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.
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.
Project description:A detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and individuals infected with SARS-CoV-2 involving high throughput quantitative (iTRAQ) proteomics analysis.
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+).
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+).
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+).
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+).
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+).
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+).
Project description:SARS-CoV-2 has created a global disease burden infecting >100 million humans in just over a year. In this study, we adopted a SISCAPA-based enrichment approach using anti-peptide antibodies generated against peptides from the nucleocapsid protein of SARS-CoV-2. We developed a targeted workflow in which nasopharyngeal samples were digested followed by enrichment of viral peptides using the anti-peptide antibodies and targeted parallel reaction monitoring (PRM) analysis using a high-resolution mass spectrometer. This workflow was applied to 41 RT-PCR-confirmed clinical nasopharyngeal swab samples and 30 negative samples. The SISCAPA-based platform described in the current study can serve as one of the alternative methods for SARS-CoV-2 viral detection.