Viruses
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA227014 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Respiratory Virus Enrichment Method for Genomic Sequencing and Identification
| PRJNA448596 | ENA
Project description:Identification of novel sugarcane viruses through high-throughput sequencing
| PRJNA242696 | ENA
Project description:To better prepare for future viral outbreaks, scalable and adaptable platforms to study emerging infections are essential. Understanding virus–host interactions, particularly the mechanisms of cell entry, is critical for developing effective therapeutics and vaccines. Current approaches often rely on live virus assays requiring high-containment facilities, limiting speed, scalability, and accessibility. As a proof-of-principle, we developed a novel screening platform—Ceudovitox—using pseudotyped viruses (PVs) bearing the chikungunya virus (CHIKV) envelope protein. These PVs were engineered to express herpes simplex virus-1 thymidine kinase, enabling selective killing of infected cells with ganciclovir. A heterogeneous CRISPR-Cas9 knockout cell pool was then screened using this "killer" PV system, allowing identification of CHIKV entry factors via next-generation sequencing.
2025-07-31 | GSE302317 | GEO
Project description:Zoonotic influenza A viruses of avian origin can cause severe disease in individuals, or even global pandemics, and thus pose a threat to human populations. Waterfowl and shorebirds are believed to be the reservoir for all influenza A viruses, but this has recently been challenged by the identification of novel influenza A viruses in bats. The major bat influenza A virus envelope glycoprotein, haemagglutinin, does not bind the canonical influenza A virus receptor, sialic acid or any other glycan, despite its high sequence and structural homology with conventional haemagglutinins. This functionally uncharacterized plasticity of the bat influenza A virus haemagglutinin means the tropism and zoonotic potential of these viruses has not been fully determined. Here we show, using transcriptomic profiling of susceptible versus non-susceptible cells in combination with genome-wide CRISPR-Cas9 screening, that the major histocompatibility complex class II (MHC-II) human leukocyte antigen DR isotype (HLA-DR) is an essential entry determinant for bat influenza A viruses. Genetic ablation of the HLA-DR α-chain rendered cells resistant to infection by bat influenza A virus, whereas ectopic expression of the HLA-DR complex in non-susceptible cells conferred susceptibility. Expression of MHC-II from different bat species, pigs, mice or chickens also conferred susceptibility to infection. Notably, the infection of mice with bat influenza A virus resulted in robust virus replication in the upper respiratory tract, whereas mice deficient for MHC-II were resistant. Collectively, our data identify MHC-II as a crucial entry mediator for bat influenza A viruses in multiple species, which permits a broad vertebrate tropism.
2022-02-04 | GSE196122 | GEO
Project description:Purpose: Next-generation sequencing (NGS) on targeted locus in Sindbis genome to determine frequency changes of artificial microRNAs expressed by viruses after passaging in cancer and normal cells Methods: RNA was harvested in Trizol 488 (Thermo Fisher). RNA was extracted using the manufacturer’s protocol and quantified by nanodrop. Sequencing was done by SeqMatic on a MiSeq v3 platform generating 75bp reads. Adapters were trimmed using Trimmomatic and adapter-free reads represent artificial microRNAs encoded by Sindbis virus in a sample. Results: We have identified changes in artificial microRNA frequency after passaging virus pool in cancer and normal cells and have identified microRNAs increasing viral fitness in cancer cells. Conclusions: Our study represents artificial microRNAs which target pathways that can aid oncolytic viral replication in cancer cells.
2022-03-02 | GSE197271 | GEO
Project description:Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, we introduce proteomics as a complementary approach for the untargeted identification of human-pathogenic viruses from patient samples. The viral proteomics workflow (vPro-MS) is based on an in-silico derived peptide library covering the human virome in UniProtKB (331 viruses, 20,386 genomes, 121,977 peptides), which was especially designed for diagnostic purposes. A scoring algorithm (vProID score) was developed to assess the confidence of virus identification from proteomics data. In combination with high-throughput diaPASEF-based data acquisition, this workflow enables the analysis of up to 60 samples per day. The specificity was determined to be > 99,9 % in an analysis of 221 plasma, swab and cell culture samples covering 18 different viruses (e.g. SARS, MERS, EBOV, MPXV). The sensitivity of this approach for the detection of SARS-CoV-2 in nasopharyngeal swabs corresponds to a PCR cycle threshold of 27 with comparable quantitative accuracy to metagenomics. vPro-MS enables the integration of untargeted virus identification in large-scale proteomic studies of biofluids such as human plasma to detect previously undiscovered virus infections in patient specimens.
2025-08-04 | PXD055135 | Pride