ABSTRACT
Background/Objectives: Genetic variants affecting host defense against pathogens may help explain COVID-19 fatal outcomes. Our aim was to identify rare genetic variants related to COVID-19 severity in a selected group of patients under 60 years who required intubation or resulting in death. Method(s): Forty-four very severe COVID-19 patients were selected from the Spanish STOP-Coronavirus cohort, which comprises more than 3,500 COVID-19 patients. Genotype was performed by whole exome sequencing and variants were selected by using a gene panel of 867 candidate genes (immune response, primary immunodeficiencies or coagulation, among other). Variants were filtered, priorized and their potential pathogenicity was assessed following ACGM criteria. Result(s): We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic (26%). Mostly, the candidate variants were located in genes related to immune response (38%), congenital disorders of glycosylation (14%) or damaged DNA binding genes (9%). A network analysis, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks enriched in carbohydrate metabolism and in DNA metabolism and repair processes. Conclusion(s): The variants identified affect different, but interrelated, functional pathways such as immune response and glycosylation. Further studies are needed for confirming the ultimate role of the new candidate genes described in the present study on COVID-19 severity.
ABSTRACT
Background. T cells are central to the early identification and clearance of viral infections and support antibody generation by B cells, making them desirable for assessing the immune response to SARS-CoV-2 infection and vaccines. We combined 2 high-throughput immune profiling methods to create a quantitative picture of the SARS-CoV-2 T-cell response that is highly sensitive, durable, diagnostic, and discriminatory between natural infection and vaccination. Methods. We deeply characterized 116 convalescent COVID-19 subjects by experimentally mapping CD8 and CD4 T-cell responses via antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I and 284 class II viral peptides. We also performed T-cell receptor (TCR) repertoire sequencing on 1815 samples from 1521 PCR-confirmed SARS-CoV-2 cases and 3500 controls to identify shared public TCRs from SARS-CoV-2-associated CD8 and CD4 T cells. Combining these approaches with additional samples from vaccinated individuals, we characterized the response to natural infection as well as vaccination by separating responses to spike protein from other viral targets. Results. We find that T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the SARS-CoV-2 T-cell response peaks about 1-2 weeks after infection and is detectable at least several months after recovery. Applying these data, we trained a classifier to diagnose past SARS-CoV-2 infection based solely on TCR sequencing from blood samples and observed, at 99.8% specificity, high sensitivity soon after diagnosis (Day 3-7 = 85.1%;Day 8-14 = 94.8%) that persists after recovery (Day 29+/convalescent = 95.4%). Finally, by evaluating TCRs binding epitopes targeting all non-spike SARS-CoV-2 proteins, we were able to separate natural infection from vaccination with > 99% specificity. Conclusion. TCR repertoire sequencing from whole blood reliably measures the adaptive immune response to SARS-CoV-2 soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points, and distinguishes post-infection vs. vaccine immune responses with high specificity. This approach to characterizing the cellular immune response has applications in clinical diagnostics as well as vaccine development and monitoring.
ABSTRACT
BACKGROUND AND AIMS: End-stage renal disease patients on haemodialysis (HD) seem more likely to develop severe COVID19 disease. Over the course of COVID disease, we observed a poor tolerance to HD sessions with a marked tendency of clinical deterioration over them. The objective is to evaluate changes on immunological system over HD session on patients affected with COVID19 compared with patients without COVID19. METHOD: Fourteen HD patients were studied including 9 confirmed COVID19 infection and 5 healthy controls. Predialysis and postdialysis blood samples were compared to study alterations on immune status. We identified cytoKines by Luminex (CCL2, CXCL10, IL1Ra, IL10, IL12p70, TNFa, IL17Ra, IL6, IL7) and adaptive lymphocyte subsets (CD4/CD8 naïve, CD4/CD8 MC, CD4/CD8 MP, CD19, CD56). Monocyte subsets (CD14+CD16-, CD14+CD16+, CD14-CD16+) were detected from peripheral blood mononuclear cells (PBMC), as well as immune activation (CD11b, HLA-DR, CD86) and migration factors (CCR2, CCR5). The supernatant of isolated CD14+ cells after 4-hour stimulation with LPS where analysed by Luminex to measure cytokines (CCL2, CXCL10, GM-CSF, IL10, IL12p70, IL17Ra, IL6, IL7, TNFa). RESULTS: Patients with COVID19 presented predialysis: (1) higher plasmatic levels of IL12p70, TNFa e IL7, (2) lymphopenia and neutrophilia, (3) higher percentage of intermediate monocytes and lower of non-classical, (4) lower membrane expression of CCR2, HLA-DR y CD86 over Cd14+ cells, and (5) higher production of CCL2, GMCSF, IL10, IL12p70 y IL17Ra by LPS stimulated monocytes compared with patients without COVID19. When analysed the fold-change between pre and postdialysis values, patients with COVID19 infection present a: (a) higher plasmatic levels of IL6, IL1Ra, CCL2 e CXCL10, (b) reductions of total lymphocites, (c) higher membrane expression of CCR2, CD33 y CD86 on CD14+ cells, and (d) higher production of TNFa, GM-CSF, IL10, IL17, IL6 e IL7 by LPS stimulated monocytes compared with patients without COVID19. No differences on lymphocite subset were found. CONCLUSION: The clinical deterioration on COVID19 infected patients over HD session could be related with monocyte activation and pro-inflammatory cytokines secretion.