swabs. After vaccination, all rabbits developed an antibody response, with titers of 1:10–1:160. Seroconversion generally occurred at 7–10 d. The duration of antibody response was ≥60 d in 12 of 13 rabbits. Sixteen animals were released and 4 were recaptured several months later, offering a glimpse into longer duration immune response. Our study has informed vaccination strategies for this species and serves as a model for protecting other vulnerable lagomorphs against RHDV2.

California↗
USGS2025

Laboratory assessment for recovery of porcine circovirus 2 and porcine reproductive and respiratory syndrome virus using two types of commercially available hollow-fiber ultrafilters

Groundwater near swine farms is an uninvestigated reservoir for porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCVs). Enteric microorganisms are often collected from groundwater via dead-end ultrafiltration, but recovery of PRRSV and PCV with this method has not been assessed. We recovered PRRSV2 and PCV2 by dead-end ultrafiltration followed by polyethylene glycol (PEG) precipitation, nucleic acid extraction, and reverse-transcription quantitative real-time PCR. We also compared 2 commercial hemodialysis ultrafilters (Asahi Kasei Rexeed-25A, Nipro Elisio-25H) and compared PRRSV2 recovery in these filters to other waterborne microorganisms. On average, 8 ± 1% of PRRSV2 was recovered by dead-end ultrafiltration and PEG precipitation, compared to 25 ± 6% for adenovirus 41. Full-process recovery of bacteria in the same filters was 5–15%; Cryptosporidium parvum recovery was 42 ± 12%. PCV2 was detected in 4 of 12 replicate filters, but low stock concentrations precluded quantitative recovery estimates. Elisio-25H ultrafilters performed similarly to Rexeed-25A filters for all organisms tested and is an effective replacement for the Rexeed-25A, which is no longer available in the United States. Our recovery of PRRSV2 and PCV2 by dead-end ultrafiltration in the laboratory suggests that PRRSV2 detection limits are as low as 3–50 genomic copies/L in sample volumes of 100–1,500 L. Based on quantitative microbial risk assessment, these concentrations are relevant to PRRSV2 infection rates in the U.S. swine herd.

Journal of Veterinary Diagnostic Investigation↗
USGS2014

West Nile Virus transmission in winter: the 2013 Great Salt Lake Bald Eagle and Eared Grebes Mortality event

West Nile Virus (WNV) infection has been reported in over 300 species of birds and mammals. Raptors such as eagles, hawks and falcons are remarkably susceptible, but reports of WNV infection in Bald Eagles (Haliaeetus leucocephalus) are rare and reports of WNV infection in grebes (Podicipediformes) even rarer. We report an unusually large wild bird mortality event involving between 15,000-20,000 Eared Grebes (Podiceps nigricollis) and over 40 Bald Eagles around the Great Salt Lake, Utah, in November-December 2013. Mortality in grebes was first reported in early November during a period when the area was unseasonably warm and the grebes were beginning to gather and stage prior to migration. Ten out of ten Eared Grebes collected during this period were WNV RT-PCR and/or isolation positive. This is the first report of WNV infection in Eared Grebes and the associated mortality event is matched in scale only by the combined outbreaks in American White Pelican (Pelecanus erythrorhynchos) colonies in the north central states in 2002-2003. We cannot be sure that all of the grebes were infected by mosquito transmission; some may have become infected through contact with WNV shed orally or cloacally from other infected grebes. Beginning in early December, Bald Eagles in the Great Salt Lake area were observed to display neurological signs such as body tremors, limb paralysis and lethargy. At least 43 Bald Eagles had died by the end of the month. Nine of nine Bald Eagles examined were infected with WNV. To the best of our knowledge, this is the largest single raptor mortality event since WNV became endemic in the USA. Because the majority of the eagles affected were found after onset of below-freezing temperatures, we suggest at least some of the Bald Eagles were infected with WNV via consumption of infected Eared Grebes or horizontal transmission at roost sites.

PLOS Current Outbreaks↗
USGS2015

Modelling the effects of seasonality and socioeconomic impact on the transmission of Rift Valley fever virus

Rift Valley fever (RVF) is an important mosquito-borne viral zoonosis in Africa and the Middle East that causes human deaths and significant economic losses due to huge incidences of death and abortion among infected livestock. Outbreaks of RVF are sporadic and associated with both seasonal and socioeconomic effects. Here we propose an almost periodic three-patch model to investigate the transmission dynamics of RVF virus (RVFV) among ruminants with spatial movements. Our findings indicate that, in Northeastern Africa, human activities, including those associated with the Eid al Adha feast, along with a combination of climatic factors such as rainfall level and hydrological variations, contribute to the transmission and dispersal of the disease pathogen. Moreover, sporadic outbreaks may occur when the two events occur together: 1) abundant livestock are recruited into areas at risk from RVF due to the demand for the religious festival and 2) abundant numbers of mosquitoes emerge. These two factors have been shown to have impacts on the severity of RVF outbreaks. Our numerical results present the transmission dynamics of the disease pathogen over both short and long periods of time, particularly during the festival time. Further, we investigate the impact on patterns of disease outbreaks in each patch brought by festival- and seasonal-driven factors, such as the number of livestock imported daily, the animal transportation speed from patch to patch, and the death rate induced by ceremonial sacrifices. In addition, our simulations show that when the time for festival preparation starts earlier than usual, the risk of massive disease outbreaks rises, particularly in patch 3 (the place where the religious ceremony will be held).

PLoS Neglected Tropical Diseases↗
USGS2011

A nuclear localization of the infectious haematopoietic necrosis virus NV protein is necessary for optimal viral growth

The nonvirion (NV) protein of infectious hematopoietic necrosis virus (IHNV) has been previously reported to be essential for efficient growth and pathogenicity of IHNV. However, little is known about the mechanism by which the NV supports the viral growth. In this study, cellular localization of NV and its role in IHNV growth in host cells was investigated. Through transient transfection in RTG-2 cells of NV fused to green fluorescent protein (GFP), a nuclear localization of NV was demonstrated. Deletion analyses showed that the 32 EGDL 35 residues were essential for nuclear localization of NV protein, and fusion of these 4 amino acids to GFP directed its transport to the nucleus. We generated a recombinant IHNV, rIHNV-NV-ΔEGDL in which the 32 EGDL 35 was deleted from the NV. rIHNVs with wild-type NV (rIHNV-NV) or with the NV gene replaced with GFP (rIHNV-ΔNV-GFP) were used as controls. RTG-2 cells infected with rIHNV-ΔNV-GFP and rIHNV-NV-ΔEGDL yielded 12- and 5-fold less infectious virion, respectively, than wild type rIHNV-infected cells at 48 h post-infection (p.i.). While treatment with poly I:C at 24 h p.i. did not inhibit replication of wild-type rIHNVs, replication rates of rIHNV-ΔNV-GFP and rIHNV-NV-ΔEGDL were inhibited by poly I:C. In addition, both rIHNV-ΔNV and rIHNV-NV-ΔEGDL induced higher levels of expressions of both IFN1 and Mx1 than wild-type rIHNV. These data suggest that the IHNV NV may support the growth of IHNV through inhibition of the INF system and the amino acid residues of 32 EGDL 35 responsible for nuclear localization are important for the inhibitory activity of NV.

PLoS ONE↗
USGS2012

Zoonotic viruses associated with illegally imported wildlife products

The global trade in wildlife has historically contributed to the emergence and spread of infectious diseases. The United States is the world's largest importer of wildlife and wildlife products, yet minimal pathogen surveillance has precluded assessment of the health risks posed by this practice. This report details the findings of a pilot project to establish surveillance methodology for zoonotic agents in confiscated wildlife products. Initial findings from samples collected at several international airports identified parts originating from nonhuman primate (NHP) and rodent species, including baboon, chimpanzee, mangabey, guenon, green monkey, cane rat and rat. Pathogen screening identified retroviruses (simian foamy virus) and/or herpesviruses (cytomegalovirus and lymphocryptovirus) in the NHP samples. These results are the first demonstration that illegal bushmeat importation into the United States could act as a conduit for pathogen spread, and suggest that implementation of disease surveillance of the wildlife trade will help facilitate prevention of disease emergence.

PLoS ONE↗
USGS2013

Molecular detection and genotyping of Japanese Encephalitis Virus in mosquitoes during a 2010 outbreak in the Republic of Korea

Japanese encephalitis virus (JEV), a mosquito-borne zoonotic pathogen, is one of the major causes of viral encephalitis. To reduce the impact of Japanese encephalitis among children in the Republic of Korea (ROK), the government established a mandatory vaccination program in 1967. Through the efforts of this program only 0-7 (mean 2.1) cases of Japanese encephalitis were reported annually in the ROK during the period of 1984-2009. However, in 2010 there was an outbreak of 26 confirmed cases of Japanese encephalitis, including 7 deaths. This represented a >12-fold increase in the number of confirmed cases of Japanese encephalitis in the ROK as compared to the mean number reported over the last 26 years and a 3.7-fold increase over the highest annual number of cases during this same period (7 cases). Surveillance of adult mosquitoes was conducted during the 2010 outbreak of Japanese encephalitis in the ROK. A total of 6,328 culicine mosquitoes belonging to 12 species from 5 genera were collected at 6 survey sites from June through October 2010 and assayed by reverse-transcription polymerase chain reaction (RT-PCR) for the presence of JEV. A total of 34/371 pooled samples tested positive for JEV (29/121 Culex tritaeniorhynchus, 4/64 Cx. pipiens, and 1/26 Cx. bitaeniorhynchus) as confirmed by sequencing of the pre-membrane and envelope protein coding genes. The maximum likelihood estimates of JEV positive individuals per 1,000 culicine vectors for Cx. tritaeniorhynchus, Cx. pipiens, and Cx. bitaeniorhynchus were 11.8, 5.6, and 2.8, respectively. Sequences of the JEV pre-membrane and envelope protein coding genes amplified from the culicine mosquitoes by RT-PCR were compared with those of JEV genotypes I-V. Phylogenetic analyses support the detection of a single genotype (I) among samples collected from the ROK in 2010.

PLoS ONE↗