Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic and phenotypic changes to Venezuelan equine encephalitis virus following treatment with β-D-N4-hydroxycytidine, an RNA mutagen

ABSTRACT: Genetic and phenotypic changes to Venezuelan equine encephalitis virus following treatment with β-D-N4-hydroxycytidine, an RNA mutagen

PROVIDER: PRJNA853786 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19899500_1.fastq.gz	Fastqsanger.gz
	SRR19899600_1.fastq.gz	Fastqsanger.gz
	SRR19899700_1.fastq.gz	Fastqsanger.gz
	SRR19899800_1.fastq.gz	Fastqsanger.gz
	SRR19899900_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1246

Similar Datasets

Genetic and phenotypic changes to Venezuelan equine encephalitis virus following treatment with β-D-N4-hydroxycytidine, an RNA mutagen

Project description:The high mutation rate of RNA viruses provides viral populations with the ability to adapt to new environments but also makes them vulnerable to extinction due to the deleterious effects of mutations, which is the conceptual basis for the antiviral activity of RNA mutagens. However, there are still gaps in the quantitative understanding of the dynamics between the mutations induced by an RNA mutagen and its effects on viral fitness. To address this, we used Venezuelan Equine Encephalitis Virus (VEEV) and the potent RNA mutagen β-d-N4-hydroxycytidine (NHC) as a model to analyze virus replication competency and mutation frequency following treatment in the total and replication-competent viral populations separately. We found that NHC induced transition mutations in a concentration dependent manner in the total population, while the replication-competent population maintained itself within an increased, yet narrow, mutation spectrum. The incorporation of NHC mainly happened during the positive sense RNA synthesis of VEEV. A growth kinetic analysis of VEEV population treated with NHC pointed to a lower but more diverse distribution in mutational fitness, demonstrating that NHC-induced mutations negatively and broadly affect the fitness of the virus. Together, our study provides mechanistic insight into how RNA mutagens affect viral population landscape and the potential of RNA mutagens as an antiviral strategy for alphaviruses.

2024-10-25 | GSE207136 | GEO

Venezuelan equine encephalitis virus

Project description:Venezuelan equine encephalitis virus Genome sequencing

| PRJNA438670 | ENA

Characterization of genetic variability of Venezuelan equine encephalitis viruses

Project description:We performed whole genome single nucleotide polymorphism (SNP) based analysis of all available Venezuelan equine encephalitis (VEE) virus antigenic complex genomes and developed a high resolution genome-wide SNP microarray. We used the SNP microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array and sequence based genotypes for previously sequenced strains, and genotyped unsequenced strains.

2016-03-24 | GSE79530 | GEO

Venezuelan equine encephalitis virus

Project description:Complete genome sequencing of a collection of the Venezuelan equine encephalitis viruses (VEEV).

| PRJNA157941 | ENA

Venezuelan equine encephalitis virus strain: LSE9910-15

Project description:Venezuelan equine encephalitis virus strain: LSE9910-15 Genome sequencing and assembly

| PRJNA546500 | ENA

The transcriptional landscape of Venezuelan equine encephalitis virus infection

Project description:The transcriptional landscape of Venezuelan equine encephalitis virus infection

| PRJNA608425 | ENA

Characterization of genetic variability of Venezuelan equine encephalitis viruses

Project description:Characterization of genetic variability of Venezuelan equine encephalitis viruses

| PRJNA316099 | ENA

The transcriptional landscape of Venezuelan equine encephalitis virus infection

Project description:No vaccines or antivirals are approved against Venezuelan equine encephalitis virus (VEEV) infection in humans. To improve our understanding of VEEV-host interactions, we simultaneously profiled host transcriptome and viral RNA (vRNA) in thousands of single cells during infection of human astrocytes. Host transcription was suppressed, and “superproducer cells” with extreme vRNA abundance and altered transcriptome emerged during the first viral life cycle. Cells with increased structural-to-nonstructural transcript ratio demonstrated upregulation of trafficking genes at later time points. Loss- and gain-of-function experiments confirmed pro- and antiviral host factors. Single-cell deep sequencing analysis identified a viral E3 protein mutation altering host gene expression. Lastly, comparison with data from other viruses highlighted common and unique pathways perturbed by infection across evolutionary scales. This study provides a high-resolution characterization of the cellular response to VEEV infection, identifies candidate targets for antivirals, and establishes a comparative single-cell approach to study the evolution of virus-host interactions.

2020-02-25 | GSE145815 | GEO

Single-cell transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection

Project description:Neurotropic alphaviruses such as Venezuelan equine encephalitis virus (VEEV) are critical human pathogens that continually expand to naïve populations and for which there are no licensed vaccines or therapeutics. The neuropathology of VEEV has been attributed to the immune response in the brain yet the underlying mechanisms and specific immune cell populations involved are not fully elucidated. In this study, a murine model of lethal VEEV infection is paired with single-cell RNA sequencing to transcriptionally profile the immune response longitudinally in the brain following infection. Infection-induced immune changes in the brain was also compared to changes in peripheral blood mononuclear cells (PBMCs). The results define an inflammatory response involving transcriptionally distinct subpopulations of activated microglia and infiltrating proinflammatory myeloid populations and cytotoxic lymphocytes. This study advances our understanding of the immune mechanisms underlying viral encephalitis toward the goal of identifying new therapeutic targets.

2024-12-09 | GSE274566 | GEO

BDGR-49 protects BALB/c mice from lethal, intranasal challenge of Venezuelan Equine Encephalitis Virus

Project description:Venezuelan, Western and Eastern Equine Encephalitis Virus (VEEV, WEEV and EEEV), genus Alphavirus, causes a febrile illness that may result in fatal neurological disease which has no FDA-approved antivirals for the prevention or treatment. To address this gap, we developed a novel brain-penetrant, small molecule, BDGR-49, which when administered subcutaneously at 6 mg/kg twice per day for 6 days conferred 100% protection against a lethal intranasal challenge of VEEV Trinidad donkey (TrD) in BALB/c mouse model. By eight days post-infection (dpi), viral load in the brain of BDGR-49-treated mice was significantly reduced whereas TrD-infected, sham-treated mice succumbed to disease on 5 dpi. Analysis of the host responses in the brains of VEEV TrD-infected, BDGR-49-treated, mice resulted in a significant reduction in expression of genes in pathways associated with inflammation and cell death.

2025-01-06 | GSE277300 | GEO

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