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:A critical factor in infectious disease control is the risk of an outbreak overwhelming local healthcare capacity. The overall demand on healthcare services will depend on disease severity, but the precise timing and size of peak demand also depends on the time interval (or clinical time delay) between initial infection, and development of severe disease. A broader distribution of intervals may draw that demand out over a longer period, but have a lower peak demand. These interval distributions are therefore important in modelling trajectories of e.g. hospital admissions, given a trajectory of incidence. Conversely, as testing rates decline, an incidence trajectory may need to be inferred through the delayed, but relatively unbiased signal of hospital admissions. Healthcare demand has been extensively modelled during the COVID-19 pandemic, where localised waves of infection have imposed severe stresses on healthcare services. While the initial acute threat posed by this disease has since subsided with immunity buildup from vaccination and prior infection, prevalence remains high and waning immunity may lead to substantial pressures for years to come. In this work, then, we present a set of interval distributions, for COVID-19 cases and subsequent severe outcomes; hospital admission, ICU admission, and death. These may be used to model more realistic scenarios of hospital admissions and occupancy, given a trajectory of infections or cases. We present a method for obtaining empirical distributions using COVID-19 outcomes data from Scotland between September 2020 and January 2022 (N = 31724 hospital admissions, N = 3514 ICU admissions, N = 8306 mortalities). We present separate distributions for individual age, sex, and deprivation of residing community. While the risk of severe disease following COVID-19 infection is substantially higher for the elderly and those residing in areas of high deprivation, the length of stay shows no strong dependence, suggesting that severe outcomes are equally severe across risk groups. As Scotland and other countries move into a phase where testing is no longer abundant, these intervals may be of use for retrospective modelling of patterns of infection, given data on severe outcomes.
Project description:Early in the COVID-19 pandemic, type 2 diabetes (T2D) was marked as a risk-factor for severe disease. Inflammation is central to the aetiology of both conditions where immune responses influence disease course. Identifying at-risk groups through immuno-inflammatory signatures can direct personalised care and help develop potential targets for precision therapy. This observational study characterised immunophenotypic variation associated with COVID-19 severity in T2D. Broad-spectrum immunophenotyping quantified 15 leukocyte populations in circulation from a cohort of 45 hospitalised COVID-19 patients with and without T2D. Lymphocytopenia, of CD8+ lymphocytes, was associated with severe COVID-19 and intensive care admission in non-diabetic and T2D patients. A morphological anomaly of increased monocyte size and monocytopenia of classical monocytes were specifically associated with severe COVID-19 in patients with T2D requiring intensive care. Over-expression of inflammatory markers reminiscent of the type-1 interferon pathway underlaid the immunophenotype associated with T2D. These changes may contribute to severity of COVID-19 in T2D. These findings show characteristics of severe COVID-19 in T2D as well as provide evidence that type-1 interferons may be actionable targets for future studies.
Project description:IntroductionChronic kidney disease (CKD) is a risk factor for acquiring severe COVID-19, but underlying mechanisms are unknown. We aimed to study the risk associated with CKD for severe COVID-19 outcomes in relation to body mass index (BMI) and diabetes because they are common risk factors for both CKD and severe COVID-19.MethodsThis nationwide case-control study with data from mandatory national registries included 4684 patients (cases) admitted to the intensive care units (ICUs) requiring mechanical ventilation and 46,840 population-based controls matched by age, sex, and district of residency. Logistic regression was used to calculate odds ratios (ORs) with 95% confidence intervals (CIs) for associations between severe COVID-19 and exposures with adjustment for confounders, in subgroups by BMI, and matched by type 2 diabetes.ResultsThe median age was 64 years, and 27.7% were female. CKD was observed in 5.4% of the cases and 1.5% of the controls, whereas 1.9% and 0.3% had end-stage CKD, respectively. CKD was associated with severe COVID-19 (OR, 2.20 [95% CI, 1.85-2.62]), continuous renal replacement therapy (CRRT) in ICU (OR, 7.36 [95% CI, 5.39-10.05]), and death any time after ICU admission (OR, 2.51 [95% CI, 1.96-3.22]). The risk associated with CKD for severe COVID-19 did not differ significantly by weight but was higher in those without diabetes (OR, 2.76 [95% CI, 2.15-3.55]) than in those with diabetes (OR, 1.88 [95% CI, 1.37-2.59]).ConclusionCKD, especially end-stage CKD, is an important risk factor for severe COVID-19 and death after ICU admission also in patients with normal BMI and without type 2 diabetes.
Project description:Despite extensive global research into genetic predisposition for severe COVID-19, knowledge on the role of rare host genetic variants and their relation to other risk factors remains limited. Here, 52 genes with prior etiological evidence were sequenced in 1,772 severe COVID-19 cases and 5,347 population-based controls from Spain/Italy. Rare deleterious TLR7 variants were present in 2.4% of young (<60 years) cases with no reported clinical risk factors (n = 378), compared to 0.24% of controls (odds ratio [OR] = 12.3, p = 1.27 × 10-10). Incorporation of the results of either functional assays or protein modeling led to a pronounced increase in effect size (ORmax = 46.5, p = 1.74 × 10-15). Association signals for the X-chromosomal gene TLR7 were also detected in the female-only subgroup, suggesting the existence of additional mechanisms beyond X-linked recessive inheritance in males. Additionally, supporting evidence was generated for a contribution to severe COVID-19 of the previously implicated genes IFNAR2, IFIH1, and TBK1. Our results refine the genetic contribution of rare TLR7 variants to severe COVID-19 and strengthen evidence for the etiological relevance of genes in the interferon signaling pathway.
Project description:Analysis of COVID-19 hospitalized patients, with different kind of symptoms, by human rectal swabs collection and 16S sequencing approach.
Project description:COVID-19 clinically manifests from asymptomatic to the critical range. Immune response provokes the pro-inflammatory interactions, which lead to the cytokines, reactive oxygen/nitrogen species, peptidases, and arachidonic acid metabolites enlargement and activation of coagulation components. Matrix metalloproteinases (MMPs) contribute to tissue destruction in the development of COVID-19. Due to the endothelial, systemic course of the disease, VEGF A participates actively in COVID-19 development, while neurotrophic and metabolic effects of BDNF recommends for the prediction of complications in COVID-19 patients. Searching for a marker that would improve and simplify the ranking in COVID-19, the study intended to evaluate the relationship of MMP-9 with VEGF A, BDNF, and MMP-8 with the COVID-19 severity. Upon admission to the hospital and before the therapy administration, 77 patients were classified into a mild, moderate, severe, or critical group. Due to the inflammatory stage in COVID-19, a comparison between groups showed related differences in leukocytes, neutrophils, lymphocytes, and platelets counts as anticipated. Only in seriously ill patients, there is a significant increase in the serum concentration of MMP-9, MMP-8, and VEGF A, while BDNF values did not show significant variations between groups. However, all those parameters positively correlated with each other. The ratio of MMP-9/BDNF markedly decreased in the severe and critically patients compared to the mild group. Testing the capability of this ratio to predict the COVID-19 stage by ROC curves, we found the MMP-9/BDNF could be a suitable marker for differentiating stages I/II (AUC 0.7597), stage I/III (AUC 0.9011), and stage I/IV (AUC 0.7727). Presented data describe for the first time the high-level systemic MMP-9/BDNF ratio in patients with COVID-19. This parameter could contribute to a more precise determination of the phase of the disease.
Project description:There are no studies which have compared the risk of severe COVID-19 and related mortality between transplant recipients and nontransplant patients. We enrolled two groups of patients hospitalized for COVID-19, that is, kidney transplant recipients (KTR) from the French Registry of Solid Organ Transplant (n = 306) and a single-center cohort of nontransplant patients (n = 795). An analysis was performed among subgroups matched for age and risk factors for severe COVID-19 or mortality. Severe COVID-19 was defined as admission (or transfer) to an intensive care unit, need for mechanical ventilation, or death. Transplant recipients were younger and had more comorbidities compared to nontransplant patients. They presented with higher creatinine levels and developed more episodes of acute kidney injury. After matching, the 30-day cumulative incidence of severe COVID-19 did not differ between KTR and nontransplant patients; however, 30-day COVID-19-related mortality was significantly higher in KTR (17.9% vs 11.4%, respectively, p = .038). Age >60 years, cardiovascular disease, dyspnea, fever, lymphopenia, and C-reactive protein (CRP) were associated with severe COVID-19 in univariate analysis, whereas transplant status and serum creatinine levels were not. Age >60 years, hypertension, cardiovascular disease, diabetes, CRP >60 mg/L, lymphopenia, kidney transplant status (HR = 1.55), and creatinine level >115 µmol/L (HR = 2.32) were associated with COVID-19-related mortality in univariate analysis. In multivariable analysis, cardiovascular disease, dyspnea, and fever were associated with severe disease, whereas age >60 years, cardiovascular disease, dyspnea, fever, and creatinine level>115 µmol/L retained their independent associations with mortality. KTR had a higher COVID-19-related mortality compared to nontransplant hospitalized patients.