Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1078389 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28015478_1.fastq.gz | Fastqsanger.gz | |||
| SRR28015478_2.fastq.gz | Fastqsanger.gz | |||
| SRR28015479_1.fastq.gz | Fastqsanger.gz | |||
| SRR28015479_2.fastq.gz | Fastqsanger.gz | |||
| SRR28015480_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 572 |
Similar Datasets
Project description:Microbiome analysis of oropharyngeal and nasopharyngeal samples of SARS-CoV-2 infected patients
2021-02-06 | GSE166281 | GEO
Project description:During the COVID-19 pandemic, thousands of pregnant women have been infected with SARS-CoV-2 worldwide. The short- and long-term implications of maternal SARS-CoV-2 infection on fetal and childhood well-being are unknown. To characterize the fetal immune response to maternal SARS-CoV-2 infection, we performed single-cell RNA sequencing and T cell receptor sequencing on cord blood mononuclear cells from infants born to mothers infected with SARS-CoV-2 in the third trimester. We identified widespread gene expression changes in cord blood leukocytes, including upregulation of interferon-stimulated genes (ISG) and of HLA genes in CD14+ monocytes; decreased activation of CD16+ monocytes; activation of plasmacytoid dendritic cells; and activation and exhaustion of NK cells and T CD8+ cells in the cord blood of infants born to SARS-CoV-2+ mothers. Lastly, we observed fetal TCR repertoire clonal expansion in cord blood T cells from pregnancies complicated by maternal SARS-CoV-2 infection. Our results suggest that even in the absence of vertical transmission, SARS-CoV-2 maternal infection in the third trimester modulates the fetal immune system.
2021-04-06 | GSE165193 | GEO
Project description:SARS-CoV-2 infection alters both the nasopharyngeal microbiota and host inflammatory environment. In this study, nasopharyngeal samples collected in Chile during different phases of the pandemic were analyzed using 16S rRNA gene sequencing (V3–V4) and RT-qPCR quantification of IL-2, TNF-α, IFN-γ and IL-1ra. Machine-learning models (Random Forest and K-Nearest Neighbors) were applied to integrate microbial community profiles, cytokine expression, and SARS-CoV-2 variants (Gamma, Lambda, Delta). The results show variant-dependent immunomicrobial signatures characterized by TNF-α-driven inflammation and the expansion of opportunistic bacterial genera such as Acinetobacter, Prevotella, and Staphylococcus. These findings provide a comprehensive overview of the interplay between viral infection, microbiome structure, and inflammatory responses and highlight the utility of combining microbiome and cytokine profiling with machine-learning approaches to discriminate infection outcomes across SARS-CoV-2 variants.
2026-01-30 | GSE311689 | GEO
Project description:Respiratory viruses such as SARS-CoV-2 are pathogens that can reach pandemic proportions. The early human response to respiratory viruses are in the nasal cavity and nasopharyngeal regions. Defining biomarkers of disease trajectory at the time of a positive test is important for opting for treatment and monitoring decisions. We hypothesize that the nasopharyngeal tRNA profiles can be used to predict symptom severity resulting from SARS-CoV-2 infection. We carried out multiplex small RNA sequencing (MSR-seq) on nasopharyngeal swaps to measure the human tRNA response to SARS-CoV-2 infection. Our result simultaneously measured full-length tRNA abundance, tRNA modifications, and tRNA fragmentation among individuals that went on to develop no/mild or severe symptoms. We identified distinct tRNA signatures that can predict the clinical outcome of SARS-CoV-2 infected individual at the time of a positive test. These results highlight the utility of using host tRNA properties as biomarkers for clinical applications.
2022-10-01 | GSE208612 | GEO
Project description:Differences in immune profiles of children and adults with COVID-19 have been previously described. However, no systematic studies have been reported from infants hospitalized with severe disease. We applied a multidimensional approach to decipher the immune responses of SARS-CoV-2 infected infants (n=26; 10 subacute, 11 moderate and 5 severe disease; median age=1.6 months) and matched controls (n=14; median age=2 months). Single cell (scRNA-seq) profiling of PBMCs revealed substantial alterations in cell composition in SARS-CoV-2 infected infants; with most cell-types switching to an interferon-stimulated gene (ISGhi) state including: (i) CD14+ monocytes co-expressing ISGs and inflammasome-related molecules, (ii) ISGhi naïve CD4+ T cells, (iii) ISGhi proliferating cytotoxic CD8+ T cells, and (iv) ISGhi naïve and transitional B cells. We observe increased serum concentrations of both interferons and inflammatory cytokines in infected infants. Antibody responses to SARS-CoV-2 are also consistently detect in the absence of anti-IFN autoantibodies. Compared with infected adults, infants display a similar ISG signature in monocytes but a markedly enhanced ISG signature in T and B cells. These findings provide insights into the distinct immune responses to SARS-CoV-2 in the first year of life and underscore the importance of further defining the unique features of early life immunity.
2025-03-31 | GSE206289 | GEO
Project description:The clinical phenotype of infants infected with respiratory syncytial virus (RSV) differs from that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. RSV is the leading cause of hospitalization for lower respiratory tract infection and carries a significant higher risk of respiratory failure compared to SARS-CoV-2, which has been generally linked to fever and croup in young infants. The underlying mechanisms these differences remain unclear. We analyzed peripheral blood mononuclear cells (PBMCs) and serum from infants infected with SARS-CoV-2 (n=30), RSV (n=19), and healthy controls (n=17) using single-cell RNA sequencing, single-nucleus ATAC sequencing and cytokine profiling. Both viruses triggered type I interferon responses across PBMC subsets but differed in their NK cell and inflammatory responses. Severe RSV cases were characterized by lower NK cell percentages, lower IFNG expression and diminished chromatin accessibility at T-BET and EOMES binding sites in NK cells. Furthermore, RSV infections were associated with increased frequencies of CD4+ TEMRA and memory Treg cells. In contrast, SARS-CoV-2 infections were marked by more pronounced pro-inflammatory signatures, including increased transcriptional and epigenetic activity at NFKB factors and higher serum TNF concentrations. These findings highlight distinct immune response pathways in RSV and SARS-CoV-2 infections that may inform future therapeutic strategies.
2026-01-15 | GSE283744 | GEO
Project description:To evaluate the gene expression profiling of peripheral leukocytes in different outcomes of SARS-CoV-2 infections, whole blood samples were collected from individuals with positive SARS-CoV-2 nasopharyngeal swab by RT-PCR (54 patients) and healthy uninfected individuals (12 volunteers). Infected patients were classified into mild, moderate, severe and critical groups according to a modified statement in the Novel Coronavirus Pneumonia Diagnosis and Treatment Guideline. Blood were collected into EDTA tubes and the buffy coat samples were stored in TRIzol reagent at -80 °C until use for RNA extraction. Affymetrix Clariom S array was used to perform the high-throughput gene expression profiling. Microarray analyses were performed using APT Affymetrix software, R packages and Bioconductor libraries. This systemic view of SARS-CoV-2 infections through blood transcriptomics will foster the understanding about molecular mechanisms and immunopathological processes involved in COVID-19 disease and its different outcomes.
2022-04-29 | E-MTAB-11240 | biostudies-arrayexpress
Project description:Healthcare workers were recruited at St Bartholomew’s Hospital, London, UK in the week of lockdown in the United Kingdom (between 23rd and 31st March 2020). Participants underwent weekly evaluation using a questionnaire and biological sample collection (including serological assays) for up to 16 weeks when attending for work and self-declared as fit to attend work at each visit, with further follow up samples collected at 24 weeks. Blood RNA sequencing data was to be used to identify host-response biomarkers of early SARS-CoV-2 infection, to evaluate existing blood transcriptomic signatures of viral infection, and to describe the underlying biology during SARS-CoV-2 infection. This submission includes a total of 172 blood RNA samples from 99 participants. Of these, 114 samples (including 16 convalescent samples collected 6 months after infection) were obtained from 41 SARS-CoV-2 cases, with the remaining 58 from uninfected controls. Participants with available blood RNA samples who had PCR-confirmed SARS-CoV-2 infection during follow-up were included as ‘cases’. Those without evidence of SARS-CoV-2 infection on nasopharyngeal swabs and who remained seronegative by both Euroimmun anti S1 spike protein and Roche anti nucleocapsid protein throughout follow-up were included as uninfected controls. ‘Cases’ include all available RNA samples, including convalescent samples at week 24 of follow-up for a subset of participants. For uninfected controls, we included baseline samples only. Sample class denotes weekly interval to positive SARS-CoV-2 PCR; non-infected controls (NIC); convalescent samples (Conv)_.
2021-07-07 | E-MTAB-10022 | biostudies-arrayexpress
Project description:The SARS-CoV-2 virus is continuously evolving, with appearance of new variants characterized by multiple genomic mutations, some of which can affect functional properties, including infectivity, interactions with host immunity, and disease severity. The rapid spread of new SARS-CoV-2 variants has highlighted the urgency to trace the virus evolution, to help limit its diffusion, and to assess effectiveness of containment strategies. We propose here a PCR-based rapid, sensitive and low-cost allelic discrimination assay panel for the identification of SARS-CoV-2 genotypes, useful for detection in different sample types, such as nasopharyngeal swabs and wastewater. The tests carried out demonstrate that this in-house assay, whose results were confirmed by SARS-CoV-2 whole-genome sequencing, can detect variations in up to 10 viral genome positions at once and is specific and highly sensitive for identification of all tested SARS-CoV-2 clades, even in the case of samples very diluted and of poor quality, particularly difficult to analyze.
2022-06-03 | E-MTAB-11261 | biostudies-arrayexpress
Project description:The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus’s effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways
2023-05-25 | E-MTAB-13028 | biostudies-arrayexpress