SARS COV-2 Genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB52543 | ENA |
REPOSITORIES: ENA
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Project description:A pivotal role of astrocytes in the pathophysiology of CNS disorders during the SARS-CoV-2 infection of brain has been proposed. Thus, the study was performed to reveal astrocyte response to infection caused by either Omicron or Delta variant.
2025-03-01 | E-MTAB-14745 | biostudies-arrayexpress
Project description:The objective of the study was to characterize the immunoreactivity profiles of IgG-reactive epitopes in COVID-19 patients with distinct disease trajectories as well as SARS-CoV-2-naïve sera, using a high-density SARS-CoV-2 whole proteome peptide microarray. The microarray comprised of a total of 5347 individual peptides, each consisting of 15 amino acids with an overlap of 13 amino acids printed in duplicate. The microarray also had a panel of the most relevant mutations from SARS-CoV-2 variants of concern like omicron, alpha, beta, gamma, delta, and others. This study consisted of 29 participants, including 10 naïve controls (5 pre-pandemic and 5 SARS-CoV-2 seronegative) and 19 RT-PCR-confirmed COVID-19 patients. The COVID-19 patients were stratified into two distinct cohorts based on their disease trajectories: the severe cohort (S), in which the patients presented moderate COVID-19 symptoms initially but eventually progressed toward severity; and the recovered cohort (R), in which severe COVID-19 patients progressed toward recovery. Our findings contribute to a deeper understanding of the immunopathogenesis of COVID-19 in patients with different disease trajectories, the effect of mutations on immunoreactivity, and potential cross-reactivity due to exposure to common cold viruses.
2025-03-31 | E-MTAB-14495 | biostudies-arrayexpress
Project description:For the assessment of host response dynamics to SARS-CoV and SARS-CoV-2 infections in human airway epithelial cells at ambient temperature corresponding to the upper or lower respiratory tract. We performed a temporal transcriptome analysis on human airway epithelial cell (hAEC) cultures infected with SARS-CoV and SARS-CoV-2, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. hAEC cultures were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq), which allows a rapid and sensitive genome-wide transcriptomic analysis in a highly multiplexed manner. Transcriptome data was obtained from a total of 7 biological donors for pairwise comparisons of SARS-CoV or SARS-CoV-2 virus-infected to unexposed hAEC cultures at respective time points and temperatures.
2020-11-27 | E-MTAB-9781 | biostudies-arrayexpress
Project description:To investigate the virological properties of a SARS-CoV-2 variant, Omicron BA.2, we generated chimeric recombinant viruses that express GFP and encodes the S gene of B.1.1 (ancestral D614G-bearing virus), Delta, BA.1 and BA.2. To verify the genome sequence of the working viruses, we performed viral RNA-sequencing of the viral stock.
2022-02-16 | GSE196649 | GEO
Project description:The recent SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent in the coming months, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Liquid chromatography-mass spectrometry (LC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers become well-established. This study demonstrates the potential to establish SARS-CoV-2 peptide markers by examining amino-acid variant-containing tryptic peptides, their MS fragmentation intensities, and their detection sensitivity in MS experiments. We have synthesized model tryptic peptides from of SARS-CoV-2 variants beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time.
2022-10-12 | PXD033777 | Pride
Project description:To explore the relationship between SARS-CoV-2 infection in different time before operation and postoperative main complications (mortality, main pulmonary and cardiovascular complications) 30 days after operation; To determine the best timing of surgery after SARS-CoV-2 infection.
| 12454 | ecrin-mdr-crc
Project description:In this study, we tested the efficacy of five commercial probes panels at detecting SARS-CoV-2 genome including panels from Illumina, Twist Bioscience and Arbor Bioscience. To do so, we used 19 patient nasal swab samples broken down into 5 series of 4 samples of equivalent SARS-CoV-2 viral load (cycle threshold (CT): low CT means a high viral load – CT26, CT29, CT32, CT35 and CT36+).
2022-06-01 | E-MTAB-11236 | biostudies-arrayexpress
Project description:HAE cultures were infected with SARS-CoV, SARS-dORF6 or SARS-BatSRBD and were directly compared to A/CA/04/2009 H1N1 influenza-infected cultures. Cell samples were collected at various hours post-infection for analysis. Time Points = 0, 12, 24, 36, 48, 60, 72, 84 and 96 hrs post-infection for SARS-CoV, SARS-dORF6 and SARS-BatSRBD. Time Points = 0, 6, 12, 18, 24, 36 and 48 hrs post-infection for H1N1. Done in triplicate for RNA Triplicates are defined as 3 different wells, plated at the same time and using the same cell stock for all replicates. Time matched mocks done in triplicate from same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) will be used for the mock infections. Infection was done at an MOI of 2 for SARS viruses and an MOI of 1 for H1N1.
2013-07-31 | E-GEOD-47962 | biostudies-arrayexpress
Project description:A critical aspect of the mechanism of SARS-CoV-2 infection is the protease-mediated activation of the viral spike (S) protein. The type II transmembrane serine protease TMPRSS2 is crucial for SARS-CoV-2 infection in lung epithelial Calu-3 cells and murine airways. However, the importance of TMPRSS2 needs to be re-examined because the ability to utilize TMPRSS2 is significantly reduced in the Omicron variants that spread globally. For this purpose, replication profiles of SARS-CoV-2 were analyzed in human respiratory organoids. All tested viruses, including Omicron variants, replicated efficiently in these organoids. Notably, all SARS-CoV-2 strains retained replication ability in TMPRSS2-gene knockout (KO) respiratory organoids, suggesting that TMPRSS2 is not essential for SARS-CoV-2 infection in human respiratory tissues. However, TMPRSS2-gene knockout significantly reduces the inhibitory effect of nafamostat, suggesting the advantage of TMPRSS2-utilizing ability for the SARS-CoV-2 infection in these organoids. Interestingly, Omicron variants regained the TMPRSS2-utilizing ability in recent subvariants. The basal infectivity would be supported mainly by cathepsins because the cathepsin inhibitor, EST, showed a significant inhibitory effect on infection with any SARS-CoV-2 strains, mainly when used with nafamostat. A supplementary contribution of other serine proteases was also suggested because the infection of the Delta variant was still inhibited partially by nafamostat in TMPRSS2 KO organoids. Thus, various proteases, including TMPRSS2, other serine proteases, and cathepsins, co-operatively contribute to SARS-CoV-2 infection significantly in the respiratory organoids. Thus, SARS-CoV-2 infection in the human respiratory tissues would be more complex than observed in cell lines or mice.
2024-11-20 | GSE279753 | GEO
Project description:HAE cultures were infected with SARS-CoV, SARS-dORF6 or SARS-BatSRBD and were directly compared to A/CA/04/2009 H1N1 influenza-infected cultures. Cell samples were collected at various hours post-infection for analysis. Time Points = 0, 12, 24, 36, 48, 60, 72, 84 and 96 hrs post-infection for SARS-CoV, SARS-dORF6 and SARS-BatSRBD. Time Points = 0, 6, 12, 18, 24, 36 and 48 hrs post-infection for H1N1. Done in triplicate or quadruplicate for RNA Triplicates/quadruplicates are defined as 3/4 different wells, plated at the same time and using the same cell stock for all replicates. Time matched mocks done in triplicate from same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) will be used for the mock infections. Infection was done at an MOI of 2.
2013-07-31 | E-GEOD-47960 | biostudies-arrayexpress