Dengue virus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA779757 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16944000_1.fastq.gz | Fastqsanger.gz | |||
| SRR16944000_2.fastq.gz | Fastqsanger.gz | |||
| SRR16944001_1.fastq.gz | Fastqsanger.gz | |||
| SRR16944001_2.fastq.gz | Fastqsanger.gz | |||
| SRR16944002_1.fastq.gz | Fastqsanger.gz |
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Project description:Our hypothesis is that dengue induces different innate immune responses in patients with mild respective severe dengue. We further hypothesize that severe dengue infection is a consequence of an over reactive inflammatory response which could be inhibited in an early stage by immune suppressants. We hypothesize that the drugs used in this study induce a down regulated inflammatory response; VP-16 by triggering apoptosis and Rosiglitazone by inhibiting NFkB related cytokine production In-vitro dengue infected U937, transcriptional assessment
2014-04-01 | E-GEOD-28985 | biostudies-arrayexpress
Project description:This study aims to understand the characteristics and diversification of Dengue specific immunoglobulin repertoires after different immunization strategies in mouse. We propose two different immunization strategies in dengue vaccine development. One is tetravalent strategy, which pre-mixed four serotype dengue DNA vaccine and administrated four times. The other one is sequential strategy, which sequentially administrated four time, each serotype vaccine for each dose as sequences of Den1, Den2, Den3 and Den4.
2020-06-30 | GSE139225 | GEO
Project description:Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples. Background Dengue is a mosquito-borne viral infection causing a major public health problem globally. Dengue virus (DENV) is the causative agent of dengue fever (DF) and dengue hemorrhagic fever (DHF) and includes four distinct serotypes (DENV-1, DENV-2, DENV-3, and DENV-4). DENV-2 and DENV-3 have been associated with severe dengue disease, consequently, laboratory testing for DENV is needed to confirm the diagnosis of DENV infection, serotype and to differentiate dengue from other febrile tropical illnesses. In addition, surveillance of mosquitoes infected with DENV is needed to monitor the infection rates within vector mosquito populations harboring specific serotype to provide an early warning sign to predict epidemics. Results In this work we have applied microarray analysis to simultaneously determine the serotype of multiple RNA samples from human or mosquitoes. The proposed microarray method can be used for i) rapid and reliable dengue diagnosis; ii) serotyping and iii) surveillance of mosquitoes infected with dengue. These microarrays were useful to confirm the presence of DENV-2 in 94 serum samples, DENV-3 in three samples from Juchitan, Oaxaca and one case from Juchitan, Oaxaca contained DENV-2 and -3. Moreover by using these microarrays we also determined DENV in pools of gravid females mosquitoes collected in several sites of nineteen Mexican states in 2005. Mosquito pools from 31 cities in the states of Yucatan, Campeche, Tabasco, Chiapas, Veracruz, Oaxaca, Guerrero, Tamaulipas and Colima were infected with DENV-2, six cities in Yucatán, Tabasco, Morelos, Tamaulipas, Colima, and Nayarit with DENV-1, three from Tabasco, Veracruz and Oaxaca with DENV 3 and two with two serotypes simultaneously (Ciudad Mante with DENV-1 and DENV-2, and Tavela with DENV-2 and DENV-3). Conclusion Here we show the success of applying microarrays assay to provide a consistently robust qualitative detection of dengue serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) in serum samples from patients or in pools of gravid female mosquitoes collected in the field of nineteen Mexican states. Interestingly, we did not detect any mosquito or serum sample containing DENV-4.
2015-11-30 | GSE26943 | GEO
Project description:Investigation of whole genome gene expression level changes in Moyo-S and Moyo-R strains of Aedes aegypti after oral infection of serotype 1, serotype 2, serotype 3 and serotype 4 of dengue virus The Moyo-S is highly suscpetible to dengue infection whereas Moyo-R is refractory to the dengue infection. They have been investigated in our previous studies incluidng Behura et al. (2011). PLoS neglected tropical diseases 5 (11), e1385; and Chauhan et al. (2012). PloS one 7 (10), e47350.
2017-12-30 | GSE56508 | GEO
Project description:Background: dengue is a potentially life-threatening viral infection. Early prognostic markers of severe complications may improve case management and reduce dengue-related mortalities. This study aimed to identify circulating microRNAs (miRNAs) as biomarkers for predicting severe dengue. Methods: Serum samples from dengue-infected patients were collected on the first day of admission. Patients were followed up for 14 days after admission to determine the final diagnosis. Participants were divided into non-severe and severe dengue, as defined by WHO 2009 criteria. Circulating microtranscriptome analysis was performed using the NanoString miRNA Expression Assay. The expression level of candidate miRNAs were then validated by quantitative reverse transcription-PCR (qRT-PCR) method. Findings: The discovery cohort (N=19) lead to the identification of 37 differentially expressed miRNAs between the two groups. Six miRNAs (miR122-5p, miR1246, miR1303, miR574-5p, miR30d-5p, and miR424-5p) were selected and further validated in the larger cohort (N=135). The qRT-PCR analysis confirmed that the six miRNAs expression levels were significantly higher in the severe dengue group compared to the non-severe group. Based on receiver operating characteristic (ROC) analysis, miR574-5p and miR1246 displayed the highest diagnostic performance in discriminating between severe from non-severe dengue (AROC curve =0·83). Additionally, miR574-5p and miR1246 had high sensitivity and high negative predictive value for detecting severe dengue. Multivariate analysis suggested that serum miR574-5p was an independent predictor of severe dengue (odds ratio 3·30, 95% CI 1·81-6·04; p<0·001). Interpretation: Circulating miRNAs, especially miR-574-5p and miR-1246, could be promising diagnostic and prognostic biomarkers for severe dengue.
2022-10-26 | GSE190749 | GEO
Project description:To study the role of Dengue virus serotype 4 NS1 in modulation of host cell transcriptome we performed gene expression profiling using data obtained from RNA- sequencing of total RNA from 3 different samples: Huh7 cells (no transfection), Huh7 cells transfected with pTracer-SV40 empty vector and Huh7 cells transfected with pTracer-SV40 encoding dengue virus serotype 4 NS1 (pDENV4 NS1).
2024-11-04 | GSE230787 | GEO
Project description:Dengue virus infection can result in severe symptoms including shock and hemorrhage, but an understanding of the molecular correlates of disease severity is lacking. Bulk transcriptomics on blood samples are difficult to interpret because the blood is composed of different cell types that may react differently to virus infection. Dengue virus RNA can be detected in human plasma, however identifying the cells carrying dengue virus through the bloodstream in vivo has proven challenging. Here we used our recently developed viscRNA-Seq approach to profile transcriptomes of thousands of single blood peripheral mononuclear cells from 6 human subjects with dengue fever and severe dengue, as well as to characterize the cell types associated with dengue virus in the human blood. We found that although no bulk transcriptome marker for severe dengue exists, the expression of MX2 in naive B cells, of CD163 in CD14+/CD16+ monocytes and of other genes in specific cell types is highly predictive for severe dengue. We detected virus-associated cells in the blood of two severe dengue patients with high viral load and discovered the majority of these to be B cells expressing germline IgM or IgD immunoglobulin chains and naive markers but also showing signs of activation and expression of CD69, CXCR4, and other surface receptors. In bystander B cells we detected signs of strong immune activation, parallel hypersomatic evolution and, in one severe degue subject, an anomalously large clone of highly mutated, IgG1 plasmablasts that could be reactive to dengue virus. This study presents a high-resolution molecular exploration into dengue virus infection in humans and can be generalized to any RNA virus.
2018-11-19 | GSE116672 | GEO
Project description:Clinical symptoms of dengue virus (DENV) infection, the most prevalent arthropod-borne viral disease, range from classical mild dengue fever to severe, life-threatening dengue shock syndrome. However, most DENV infections cause few or no symptoms. Asymptomatic DENV-infected patients provide a unique opportunity to decipher the host immune responses leading to virus elimination without negative impact on an individual’s health. We used an integrated approach of transcriptional profiling and immunological analysis to compare a Cambodian population of strictly asymptomatic viremic individuals with clinical dengue patients. Whereas inflammatory pathways and innate immune response pathways were similar between asymptomatic individuals and clinical dengue patients, expression of proteins related to antigen presentation and subsequent T and B cell activation pathways were differentially regulated, independent of viral load and previous DENV infection history. Feedback mechanisms controlled the immune response in asymptomatic viremic individuals, as demonstrated by increased activation of T cell apoptosis-related pathways and FcγRIIB signaling associated with decreased anti-DENV specific antibody concentrations. Taken together, our data illustrate that symptom-free DENV infection in children is associated with determined by increased activation of the adaptive immune compartment and proper control mechanisms, leading to elimination of viral infection without excessive immune activation, with implications for novel vaccine development strategies
2017-09-05 | GSE100299 | GEO
Project description:This pilot study, aimed to profile the host transcriptome as a potential strategy for identifying specific biomarkers for dengue prediction and detection. High-throughput RNA-sequencing (RNA-seq) was employed to generate host transcriptome profiles in 16 dengue patients and 10 healthy controls. Differentially expressed genes (DEGs) were identified in patients with severe dengue and those with dengue with warning signs compared to healthy individuals. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the functions of upregulated and downregulated genes. Compared to healthy controls, 6466 genes were significantly differentially expressed (P < 0.05) in the dengue with warning signs group and 3082 genes in the severe dengue group, with over half being upregulated. The major KEGG pathways implicated included transport and catabolism (14.4%-16.3%), signal transduction (6.6%-7.3%), global and overview maps (6.7%-7.1%), viral diseases (4.6%-4.8%), and the immune system (4.4%-4.6%). Several genes exhibited consistent and significant upregulation across all dengue patients, regardless of severity: Interferon alpha inducible protein 27 (IFI27), Potassium Channel Tetramerisation Domain Containing 14 (KCTD14), Syndecan 1 (SDC1), DCC netrin 1 receptor (DCC), Ubiquitin C-terminal hydrolase L1 (UCHL1), Marginal zone B and B1 cell specific protein (MZB1), Nestin (NES), C-C motif chemokine ligand 2 (CCL2), TNF receptor superfamily member 17 (TNFSF17), and TNF receptor superfamily member 13B (TNFRSF13B). Further analysis revealed potential biomarkers for severe dengue prediction, including TNF superfamily member 15 (TNFSF15), Plasminogen Activator Inhibitor-2 (SERPINB2), motif chemokine ligand 7 (CCL7), aconitate decarboxylase 1 (ACOD1), Metallothionein 1G (MT1G) and Myosin Light Chain Kinase (MYLK2), which were expressed 3.5 times, 2.9 times, 2.3 times, 2.1 times, 1.7 times, and 1.4 times greater, respectively, than dengue patients exhibiting warning signs. The identification of these host biomarkers through RNA-sequencing holds promising implications and potential to augment existing dengue detection algorithms, contributing significantly to improved diagnostic and prognostic capabilities.
2024-10-10 | GSE279208 | GEO
Project description:Dengue viruses cause two severe diseases that alter vascular fluid barrier functions, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). While the mechanisms that lead to vascular permeability are unknown, the endothelium plays a central role in regulating fluid and cellular efflux from capillaries. Thus, dysregulation of endothelial cells functions by dengue virus infection may contribute to pathogenesis and severe disease. We used microarrays to investigate the effect of dengue virus infection on gene expression within primary human endothelial cells at various times post infection and identified numerous upregulated antiviral and immune response genes. Early passage primary endothelial cells (HUVECs) were mock infected (no virus) or infected with dengue virus and total RNA collected at 3 timepoints: 12, 24, and 48 hours post infection. Multiple timepoints were analyzed to identify changes in gene expression levels over time. Gene expression from both mock infected and dengue virus infected endothelial cells was evaluated to determine fold induction at each timepoint.
2012-04-10 | E-GEOD-34628 | biostudies-arrayexpress