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Single cell transcriptional dynamics of flavivirus infection

ABSTRACT: Single cell transcriptional dynamics of flavivirus infection

PROVIDER: PRJNA433871 | ENA |

REPOSITORIES: ENA

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Single cell transcriptional dynamics of flavivirus infection

Project description:Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.

2018-02-27 | GSE110496 | GEO

Single-cell transcriptional dynamics of flavivirus infection.

Project description: Not available

| S-EPMC5826272 | biostudies-literature

TMEM41B is a pan-flavivirus host factor

Project description:Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection. Based on our mechanistic studies we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.

2020-11-24 | GSE162040 | GEO

Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics

Project description:Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics

| PRJNA665227 | ENA

RIPK3-dependent transcriptional program in flavivirus-infected neurons

Project description:RIPK3-dependent transcriptional program in flavivirus-infected neurons

| PRJNA503843 | ENA

Oligodendrocyte-derived IL-33 functions as a microglial survival factor during neuroinvasive flavivirus infection

Project description:In order to recover from infection, organisms must balance robust immune responses to pathogens with the tolerance of immune-mediated pathology. This balance is particularly critical within the central nervous system, whose complex architecture, essential function, and limited capacity for self-renewal render it susceptible to both pathogen- and immune-mediated pathology. Here, we identify the alarmin IL-33 and its receptor ST2 as critical for host survival to neuroinvasive flavivirus infection. We identify oligodendrocytes as the critical source of IL-33, and microglia as the key cellular responders. Notably, we find that the IL-33/ST2 axis does not impact viral control or adaptive immune responses; rather, it is required to promote the activation and survival of microglia. In the absence of intact IL-33/ST2 signaling in the brain, neuroinvasive flavivirus infection triggered aberrant recruitment of monocyte-derived peripheral immune cells, increased neuronal stress, and neuronal cell death, effects that compromised organismal survival. These findings identify IL-33 as a critical mediator of CNS tolerance to pathogen-initiated immunity and inflammation.

2023-11-08 | GSE241804 | GEO

Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

Project description:Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

| PRJNA854905 | ENA

Flavivirus

Project description:Flavivirus, Zika virus Genome sequencing and assembly

| PRJNA394139 | ENA

An RNA-centric dissection of host complexes controlling flavivirus infection

Project description:An RNA-centric dissection of host complexes controlling flavivirus infection

| PRJNA430080 | ENA

A multiplex targeted mass spectrometry assay for one-shot flavivirus diagnosis

Project description:Targeted proteomic mass spectrometry is emerging as a salient clinical diagnostic tool to track protein biomarkers. Yet, its strong analytical properties have not been exploited in the diagnosis and typing of flavivirus. Here, we report the development of a highly sensitive and specific single-shot robust assay for flavivirus typing and diagnosis using targeted mass spectrometry technology. Our flavivirus parallel reaction monitoring assay (fvPRM) has the ability to track secreted flaviviral non-structural protein 1 (NS1) over a broad diagnostic and typing window with high sensitivity, specificity, extendibility and multiplexing capability. These features, pivotal and pertinent to efficient response towards flavivirus outbreaks, including newly emerging flavivirus strains, and circumvent the limitations of current diagnostic assays. fvPRM thus carries high potential in positioning itself as a forerunner in delivering early and accurate diagnosis for disease management.

2019-03-25 | PXD006922 | Pride

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