Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In situ detection of Australian gill-associated virus with a yellow head virus gene probe.

ABSTRACT: A digoxigenin-labeled gene probe for yellow head virus (YHV) was used to detect gill-associated virus (GAV) in Penaeus monodon from Australia via in situ hybridization. In GAV-infected shrimp, positively reacting tissues included: lymphoid organ, gills, antennal gland, and cuticular epithelium of the stomach. This demonstrates that a YHV probe can be used as a diagnostic tool for GAV and supports previous suggestions that these two viruses are closely related.

SUBMITTER: Tang KF

PROVIDER: S-EPMC7172130 | biostudies-literature | 2002 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

In situ detection of Australian gill-associated virus with a yellow head virus gene probe.

Tang Kathy F-J KF Spann Kirsten M KM Owens Leigh L Lightner Donald V DV

Aquaculture. 20020129 1

A digoxigenin-labeled gene probe for yellow head virus (YHV) was used to detect gill-associated virus (GAV) in <i>Penaeus monodon</i> from Australia via in situ hybridization. In GAV-infected shrimp, positively reacting tissues included: lymphoid organ, gills, antennal gland, and cuticular epithelium of the stomach. This demonstrates that a YHV probe can be used as a diagnostic tool for GAV and supports previous suggestions that these two viruses are closely related. ...[more]

PMID: 32336809

Similar Datasets

Yellow Head Virus

Project description:Yellow head virus (YHV) infects the black tiger shrimp (Penaeus monodon) – one of the world's major aquaculture species. It is a highly virulent pathogen that can cause 100% mortality within a few days of the first signs of disease in a pond. YHV is a rod-shaped, enveloped (+) single-stranded RNA (ssRNA) virus with a helical nucleocaspsid. In genome organization and transcription strategy, it resembles coronaviruses, toroviruses, and arteriviruses with which it has been classified within the order Nidovirales (genus Okavirus, family Roniviridae). The 26 662 nt genome comprises four long open reading frames (ORFs). ORF1a and ORF1b encode nonstructural proteins that are expressed as polyproteins (pp1a and pp1ab) and processed to generate elements of a replicase complex. ORF1b is expressed only as an extension of ORF1a via a ribosomal frameshift. ORF2 encodes the nucleocapsid protein (p20). ORF3 encodes envelope glycoproteins (gp64 and gp116) and a small, nonstructural, triple-membrane-spanning protein (p22). YHV is one genotype in a complex of closely related viruses that are endemic in black tiger shrimp in the Indo-Pacific region. These include gill-associated virus which has been associated with less severe forms of disease in Australia and at least four other genotypes that cause low-level chronic infections in healthy shrimp.

| S-EPMC7173420 | biostudies-literature

Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene.

Project description:The genus Okavirus (order Nidovirales) includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of approximately 26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.

| S-EPMC2805633 | biostudies-literature

Detection of yellow head virus in shrimp by loop-mediated isothermal amplification (LAMP).

Project description:Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting the structural glycoprotein gene of yellow head virus (YHV). The RT-LAMP assay is a novel method of gene amplification that amplifies nucleic acid with high specificity, sensitivity and rapidity under isothermal conditions with a set of four specially designed primers that recognize six distinct sequences of the target. The whole procedure is very simple and rapid, and reaction time and temperatures were optimized for 60 min at 65 degrees C, respectively. Detection of gene amplification could be accomplished by agarose gel electrophoresis. The standardized RT-LAMP procedure was used to detect YHV in the heart and gill from infected shrimp. Thus, the RT-LAMP assay is extremely rapid, cost-effective, sensitive and specific and has potential usefulness for rapid diagnosis for YHV detection in shrimp.

| S-EPMC7172593 | biostudies-literature

Gene expression kinetics of the yellow head virus in experimentally infected Litopenaeus vannamei.

Project description:The yellow head virus (YHV) has been reported to be one of most pathogenic viruses for cultivated shrimp; however, serious problems have only been reported in farms in south and southeastern Asian. Recently, a YHV strain was detected in Litopenaeus vannamei cultivated in Mexican farms that lacked virus-associated mortalities or epizooties, and the animals were apparently healthy. The identity of the virus was confirmed by sequencing replicative and structural protein-encoding regions and comparing with homologous virus sequences. Phylogenic relationships and genetic distances were also determined and, although some differences were observed, an influence on virulence was uncertain. In addition, the expression levels of several transcripts (3CLPRO, POL, GP64 and GP116) were evaluated by quantitative real-time polymerase chain reaction during an experimental infection. Although the transcript showed varying kinetics, viral genes were expressed in infected L. vannamei, demonstrating the replicative capability of this YHV strain.

| S-EPMC7159739 | biostudies-literature

Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of yellow head virus in shrimp.

Project description:A real-time reverse transcription loop-mediated isothermal amplification (real-time RT-LAMP) method was applied for detecting the replicase polyprotein-encoding gene of yellow head virus (YHV) in shrimp, Penaeus monodon. It is a novel, gene-specific assay that amplifies nucleic acid with high specificity, sensitivity and rapidity under isothermal conditions using a set of six specially designed primers that recognize eight distinct sequences of the target gene. This method works with even low copies of DNA and is based on magnesium pyrophosphate turbidity detection by an inexpensive photometer for quantitative analysis. A user-friendly protocol was developed with optimal conditions standardized at 63 degrees C for 60 min. With this protocol, the assay sensitivity was 10 times higher than the widely used YHV nested RT-PCR system. Cross-reactivity analysis using other shrimp virus DNA/cDNA and YHV-negative shrimp demonstrated high specificity of the assay. The real-time RT-LAMP method was performed also for an internal control gene, EF-1alpha, to compare with the expressions of the YHV gene in different organs of infected shrimp, and the resulting standard curves showed high correlation coefficient values. These results suggest that this assay is applicable widely as a new quantitative detection method in the pursuit of YHV-free shrimp culture.

| S-EPMC7112779 | biostudies-literature

Detection of carp interstitial nephritis and gill necrosis virus in fish droppings.

Project description:Carp interstitial nephritis and gill necrosis virus (CNGV) is an unclassified large DNA virus that morphologically resembles members of the Herpesviridae but contains a large (ca. approximately 280-kbp) linear double-stranded DNA. This virus has also been named koi herpesvirus, koi herpes-like virus, and cyprinid herpesvirus 3. CNGV is the cause of a lethal disease that afflicts common carp and koi. By using immunohistochemistry, molecular analysis, and electron microscopy we previously demonstrated that this virus is present mainly in the intestine and kidney of infected fish. Based on these observations, we postulated that viruses and/or viral components may appear in droppings of infected carp. Here we report that (i) by using PCR we demonstrated that fish droppings contain viral DNA, (ii) fish droppings contain viral antigens which are useful for CNGV diagnosis, and (iii) fish droppings contain active virus which can infect cultured common carp brain cells and induce the disease in naïve fish following inoculation. Thus, our findings show that CNGV can be identified by using droppings without taking biopsies or killing fish and that infectious CNGV is present in the stools of sick fish. The possibility that fish droppings preserve viable CNGV during the nonpermissive seasons is discussed.

| S-EPMC1287658 | biostudies-literature

Detection of Corchorus golden mosaic virus Associated with Yellow Mosaic Disease of Jute (Corchorus capsularis).

Project description:Yellow mosaic disease, caused by a whitefly transmitted New World Begomovirus, named Corchorus golden mosaic virus (CoGMV), is emerging as a serious biotic constraint for jute fibre production in Asia. For rapid and sensitive diagnosis of the Begomovirus associated with this disease, a non-radiolabelled diagnostic probe, developed against the DNA A component of the east Indian isolate of CoGMV, detected the presence of the virus in infected plants and viruliferous whiteflies following Southern hybridization and nucleic acid spot hybridization tests. Presence of the virus was also confirmed when polymerase chain reaction amplification was performed using virus-specific primers on DNA templates isolated from infected plants and viruliferous whiteflies.

| S-EPMC3550811 | biostudies-literature

Structural and antigenic analysis of the yellow head virus nucleocapsid protein p20.

Project description:Yellow head virus (YHV) is an invertebrate nidovirus that is highly pathogenic for marine shrimp. Nucleotide sequence analysis indicated that the YHV ORF2 gene encodes a basic protein (pI = 9.9) of 146 amino acids with a predicted molecular weight of 16,325.5 Da. The deduced amino acid sequence indicated a predominance of basic (15.1%), acidic (9.6%) and hydrophilic polar (34.3%) residues and a high proportion proline and glycine residues (16.4%). The ORF2 gene was cloned and expressed in Escherichia coli as a M(r) = 21 kDa His(6)-protein that reacted with YHV nucleoprotein (p20) monoclonal antibody. Segments representing the four linear quadrants of the nucleoprotein were also expressed in E. coli as GST-fusion proteins. Immunoblot analysis using YHV polyclonal rabbit antiserum indicated the presence of linear epitopes in all except the V(37)-Q(74) quadrant. Immunoblot analysis of the GST-fusion proteins and C-terminally truncated segments of the nucleoprotein allowed mapping of YHV monoclonal antibodies Y19, Y20 and YII4 to linear epitopes in the acidic domain between amino acids I(116) and E(137). The full-length nucleoprotein was expressed at high level in E. coli and was easily purified in quantity from the soluble cell fraction by Ni(+)-NTA affinity chromatography.

| S-EPMC7172242 | biostudies-literature

Successful yellow head virus infection of Penaeus monodon requires clathrin heavy chain.

Project description:Viral disease caused by the Yellow head virus (YHV) had great impact on economic loss in the aquaculture industry. Prevention or curing YHV disease is still not possible due to the lack of understanding of the basic mechanisms of YHV infection. In this report, the endocytosis inhibitors (chlorpromazine (CPZ), amiloride and methyl-β-cyclodextrin (MβCD)) were used to identify the cellular entry pathway of YHV. Pretreating shrimp with CPZ but not amiloride or MβCD followed by YHV challenge resulted in a significant reduction of YHV levels, suggesting that YHV entered the shrimp cells via clathrin-mediated endocytosis. Next, the major component of the clathrin-coated vesicle, Penaeus monodon clathrin heavy chain (PmCHC) was cloned and characterized. The complete coding sequence of PmCHC is 5055 bp encoding a putative protein of 1684 amino acids. Specific silencing of PmCHC mRNA by dsRNA-PmCHC showed an inhibition of YHV replication for 48 h post YHV injection as well as exhibiting a delay in shrimp mortality. These results indicated that PmCHC was an essential component for YHV infection of shrimp cells.

| S-EPMC7112056 | biostudies-literature

Homology modeling and virtual screening for antagonists of protease from yellow head virus.

Project description:Yellow head virus (YHV) is one of the causative agents of shrimp viral disease. The prevention of YHV infection in shrimp has been developed by various methods, but it is still insufficient to protect the mass mortality in shrimp. New approaches for the antiviral drug development for viral infection have been focused on the inhibition of several potent viral enzymes, and thus the YHV protease is one of the interesting targets for developing antiviral drugs according to the pivotal roles of the enzyme in an early stage of viral propagation. In this study, a theoretical modeling of the YHV protease was constructed based on the folds of several known crystal structures of other viral proteases, and was subsequently used as a target for virtual screening-molecular docking against approximately 1364 NCI structurally diversity compounds. A complex between the protease and the hit compounds was investigated for intermolecular interactions by molecular dynamics simulations. Five best predicted compounds (NSC122819, NSC345647, NSC319990, NSC50650, and NSC5069) were tested against bacterial expressed YHV. The NSC122819 showed the best inhibitory characteristic among the candidates, while others showed more than 50 % of inhibition in the assay condition. These compounds could potentially be inhibitors for curing YHV infection.

| S-EPMC7087857 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data