scholarly journals Molecular Confirmation of Ranavirus Infection in Amphibians From Chad, Africa

2021 ◽  
Vol 8 ◽  
Author(s):  
Erin K. Box ◽  
Christopher A. Cleveland ◽  
Kuttichantran Subramaniam ◽  
Thomas B. Waltzek ◽  
Michael J. Yabsley
Keyword(s):  
Ribonucleotide Reductase ◽  
Incidental Finding ◽  
Sister Group ◽  
Global Scale ◽  
Population Declines ◽  
Full Genome Sequencing ◽  
Tissue Samples ◽  
Dna Viruses ◽  
Frog Virus ◽  
Individual Gene

Ranaviruses are DNA viruses (Family Iridoviridae; Subfamily Alphairidovirinae) and ranaviral disease is considered an emerging infectious disease of ectothermic vertebrates. Ranavirus infection can have varying pathological effects on infected amphibians, reptiles, and fish, most notably causing significant mortality events and population declines. Despite having a broad global range with reports from six continents, only a single incidental finding in Xenopus longipes from mainland Africa (Cameroon) is known and lacks molecular confirmation. Thus, there is a considerable knowledge gap concerning ranaviruses in Africa. We opportunistically obtained tissue samples from 160 amphibians representing five genera (Hoplobatrachus, Hylarana, Ptychadena, Pyxicephalus, and Xenopus) and two turtles (Pelomedusa sp.) from Chad, Africa. Samples were tested for ranavirus infection using a conventional PCR assay targeting the major capsid protein (MCP). A total of 25/160 (16%) frogs tested positive including 15/87 (17%) Hoplobatrachus occipitalis, 10/58 (17%) Ptychadena spp., 0/3 Pyxicephalus spp., 0/9 Xenopus spp., and 0/3 Hylarana spp. One of two turtles tested positive. Partial MCP gene sequences indicated all samples were >98% similar to several frog virus 3 (FV3)-like sequences. Additional gene targets (DNA polymerase [DNApol], ribonucleotide reductase alpha [RNR- α], ribonucleotide reductase beta subunit [RNR- β]) were sequenced to provide further detailed classification of the virus. Sequences of individual gene targets indicate that the ranavirus detected in frogs in Chad is most similar to tiger frog virus (TFV), a FV3-like virus previously isolated from diseased amphibians cultured in China and Thailand. Full genome sequencing of one sample indicates that the Chad frog virus (CFV) is a well-supported sister group to the TFVs previously determined from Asia. This work represents the first molecular confirmation of ranaviruses from Africa and is a first step in comparing ranavirus phylogeography on a local and global scale.

scholarly journals Identification of Poxvirus Genome Uncoating and DNA Replication Factors with Mutually Redundant Roles

2018 ◽  
Vol 92 (7) ◽  
Author(s):  
Baoming Liu ◽  
Debasis Panda ◽  
Jorge D. Mendez-Rios ◽  
Sundar Ganesan ◽  
Linda S. Wyatt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Vaccinia Virus ◽  
Deletion Mutant ◽  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Early Gene ◽  
Late Gene Expression ◽  
Dna Viruses ◽  
Individual Gene

ABSTRACTGenome uncoating is essential for replication of most viruses. For poxviruses, the process is divided into two stages: removal of the envelope, allowing early gene expression, and breaching of the core wall, allowing DNA release, replication, and late gene expression. Subsequent studies showed that the host proteasome and the viral D5 protein, which has an essential role in DNA replication, are required for vaccinia virus (VACV) genome uncoating. In a search for additional VACV uncoating proteins, we noted a report that described a defect in DNA replication and late expression when the gene encoding a 68-kDa ankyrin repeat/F-box protein (68k-ank), associated with the cellular SCF (Skp1, cullin1, F-box-containing complex) ubiquitin ligase complex, was deleted from the attenuated modified vaccinia virus Ankara (MVA). Here we showed that the 68k-ank deletion mutant exhibited diminished genome uncoating, formation of DNA prereplication sites, and degradation of viral cores as well as an additional, independent defect in DNA synthesis. Deletion of the 68k-ank homolog of VACV strain WR, however, was without effect, suggesting the existence of compensating genes. By inserting VACV genes into an MVA 68k-ank deletion mutant, we discovered that M2, a member of the poxvirus immune evasion (PIE) domain superfamily and a regulator of NF-κB, and C5, a member of the BTB/Kelch superfamily associated with cullin-3-based ligase complexes, independently rescued the 68k-ank deletion phenotype. Thus, poxvirus uncoating and DNA replication are intertwined processes involving at least three viral proteins with mutually redundant functions in addition to D5.IMPORTANCEPoxviruses comprise a family of large DNA viruses that infect vertebrates and invertebrates and cause diseases of medical and zoological importance. Poxviruses, unlike most other DNA viruses, replicate in the cytoplasm, and their large genomes usually encode 200 or more proteins with diverse functions. About 90 genes may be essential for chordopoxvirus replication based either on their conservation or individual gene deletion studies. However, this number may underestimate the true number of essential functions because of redundancy. Here we show that any one of three seemingly unrelated and individually nonessential proteins is required for the incompletely understood processes of genome uncoating and DNA replication, an example of synthetic lethality. Thus, poxviruses appear to have a complex genetic interaction network that has not been fully appreciated and which will require multifactor deletion screens to assess.

scholarly journals Characterization of Primary and Memory CD8 T-Cell Responses against Ranavirus (FV3) in Xenopus laevis

2006 ◽  
Vol 81 (5) ◽  
pp. 2240-2248 ◽  
Author(s):  
Heidi D. Morales ◽  
Jacques Robert
Keyword(s):  
T Cells ◽  
T Cell ◽  
Xenopus Laevis ◽  
Viral Infections ◽  
Protective Antigen ◽  
Secondary Infection ◽  
Viral Immunity ◽  
Dna Viruses ◽  
Frog Virus

ABSTRACT In mammals, resistance to primary and secondary viral infections critically involves major histocompatibility complex class I-restricted cytotoxic CD8+ T lymphocytes (CTLs). Although many gene homologues involved in CTL function have been identified in all vertebrate classes, antiviral CTL responses have been poorly characterized for ectothermic vertebrates. Because of the threat of emerging wildlife viral diseases to global biodiversity, fundamental research on comparative viral immunity has become crucial. Ranaviruses (family Iridoviridae) are double-stranded DNA viruses possibly implicated in the worldwide decline of amphibian populations. We used the frog Xenopus laevis as a model to evaluate adaptive immune responses to the ranavirus frog virus 3 (FV3). FV3 infects the kidneys of adults but is cleared within 4 weeks, with faster clearance upon secondary infections. In vivo depletion of CD8+ T cells markedly decreases the survival of adults after viral infection. To further investigate the involvement of anti-FV3 CD8+ T-cell effectors in host resistance in vivo, we determined the proliferation kinetics of CD8+ T cells in the spleen by bromodeoxyuridine incorporation and their infiltration of kidneys by immunohistology. Upon primary infection, CD8+ T cells significantly proliferate in the spleen and accumulate in infected kidneys from day 6 onward, in parallel with virus clearance. Earlier proliferation and infiltration associated with faster viral clearance were observed during a secondary infection. These results provide in vivo evidence of protective antigen-dependent CD8+ T-cell proliferation, recognition, and memory in fighting a natural pathogen in Xenopus.

scholarly journals The Genome of Gryllus bimaculatus Nudivirus Indicates an Ancient Diversification of Baculovirus-Related Nonoccluded Nudiviruses of Insects

2007 ◽  
Vol 81 (10) ◽  
pp. 5395-5406 ◽  
Author(s):  
Yongjie Wang ◽  
Regina G. Kleespies ◽  
Alois M. Huger ◽  
Johannes A. Jehle
Keyword(s):  
Sequence Similarity ◽  
Heliothis Zea ◽  
Direct Repeat ◽  
Sister Group ◽  
Open Reading Frames ◽  
Gryllus Bimaculatus ◽  
Structural Genomic ◽  
Protein Coding ◽  
Dna Viruses ◽  
Core Genes

ABSTRACT The Gryllus bimaculatus nudivirus (GbNV) infects nymphs and adults of the cricket Gryllus bimaculatus (Orthoptera: Gryllidae). GbNV and other nudiviruses such as Heliothis zea nudivirus 1 (HzNV-1) and Oryctes rhinoceros nudivirus (OrNV) were previously called “nonoccluded baculoviruses” as they share some similar structural, genomic, and replication aspects with members of the family Baculoviridae. Their relationships to each other and to baculoviruses are elucidated by the sequence of the complete genome of GbNV, which is 96,944 bp, has an AT content of 72%, and potentially contains 98 predicted protein-coding open reading frames (ORFs). Forty-one ORFs of GbNV share sequence similarities with ORFs found in OrNV, HzNV-1, baculoviruses, and bacteria. Most notably, 15 GbNV ORFs are homologous to the baculovirus core genes, which are associated with transcription (lef-8, lef-9, lef-4, vlf-1, and lef-5), replication (dnapol), structural proteins (p74, pif-1, pif-2, pif-3, vp91, and odv-e56), and proteins of unknown function (38K, ac81, and 19kda). Homologues to these baculovirus core genes have been predicted in HzNV-1 as well. Six GbNV ORFs are homologous to nonconserved baculovirus genes dnaligase, helicase 2, rr1, rr2, iap-3, and desmoplakin. However, the remaining 57 ORFs revealed no homology or poor similarities to the current gene databases. No homologous repeat (hr) sequences but fourteen short direct repeat (dr) regions were detected in the GbNV genome. Gene content and sequence similarity suggest that the nudiviruses GbNV, HzNV-1, and OrNV form a monophyletic group of nonoccluded double-stranded DNA viruses, which separated from the baculovirus lineage before this radiated into dipteran-, hymenopteran-, and lepidopteran-specific clades of occluded nucleopolyhedroviruses and granuloviruses. The accumulated information on the GbNV genome suggests that nudiviruses form a highly diverse and phylogenetically ancient sister group of the baculoviruses, which have evolved in a variety of highly divergent host orders.

scholarly journals No pervasive relationship between species size and local abundance trends

2021 ◽  
Author(s):  
J. Christopher D. Terry ◽  
Jacob D. O’Sullivan ◽  
Axel G. Rossberg
Keyword(s):  
Potential Role ◽  
Global Scale ◽  
Clear Correlation ◽  
Population Declines ◽  
Multiple Trait ◽  
Abundance Trends ◽  
Local Abundance ◽  
Over Time ◽  
Consistent Tendency

AbstractAlthough there is some evidence that larger species could be more prone to population declines, the potential role of size traits in determining changes in community composition has been underexplored in global-scale analyses. Here, we combine a large cross-taxon assemblage time series database (BioTIME) with multiple trait databases to show that there is no clear correlation within communities between size traits and changes in abundance over time, suggesting that there is no consistent tendency for larger species to be doing proportionally better or worse than smaller species at local scales.

Circular DNA viruses identified in short-finned pilot whale and orca tissue samples

Virology ◽  
2021 ◽  
Author(s):  
Kendal Smith ◽  
Russell Fielding ◽  
Kelsie Schiavone ◽  
Katharine R. Hall ◽  
Vincent S. Reid ◽  
...  
Keyword(s):  
Pilot Whale ◽  
Tissue Samples ◽  
Dna Viruses ◽  
Circular Dna

scholarly journals SURVEYING FOR RANAVIRUS IN GREEN FROGS (LITHOBATES CLAMITANS) AT FIVE LOCATIONS IN INDIANA

2016 ◽  
pp. 23-26
Author(s):  
Megan E. Winzeler ◽  
Rod N. Williams ◽  
Steven J. A. Kimble
Keyword(s):  
United States ◽  
The United States ◽  
The State ◽  
Green Frog ◽  
Emerging Pathogen ◽  
Tissue Samples ◽  
Frog Virus ◽  
The Status ◽  
Pcr Method ◽  
Management And Conservation

Ranaviruses are an emerging pathogen within the United States that infects amphibians, reptiles, and fish. A Frog Virus 3-like (FV3) ranavirus has been detected at only two locations in Indiana; however, there have been few attempts to broadly sample for ranaviruses to determine their distribution across the state. This knowledge is necessary for the continued management and conservation of native amphibian populations. Our objective was to assess the occurrence of FV3-like ranaviruses in larval Green Frog (Lithobates clamitans) populations at five sites located in different regions of Indiana. Tissue samples were collected from 166 individuals and were assayed using both conventional and qPCR methods. We did not detect the presence of any FV3-like ranaviruses at any of the five sites with either PCR method, suggesting the possibility that at these sites, FV3-like ranaviruses may not be present. However, continued sampling should be carried out to monitor the status of the presence of ranaviruses in this portion of the Midwest.

scholarly journals Effects of dams on downstream molluscan predator–prey interactions in the Colorado River estuary

2018 ◽  
Vol 285 (1879) ◽  
pp. 20180724 ◽  
Author(s):  
Jansen A. Smith ◽  
John C. Handley ◽  
Gregory P. Dietl
Keyword(s):  
Colorado River ◽  
Salinity Gradient ◽  
River Estuary ◽  
Null Model ◽  
Global Scale ◽  
Ecological Change ◽  
Population Declines ◽  
Prey Biomass ◽  
Resource Data ◽  
Drill Holes

River systems worldwide have been modified for human use and the downstream ecological consequences are often poorly understood. In the Colorado River estuary, where upstream water diversions have limited freshwater input during the last century, mollusc remains from the last several hundred years suggest widespread ecological change. The once abundant clam Mulinia modesta has undergone population declines of approximately 94% and populations of predators relying on this species as a food source have probably declined, switched to alternative prey species or both. We distinguish between the first two hypotheses using a null model of predation preference to test whether M. modesta was preyed upon selectively by the naticid snail, Neverita reclusiana , along the estuary's past salinity gradient. To evaluate the third hypothesis, we estimate available prey biomass today and in the past, assuming prey were a limiting resource. Data on the frequency of drill holes—identifiable traces of naticid predation on prey shells—showed several species, including M. modesta , were preferred prey. Neverita reclusiana was probably able to switch prey. Available prey biomass also declined, suggesting the N. reclusiana population probably also declined. These results indicate a substantial change to the structure of the benthic food web. Given the global scale of water management, such changes have probably also occurred in many of the world's estuaries.

scholarly journals First record of ranavirus (Ranavirus sp.) in Siberia, Russia

2021 ◽  
Author(s):  
Artem Lisachov ◽  
Lada Lisachova ◽  
Evgeniy Simonov
Keyword(s):  
Western Europe ◽  
West Siberia ◽  
First Record ◽  
The Arctic ◽  
Amphibian Species ◽  
Northern Asia ◽  
Tissue Samples ◽  
Dna Viruses ◽  
Arctic Regions ◽  
In The Wild

Ranaviruses are a group of double-strand DNA viruses that infect fish, amphibians and reptiles. These viruses are responsible for mass fish and amphibian mortality events worldwide, both in the wild and at the fish and amphibian farms. The number of detected epizootics has grown significantly in recent years. In Eastern Europe and Northern Asia, including Russia, very few ranavirosis monitoring studies have been conducted, in contrast with Western Europe and America. In the present work, we used a qPCR assay to survey for the first time the amphibian populations of West Siberia (Russia) for the presence of ranaviruses. In total, we studied 252 tissue samples from six amphibian species, collected across West Siberia from the south to the Arctic regions. We report a single infected sample: a common toad (Bufo bufo) captured near Tyumen city. The phylogenetic analysis showed that the detected virus strain belongs to the CMTV lineage. This is only the second observation of Ranavirus in Russia.

Comprehensive landscape of gene amplifications (amps) in tissue and circulating tumor DNA (ctDNA) in metastatic colorectal cancer (mCRC).

2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 604-604
Author(s):  
Kanwal Pratap Singh Raghav ◽  
Rona Yaeger ◽  
Jonathan M. Loree ◽  
Arvind Dasari ◽  
Van K. Morris ◽  
...  
Keyword(s):  
Copy Number ◽  
Acquired Resistance ◽  
High Sensitivity ◽  
Circulating Tumor Dna ◽  
Tissue Samples ◽  
Individual Gene ◽  
Therapeutic Implications ◽  
Oncogenic Pathways ◽  
Number Variation ◽  
Tumor Dna

604 Background: Amps, as oncogenic and resistance drivers, have therapeutic implications, but unlike mutations, have been sparsely described in mCRC. Functional account is piecemeal due to vague definitions, limited data on co-occurring alterations and use of primary tissue samples nonrepresentative of tumor heterogeneity. Our aim was to define the amp landscape in mCRC using tissue and ctDNA sequencing. Methods: We performed systematic analyses of copy-number variation in 2 cohorts of mCRC patients (pts) [tissue (TC) (N = 1,134) and ctDNA (BC) (N = 3,218)] who had high sensitivity targeted sequencing with MSK-IMPACT (341-468 genes) or Guardant Health (70-73 genes) panel, respectively. For BC, plasma copy number was adjusted (ApCN) to account for variable tumor DNA shedding using max allele frequency and high amp (HAmp) was defined as > 4 copies (similar to predefined tissue cutoff). Results: 166 (15%) and 405 (13%) pts in TC and BC harbored amp in at least one of 18 genes assessed by both panels (Table). Amp prevalence for individual gene was similar in both cohorts ( r = 0.9; P < .01) with RTK amps ( EGFR, ERBB2, MET, FGFR1/2, PDGFRA) seen in 8% pts. Key RTK amps were enriched in RAS/BRAF wild type (RB WT) compared to mutant (RB MUT) (OR 3.5; P < .01) pts in both cohorts, in contrast to low prevalence RTK and non-RTK amps. Median ApCN was higher for RTKs in RB WT vs MUT cases ( ERBB2: 12 vs 5; P = .02). Using validated EGFRab exposure (EGFRi) ctDNA signature, we found that EGFRi pts had higher prevalence of EGFR, MET, BRAF, KRAS, PIK3CA and FGFR1 amps compared to EGFRab naïve pts. Conclusions: While individually uncommon, amps occur across key oncogenic pathways in mCRC and after adjusting for ctDNA shedding, are seen at similar prevalence in tissue and plasma. Amps in RTKs are seen in 10-12% of RB WT tumors, suggesting clinically relevant roles as oncogenic effectors and targets. After EGFRi, a number of amps emerge, including PIK3CA and FGFR1 amps, not previously implicated in acquired resistance. [Table: see text]

scholarly journals Persistent ecological shifts in marine molluscan assemblages across the end-Cretaceous mass extinction

2015 ◽  
Vol 112 (23) ◽  
pp. 7207-7212 ◽  
Author(s):  
Martin Aberhan ◽  
Wolfgang Kiessling
Keyword(s):  
Mass Extinction ◽  
Biodiversity Loss ◽  
Global Scale ◽  
Population Declines ◽  
Feeding Mode ◽  
Geological Past ◽  
Irreversible Effects ◽  
Ecological Shifts ◽  
Modes Of Life ◽  
And Function

Contemporary biodiversity loss and population declines threaten to push the biosphere toward a tipping point with irreversible effects on ecosystem composition and function. As a potential example of a global-scale regime shift in the geological past, we assessed ecological changes across the end-Cretaceous mass extinction based on molluscan assemblages at four well-studied sites. By contrasting preextinction and postextinction rank abundance and numerical abundance in 19 molluscan modes of life—each defined as a unique combination of mobility level, feeding mode, and position relative to the substrate—we find distinct shifts in ecospace utilization, which significantly exceed predictions from null models. The magnitude of change in functional traits relative to normal temporal fluctuations at far-flung sites indicates that molluscan assemblages shifted to differently structured systems and faunal response was global. The strengths of temporal ecological shifts, however, are mostly within the range of preextinction site-to-site variability, demonstrating that local ecological turnover was similar to geographic variation over a broad latitudinal range. In conjunction with varied site-specific temporal patterns of individual modes of life, these spatial and temporal heterogeneities argue against a concerted phase shift of molluscan assemblages from one well-defined regime to another. At a broader ecological level, by contrast, congruent tendencies emerge and suggest deterministic processes. These patterns comprise the well-known increase of deposit-feeding mollusks in postextinction assemblages and increases in predators and predator-resistant modes of life, i.e., those characterized by elevated mobility and infaunal life habits.

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