Ontology highlight
ABSTRACT:
PROVIDER: PRJNA926971 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Zika virus reinfection events evidenced through intra-host genomic diversity and antibody response analysis
| PRJEB63302 | ENA
Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. ZIKV infections are associated with neurodevelopmental deficiencies termed Congenital Zika Syndrome. ZIKV strains are grouped into three phylogenetic lineages: East African, West African, and Asian, which contains the American lineage. RNA virus genomes exist as genetically-related sequences. The heterogeneity of these viral populations is implicated in viral fitness, and genome diversity is correlated to virulence. This study examines genetic diversity of representative ZIKV strains from all lineages utilizing next generation sequencing (NGS). Inter-lineage diversity results indicate that ZIKV lineages differ broadly from each other; however, intra-lineage comparisons of American ZIKV strains isolated from human serum or placenta show differences in diversity when compared to ZIKVs from Asia and West Africa. This study describes the first comprehensive NGS analysis of all ZIKV lineages and posits that sub-consensus-level diversity may provide a framework for understanding ZIKV fitness during infection.
2018-12-31 | E-MTAB-5945 | biostudies-arrayexpress
Project description:To better understand the critical drivers of Zika virus pathogenicity, we used microarray analysis to evaluate the host responses triggered by Zika virus infection in MRC-5 cells.
2021-03-23 | E-MTAB-10292 | biostudies-arrayexpress
Project description:To search for host factors regulating Zika virus infection, we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid human ESCs. The regulators were identified by the quantification of enrichment of their mutant clones within a pooled loss-of-function library upon Zika virus infection.
2023-05-31 | E-MTAB-11945 | biostudies-arrayexpress
Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. Live attenuated vaccines have been successfully used to combat infection by flaviviruses, such as yellow fever and Japanese encephalitis viruses. A Zika virus harboring combined mutations in the envelope protein glycosylation site and in the nonstructural 4B protein amino acid 36 (ZE4B-36) was generated and assessed for stability, attenuation, and protection against infection. To determine the genetic stability of its RNA genome, ZE4B-36 was serially passaged in vitro in Vero cells. Virus harvested from passages (P)1 to P6 was subjected to next generation sequencing and downstream analysis to determine its nucleotide sequence variability. Specifically, single nucleotide variant analysis showed that the ZE4B-36 genome decreased its genetic diversity and resulted in a more stable nucleotide sequence. Thus, in addition to showing attenuation and protection, ZE4B-36 is a stable live attenuated virus that possesses characteristics important for a vaccine to combat Zika disease.
2021-12-31 | E-MTAB-9496 | biostudies-arrayexpress
Project description:Host and genetic viral adaptations enable development of an immunocompetent mouse model of Zika virus infection. This study explored the effect of wildtype Zika virus (ZIKV) and mouse adapted ZIKV infection on the transcriptional profile of mouse adult neuronal stem cells.
2018-04-05 | GSE112711 | GEO
Project description:Zika virus was inoculated at mid gestation (day 50) in to either intra cerebrally, or interperotoneally and intra amniotic. Controls were mock injected and subject to similar surgical proceedures. Fetal tissue were obtained. Sampled fetal brains are from littermates and are not the fetus directly infected. After 28 days post infection.
2017-09-18 | GSE103932 | GEO
Project description:Purpose: The goal of this study was to compare NGS-derived mRNA transcriptome and miRNA expression profiles between Zika virus-infected A549 cells and control A549 cells to identify differentially expressed mRNAs and miRNAs. Methods: Zika virus-infected A549 cells and control A549 cells were subjected to mRNA sequencing and small RNA sequencing in biological triplicates using the Illumina HiSeq 4000 platform. For mRNA sequencing analysis, transcriptome profiles were generated by deep sequencing. The mapped reads of each sample were assembled by StringTie (v1.3.1) using a reference-based approach to assemble and quantify full-length transcripts representing multiple splice variants for each gene locus. For small RNA sequencing analysis, miRNA expression profiles were generated from small RNA sequencing data. Raw small RNA sequencing reads were filtered to obtain clean reads, which were aligned to the human reference genome using Bowtie. The DESeq R package (version 1.8.3) was used to identify differentially expressed miRNAs between Zika virus-infected and control A549 cells. Results: Sequencing analysis identified differentially expressed mRNAs and miRNAs between Zika virus-infected and control A549 cells. The sequencing data provide comprehensive mRNA and miRNA expression profiles for further analysis of host responses following Zika virus infection. Conclusions: This study provides a comprehensive characterization of the transcriptome and miRNA expression profiles of A549 cells following Zika virus infection using next-generation sequencing approaches. These sequencing data will facilitate further studies of host responses associated with Zika virus infection.
2020-03-06 | GSE146423 | GEO
Project description:In individuals highly exposed to hepatitis C virus (HCV), reinfection is common, suggesting that natural development of sterilising immunity is difficult. In those that are reinfected, some will develop a persistent infection, while a small proportion repeatedly clear the virus, suggesting natural protection is possible. The aim of this study was to characterise immune responses associated with rapid natural clearance of HCV reinfection. Broad neutralising antibodies (BnAbs) and Envelope 2 (E2)-specific memory B cell (MBCs) responses were examined longitudinally in 15 subjects with varied reinfection outcomes. BnAb responses were associated with MBC recall, but not with reinfection clearance. Strong evidence of antigen imprinting was found, and the B cell receptor repertoire showed a high level of clonality with ongoing somatic hypermutation of many clones over subsequent reinfection events. Single cell transcriptomic analyses showed that cleared reinfections featured an activated transcriptomic profile in HCV-specific B cells that rapidly expanded upon reinfection. MBC quality, but not necessarily breadth of nAb responses, is important for protection against antigenically diverse variants, which is encouraging for HCV vaccine development.
2024-06-13 | GSE269792 | GEO
Project description:Zika virus (ZIKV) jeopardizes fetal health through both vertical transmission and placental disorders, while the regulatory mechanisms and therapeutic opportunities remain elusive. Here, we reveal cyclophilin A (CypA) as a critical host factor necessary for placental ZIKV replication, functioning independently of its isomerase activity and calcineurin-dependent pathway.
2026-04-22 | GSE308795 | GEO