Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1038769 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:One of three models used to describe dynamics of COVID-19 spread in Ethiopia. Here the two investigated population groups healthcare workers and community members are modeled as separate but interacting groups.
Results are published in https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(21)00386-7/fulltext
2023-01-04 | MODEL2212310001 | BioModels
Project description:Variations in the susceptibility to SARS-CoV-2 infection and risk of severe disease are yet not well understood. The information on the human pathways and active members of the microbiome that can affect SARS-CoV-2 susceptibility and disease progression in the saliva is very scarce. Here, we studied 10 hospitalized patients with severe and moderate COVID-19 (Scov and Mcov) at an early stage of the disease during April to June 2020, compared to 10 uninfected individuals, including healthcare workers with repeated high-risk exposures to the virus but not infected (Non-susceptible, Nsus) and subjects who became infected during the follow-up (susceptible, Non-COVID, Ncov). We performed high-throughput proteomic profiling in saliva to determine the human pathways and active members of the microbiome across individuals. We detected differentially expressed proteins between groups, being the differences especially remarkable in the comparison between the non-infected vs the non-susceptible groups. In a functional analysis to correlate the putative protein biomarkers with relevant biological functions, we found increased expression of proteins related to inflammatory responses and central cellular processes and decreased expression of molecules involved in antiviral activity. The most noteworthy are the Cystatin family, protective molecules present at the oral cavity, the Calprotectin family involved in cell cycle progression, or the Histone family related to nucleosome functions. Furthermore, since proteomics allows checking microbiome functionality, we explored bacterial products and found in the COVID-19+ group 4 overrepresented genera and 2 phyla together with 4 main functional features (KOs) related to ribosomal proteins. Finally, we studied correlations with the plasma activity of the molecular target of SARS-CoV-2, ACE2, and found a link with two proteins related to protein transport through the microtubules in the cytoplasm (DYBC1 and MAPR1). Our study delineates new mechanisms of SARS-CoV-2 susceptibility and progression to severe disease that may help find better therapies for COVID-19.
2024-05-31 | PXD032333 | Pride
Project description:Fifty healthcare workers (HCW) who had received Mycobacterium-w (Mw) and at least one dose of ChAdOx1 nCoV-19 vaccine subsequently (Mw+ChAdOx1 group) were monitored for symptomatic COVID-19, during a major outbreak with the delta variant of SARS-CoV-2 (April-June, 2021) in India, along with 201 HCW receiving both doses of the vaccine without Mw (ChAdOx1 group). Bulk RNA-Seq analysis was carried out on 4 subjects enrolled from each group.
2023-02-28 | GSE216811 | GEO
Project description:The role of geospatial disparities in the dynamics of the COVID-19 pandemic is poorly understood. We developed a spatially-explicit mathematical model to simulate transmission dynamics of COVID-19 disease infection in relation with the uneven distribution of the healthcare capacity in Ohio, U.S. The results showed substantial spatial variation in the spread of the disease, with localized areas showing marked differences in disease attack rates. Higher COVID-19 attack rates experienced in some highly connected and urbanized areas (274 cases per 100,000 people) could substantially impact the critical health care response of these areas regardless of their potentially high healthcare capacity compared to more rural and less connected counterparts (85 cases per 100,000). Accounting for the spatially uneven disease diffusion linked to the geographical distribution of the critical care resources is essential in designing effective prevention and control programmes aimed at reducing the impact of COVID-19 pandemic.
2024-09-02 | BIOMD0000000969 | BioModels
Project description:Prediction of baseline oral microbiota for clinical classification post COVID-19 infection
| PRJNA1108339 | ENA
Project description:The on-going COVID-19 pandemic requires a deeper understanding of the long-term antibody responses that persist following SARS-CoV-2 infection. To that end, we determined epitope-specific IgG antibody responses in COVID-19 convalescent sera collected at 5 months post-diagnosis and compared that to sera from naïve individuals. Each serum sample was reacted with a high-density peptide microarray representing the complete proteome of SARS-CoV-2 as 15 mer peptides with 11 amino acid overlap and homologs of spike glycoprotein, nucleoprotein, membrane protein, and envelope small membrane protein from related human coronaviruses. Binding signatures were compared between COVID-19 convalescent patients and naïve individuals using the web service tool EPIphany.
2022-02-05 | E-MTAB-10740 | biostudies-arrayexpress
Project description:We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found.
2021-03-03 | GSE168018 | GEO
Project description:We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found.
2021-03-03 | GSE168017 | GEO
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to coronavirus disease 2019 (Covid-19) which has caused worldwide pandemic infection. Yet due to unknown reason, certain COVID-19 patients exhibit severe inflammatory reactions associated with cytokine storm and neutrophil infiltration and neutrophil extracellular traps (NETs) in the lung, leading to further complications of SARS-CoV-2 infection. To find out whether the cause of lung injury in COVID-19 patients is due to increased reactive oxygen species and subsequently NET formation we have compared the post-mortem lung biopsies of deceased COVID-19 patients to normal lung tissues using RNA-Seq analysis.
2023-01-31 | GSE208076 | GEO