Project description:We retrospectively analysed the expression of 579 immunological genes in 60 COVID-19 subjects (SARS +ve) and 59 COVID-negative (SARS -ve) subjects using the NanoString nCounter (Immunology panel), a technology based on multiplexed single-molecule counting. Biobanked Human peripheral blood mononuclear cells (PBMCs) samples underwent Nucleic Acid extraction and digital detection of mRNA to evaluate changes in antiviral gene expression between SARS -ve controls and patients with mild (SARS +ve Mild) and moderate/severe (SARS +ve Mod/Sev) disease.
Project description:The objective of this experiment was to compare the transcriptomic profile (NanoString platform) of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with mild disease, and patients with severe COVID-19 with and without dexamethasone treatment, and healthy controls. We analyzed PBMCs from 4 mild COVID patients, 3 severe COVID patients,4 severe COVID patients treated with dexamethasone, and 5 healthy controls
Project description:Protective immunity against COVID-19 likely depends on the production of SARS-CoV-2 binding plasma cells and memory B cells after infection or vaccination. Previous work has shown evidence that germinal center reactions, a critical component of the B cell response, are disrupted in severe COVID-19. This may adversely affect protective immunity from re-infection. Consistent with an extrafollicular B cell response, severe COVID-19 patients have large scale changes in B cell populations such as elevated frequencies of clonally expanded, class switched, unmutated plasmablasts. However, it is not clear whether mild or asymptomatically infected individuals show similar differences in B cell repertoires. Here, we use single cell RNA sequencing of B cells to show that, in contrast to hospitalized COVID-19 patients, mildly symptomatic COVID-19 subjects have B cell repertoires skewed towards clonally diverse, somatically hypermutated memory B cells approximately 30 days after the onset of symptoms. This provides evidence that B cell responses are less disrupted in mild COVID-19, and that the infection resolves with the production of memory B cells.
Project description:Protective immunity against COVID-19 likely depends on the production of SARS-CoV-2 binding plasma cells and memory B cells after infection or vaccination. Previous work has shown evidence that germinal center reactions, a critical component of the B cell response, are disrupted in severe COVID-19. This may adversely affect protective immunity from re-infection. Consistent with an extrafollicular B cell response, severe COVID-19 patients have large scale changes in B cell populations such as elevated frequencies of clonally expanded, class switched, unmutated plasmablasts. However, it is not clear whether mild or asymptomatically infected individuals show similar differences in B cell repertoires. Here, we use single cell RNA sequencing of B cells to show that, in contrast to hospitalized COVID-19 patients, mildly symptomatic COVID-19 subjects have B cell repertoires skewed towards clonally diverse, somatically hypermutated memory B cells approximately 30 days after the onset of symptoms. This provides evidence that B cell responses are less disrupted in mild COVID-19, and that the infection resolves with the production of memory B cells.
Project description:The SARS-CoV-2 infection elicits widespread immunological reactions and causes severe diseases in some individuals. However, the molecular basis behind the excessive, yet non-productive immune response in COVID-19 patients with severe diseases is not fully understood. Nor is it fully known of the molecular and cellular discrepancies between severe COVID-19 and sepsis caused by other infections. To gain systems-level insights into the pathogenesis of COVID-19, we compared the blood proteome and phosphoproteome of patients under intensive care with or without SARS-CoV-2 infection, and healthy control subjects by quantitative mass spectrometry. SARS-CoV-2 infection causes global reprogramming of the kinome and the phosphoproteome, resulting in incomplete adaptive immune responses mediated by B cells and T cells, compromised innate immune response via inhibitory SIGLEC and SLAM family receptor signaling, and excessive JAK/STAT signaling. Our work identifies the kinases CK2, SYK, JAK2/3, TYK2, and the cytokine IL-12 as potential targets for the immunomodulatory treatment of severe COVID-19 and provides a valuable resource for deciphering the mechanism of pathogen-host interactions.
Project description:Although most SARS-CoV-2-infected individuals experience mild COVID-19, some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly upregulation of the TNF/IL-1beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1beta-driven inflammation, and this was not seen in patients with milder COVID-19 infection. Based on this, we propose that the type I IFN response exacerbates inflammation in patients with severe COVID-19 infection.
Project description:The immunological signatures driving COVID-19 severity in Ghanaians are not well understood. We, therefore, performed bulk transcriptome sequencing of nasopharyngeal samples from SARS-CoV-2-infected Ghanaians with mild and severe COVID-19 and healthy controls to characterize immune signatures at the primary SARS-CoV-2 infection site and identified drivers of disease severity. Generally, a heightened antiviral response was observed in SARS-CoV-2-infected Ghanaians compared with uninfected controls. COVID-19 severity was associated with a dysregulated inflammatory response occasioned by overexpression of IL1A, S100A7, CRNN, and IL23A proinflammatory cytokines and hyperactivation of the NF-κB pathway through MAL signaling. SAMD9L was also among the differentially regulated interferon-stimulated genes (ISGs) in our mild and severe disease cohorts, suggesting that it may be playing a critical role in SARS-CoV-2 pathogenesis. We noted differences in antiviral gene expression by comparing our data with a publicly available dataset from a non-African (Indians) (GSE166530) cohort. Overall, the study identifies immune signatures driving COVID-19 severity in Ghanaians that could serve as potential prognostic markers. It further provides preliminary evidence suggesting differences in antiviral response at the upper respiratory interface in sub-Saharan Africans (Ghanaians) and non-Africans (Indians), which could be contributing to the differences in disease outcomes. Further studies using a larger dataset from different populations will expand on these findings. Keywords: Nasopharyngeal swab, SARS-Cov-2, RNA-Seq, Ghanaians, immunological signatures
Project description:In order to identify differentially abundant proteins, human plasma samples from COVID-19 patients with either a mild or moderate (MM) or a critical or severe (CS) disease course from acute phase of infection were analyzed on antibody microarrays 998 different proteins by 1,425 antibodies.
Project description:In order to identify differentially abundant proteins, human plasma samples from COVID-19 patients with either a mild or moderate (MM) or a critical or severe (CS) disease course from the acute phases of infection were analyzed on antibody microarrays targeting 351 different proteins by 517 antibodies.
Project description:The causative organism, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibits a wide spectrum of clinical manifestations in disease-ridden patients. Differences in the severity of COVID-19 ranges from asymptomatic infections and mild cases to the severe form, leading to acute respiratory distress syndrome (ARDS) and multiorgan failure with poor survival. MiRNAs can regulate various cellular processes, including proliferation, apoptosis, and differentiation, by binding to the 3′UTR of target mRNAs inducing their degradation, thus serving a fundamental role in post-transcriptional repression. Alterations of miRNA levels in the blood have been described in multiple inflammatory and infectious diseases, including SARS-related coronaviruses. We used microarrays to delineate the miRNAs and snoRNAs signature in the peripheral blood of severe COVID-19 cases (n=9), as compared to mild (n=10) and asymptomatic (n=10) patients, and identified differentially expressed transcripts in severe versus asymptomatic, and others in severe versus mild COVID-19 cases. A cohort of 29 male age-matched patients were selected. All patients were previously diagnosed with COVID-19 using TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, Waltham, Massachusetts), or Cobas SARS-CoV-2 Test (Roche Diagnostics, Rotkreuz, Switzerland), with a CT value < 30. Additional criterion for selection was age between 35 and 75 years. Participants were grouped into severe, mild and asymptomatic. Classifying severe cases was based on requirement of high-flow oxygen support and ICU admission (n=9). Whereas mild patients were identified based on symptoms and positive radiographic findings with pulmonary involvement (n=10). Patients with no clinical presentation were labelled as asymptomatic cases (n=10).