CIHR-CORONABIO DATASET

Resumen

<strong>Title</strong> CIHR - CORONABIO Project Dataset <strong>Description</strong> A total of 250 adult patients with a positive nasopharyngeal swab polymerase chain reaction (PCR) test for SARS-CoV-2 performed at participating hospitals were recruited during the first pandemic wave in Spain from March 16th to the 15th of April 2020. The patients recruited were of three different categories. The first corresponded to patients examined at an emergency room and discharged within the first 24 h (outpatients group, n=50). The second group were patients hospitalized to pneumology, infectious diseases or internal medicine wards (wards group, n=100). Patients who required critical care or died during hospitalization were excluded from this group. The third group corresponded to patients admitted to the ICU (n=100). Twenty healthy blood donors were included as controls. These controls were recruited during the pandemics, in parallel to the SARS-CoV-2 infected patients, and were negative for SARS-CoV-2 IgG. This study was registered at Clinicaltrials.gov with the identification NCT04457505. Plasma from blood collected in EDTA tubes samples was obtained from the three groups of patients in the first 24 h following admission to the emergency room, to the ward, or to the ICU. Viral RNA detection and quantification in plasma was performed using droplet digital PCR, targeting the N1 and N2 regions of the SARS-CoV-2 nucleoprotein gene. A panel of protein biomarkers was profiled by using the Ella-SimplePlex™ immunoassay. Anti-SARS-CoV-2 S IgG antibodies were quantified in plasma using an specific immunoassay. <strong>Dataset</strong> <strong>ID: </strong>Number of patient <strong>WARD_patients: </strong>Patients hospitalized to pneumology, infectious diseases or internal medicine wards (0=No; 1=Yes) <strong>ICU_patients: </strong>Patients admitted to the ICU (0=No; 1=Yes) <strong>HC0_OU1_W2_ICU3: </strong>Healthy Controls; outpatients; ward patients; ICU patients (Healthy controls=0; Outpatients=1; ward patients=2; ICU patients=3) <strong>Hospital_admission_yes_no: </strong>Patients hospitalized (0=No; 1=Yes) <strong>Hospital_admission_date: </strong>Date of hospital admission <strong>Hospital_discharge_date: </strong>Date of hospital discharge <strong>ICU_admission_date: </strong>Date of ICU admission <strong>ICU_discharge_date: </strong>Date of ICU discharge <strong>Date_Emergency_HOSP_ICU_Admission: </strong>Date of admission to the emergency room, to the ward or to the ICU <strong>Date_sample_extraction: </strong>Date of blood sample extraction <strong>Exitus: </strong>Exitus lethalis during hospital stay (0=No; 1=Yes) <strong>Exitus_date: </strong>Date of exitus <strong>Causes_of_mortality: </strong>Causes of hospital mortality <strong>Date_hosp_discharge_or_exitus: </strong>Date of hospital discharge or date of exitus <strong>Symptoms_onset_date : </strong>Date of symptoms onset <strong>SARSCOV2_N1_copies_mL_plasma: </strong>Copies of SARS-CoV-2 N1 per ml of plasma (dPCR) <strong>SARSCOV2_N2_copias_mL_plasma: </strong>Copies of SARS-CoV-2 N2 per ml of plasma (dPCR) <strong>RNAemia_SARSCOV2_plasma: </strong>Presence of SARS-CoV-2 RNA in plasma (0=No; 1=Yes) <strong>Rnase_P_copias_mL_plasma: </strong>Copies of human ribonuclease (Rnase) P<strong> </strong>per ml of plasma <strong>IgG_anti_SARS_CoV2: </strong>Presence of anti-SARS-CoV-2 IgG (0=No; 1=Yes) <strong>Age: </strong>Age (years) <strong>Sex: </strong>Sex (0=Female; 1=Male) <strong>Current_smoker: </strong>Current smoker (0=No; 1=Yes) <strong>Alcoholism: </strong>Alcoholism (0=No; 1=Yes) <strong>Drugs_abuse: </strong>Drugs abuse (0=No; 1=Yes) <strong>Obesity : </strong>Obesity, BMI &gt; 30 (0=No; 1=Yes) <strong>Hypertension: </strong>Hypertension (0=No; 1=Yes) <strong>Diabetes_type1: </strong>Diabetes type I (0=No; 1=Yes) <strong>Diabetes_type2: </strong>Diabetes type II (0=No; 1=Yes) <strong>Dyslipidemia: </strong>Dyslipidemia (0=No; 1=Yes) <strong>Chronic_cardiac_disease: </strong>Chronic cardiac disease (0=No; 1=Yes) <strong>Peripheral_vascular_disease: </strong>Peripheral vascular disease (0=No; 1=Yes) <strong>Ictus: </strong>Ictus (0=No; 1=Yes) <strong>Chronic_neurological_disease: </strong>Chronic neurological disease (0=No; 1=Yes) <strong>Chronic_pulmonary_disease: </strong>Chronic pulmonary disease (0=No; 1=Yes) <strong>Asthma: </strong>Asthma 0=No; 1=Yes) <strong>Chronic_kidney_disease: </strong>Chronic kidney disease (0=No; 1=Yes) <strong>Dialysis:</strong> Dialysis (0=No; 1=Yes) <strong>Cancer: </strong>Active cancer (0=No; 1=Yes) <strong>Hemiplegia_paraplegia: </strong>Hemiplegia or paraplegia (0=No; 1=Yes) <strong>Inflammatory_bowel_disease: </strong>Inflammatory bowel disease (0=No; 1=Yes) <strong>Chronic_liver_disease: </strong>Chronic liver disease (0=No; 1=Yes) <strong>HIV:</strong> Human immunodeficiency virus infection (0=No; 1=Yes) <strong>Autoimmune_disease: </strong>Autoimmune disease (0=No; 1=Yes) <strong>Splenectomy: </strong>Splenectomized patient (0=No; 1=Yes) <strong>Inhaled_corticosteroids_treatment: </strong>Inhaled corticosteroids treatment within 3 months before (0=No; 1=Yes) <strong>Oral_corticosteroids_treatment: </strong>Oral corticosteroids treatment within 3 months before (0=No; 1=Yes) <strong>Chemotherapy: </strong>Chemotherapy treatment (0=No; 1=Yes) <strong>Radiotherapy:</strong> Radiotherapy treatment (0=No; 1=Yes) <strong>Pregnancy: </strong>Pregnancy at the time of admission (0=No; 1=Yes) <strong>Temperature: </strong>Temperature in ºC <strong>Systolic_pressure_mmHg: </strong>Arterial systolic pressure in mmHg <strong>Oxygen_saturation: </strong>Oxygen saturation % <strong>Bilateral_pulmonary_infiltrate: </strong>Presence of bilateral pulmonary infiltrate (0=No; 1=Yes) <strong>PaO2_FiO2: </strong>PaO2/FiO2 <strong>CURB65_score:</strong> CURB65 score <strong>APACHE_score: </strong>Acute Physiology And Chronic Health Evaluation II <strong>SOFA_score: </strong>Sepsis related Organ Failure Assessment Score <strong>Complications: </strong>Complications during hospital stay (0=No; 1=Yes) <strong>ARDS: </strong>Acute respiratory distress syndrome (0=No; 1=Yes) <strong>Sepsis: </strong>Sepsis (0=No; 1=Yes) <strong>Septic_shocK: </strong>Hypotension, administration of vasopressors (MAP of 65 mmHg) and lactate &gt; 2mmol/L (0=No; 1=Yes) <strong>Pulmonary_thromboembolism: </strong>Pulmonary thromboembolism (0=No; 1=Yes) <strong>Deep_vein_thrombosis: </strong>Deep vein thrombosis (0=No; 1=Yes) <strong>Ictus_c: </strong>Ictus (0=No; 1=Yes) <strong>Myocardial_infarction: </strong>Myocardial infarction (0=No; 1=Yes) <strong>Acute_arrhythmia: </strong>Acute arrhythmia (0=No; 1=Yes) <strong>Heart_failure: </strong>Heart failure (0=No; 1=Yes) <strong>Myocarditis: </strong>Myocarditis (0=No; 1=Yes) <strong>DIC: </strong>Disseminated intravascular coagulation (0=No; 1=Yes) <strong>Secondary_infections: </strong>Secondary infections (0=No; 1=Yes) <strong>Microorganisms: </strong>Results of microorganisms culture <strong>Hydroxychloroquine: </strong>Hydroxychloroquine (0=No; 1=Yes) <strong>Chloroquine: </strong>Chloroquine treatment (0=No; 1=Yes) <strong>Corticoids: </strong>Corticoids treatment (0=No; 1=Yes) <strong>Azithromycin: </strong>Azithromycin treatment (0=No; 1=Yes) <strong>Other_antibiotics: </strong>Other antibiotics treatment (0=No; 1=Yes) <strong>Antibiotics_oral0_IV1: </strong>Oral or intravenous antibiotics (0=Oral; 1=Intravenous) <strong>Antipyretic_analgesics: </strong>Antipyretics analgesics (0=No; 1=Yes) <strong>Antipyretic_analgesics_oral0_IV1: </strong>Oral or intravenous antipyretic analgesics (0=Oral; 1=Intravenous) <strong>Remdesivir_treatment: </strong>Remdesivir treatment (0=No; 1=Yes) <strong>Tocilizumab_treatment : </strong>Tocilizumab treatment (0=No; 1=Yes) <strong>Lopinavir_treatment: </strong>Lopinavir treatment (0=No; 1=Yes) <strong>Interferon_alpha_treatment: </strong>Interferon alpha treatment (0=No; 1=Yes) <strong>Interferon_beta_treatment:</strong> Interferon beta treatment (0=No; 1=Yes) <strong>Fluid_therapy: </strong>Fluid therapy (0=No; 1=Yes) <strong>Other_treatments:</strong> Other treatments (0=No; 1=Yes) <strong>CT_scan: </strong>Computed tomography scan (0=No; 1=Yes) <strong>CT_scan_findings: </strong>Findings of computed tomography scan <strong>Oxygen_therapy</strong>: Oxygen therapy (0=No; 1=Yes) <strong>Non_invasive_mechanical_ventilation: </strong>Non invasive mechanical ventilation (0=No; 1=Yes) <strong>Invasive_mechanical_ventilation</strong>: Invasive mechanical ventilation (0=No; 1=Yes) <strong>Vasopressors:</strong> Vasopressors (0=No; 1=Yes) <strong>Date_blood_analysis: </strong>Date of blood analysis <strong>Lymphocytes_cells_mm3: </strong>Lymphocytes count (cells/mm^3) <strong>Monocytes_cells_mm3 : </strong>Monocytes count (cells/mm^3) <strong>Neutrophils_cells_mm3 : </strong>Neutrophils count (cells/mm^3) <strong>CRP_mg_dl: </strong>C-Reactive Protein (mg/dl) <strong>Creatinine_mg_dl: </strong>Creatinine (mg/dl) <strong>Glucose_mg_dl: </strong>Glucose (mg/dl) <strong>Na_mEq_L: </strong>Na (mEq/L) <strong>K_mEq_L: </strong>K (mEq/L) <strong>Platelets_x103_uL: </strong>Platelets count (cells x 10³/uL) <strong>INR: </strong>International normalized prothrombin ratio (INR) <strong>LDH_UI_L: </strong>Lactate dehydrogenase (UI/L) <strong>GPT_UI_L: </strong>Glutamic pyruvic transaminase (GPT) (UI/L) <strong>WBC_cells_mm3: </strong>White Blood Cells (cells/mm^3) <strong>Eosinophils_cells_mm3: </strong>Eosinophils count (cells/mm^3) <strong>Basophils_cells_mm3: </strong>Basophils count (cells/mm^3) <strong>Procalcitonin_ug_L: </strong>Procalcitonin (ug/L) <strong>Fibrinogen_mg_dl: </strong>Fibrinogen (mg/dl) <strong>TTPA_seg:</strong> Activated partial thromboplastin time <strong>D_Dimer_ng_ml: </strong>D Dimer (ng/ml) <strong>Ferritin_ug_L:</strong> Ferritin (ug/L) <strong>CPK_UI_L: </strong>Creatine phospho kinase (UI/L) <strong>Bilirrubin_mg_dl:</strong> Bilirrubin (mg/dl) <strong>GOT_UI_L: </strong>Glutamic oxaloacetic transaminase (UI/L) <strong>Blood_total_proteins_g_dl: </strong>Blood total proteins (g/dl) <strong>Albumin_g_dl: </strong>Albumin (g/dl) <strong>Troponin_T_ng_L: </strong>Troponin T (ng/L) <strong>Troponin_T_high_sensitivity_test: </strong>Troponin T high sensitivity test <strong>Troponin_I_ng_L: </strong>Troponin I (ng/L) <strong>Troponin_I_high_sensitivity_test: </strong>Troponin I high sensitivity test <strong>Arterial_lactate_mmol_L: </strong>Arterial lactate (mmol/L) <strong>Arterial_pH: </strong>Arterial pH <strong>Arterial_bicarbonate: </strong>Arterial bicarbonate <strong>Arterial_PaO2: </strong>Arterial partial pressure of oxygen <strong>Arterial_PaCO2: </strong>Arterial partial pressure of carbon dioxide <strong>ICAM_pg_ml_plasma: </strong>Intercellular adhesion molecule 1(pg/ml plasma) <strong>LIPO_pg_ml_plasma:</strong> Lipocalin-2 (pg/ml plasma) <strong>MPO_pg_ml_plasma: </strong>Myeloperoxidase (pg/ml plasma) <strong>VCAM1_pg_ml_plasma : </strong>Vascular Cell Adhesion Molecule 1 (pg/ml plasma) <strong>PDL1_pg_ml_plasma: </strong>Programmed death-ligand 1 <strong>(</strong>pg/ml plasma) <strong>GCSF_pg_ml_plasma: </strong>Granulocyte colony-stimulating factor (pg/ml plasma) <strong>IL1b_pg_ml_plasma: </strong>Interleukin (IL)-1β (pg/ml plasma) <strong>VEGFC_pg_ml_plasma: </strong>Vascular endothelial growth factor (pg/ml plasma) <strong>DDIMER_pg_ml_plasma: </strong>DDIMER (pg/ml plasma) <strong>ESELECTIN_pg_ml_plasma: </strong>ESELECTIN (pg/ml plasma) <strong>FERRITIN_pg_ml_plasma: </strong>FERRITIN (pg/ml plasma) <strong>SPD_pg_ml_plasma: </strong>Surfactant protein D (pg/ml plasma) <strong>IL10_pg_ml_plasma: </strong>Interleukin 10 (pg/ml plasma) <strong>IL17A_pg_ml_plasma: </strong>Interleukin-17A (pg/ml plasma) <strong>GMCSF_pg_ml_plasma : </strong>Granulocyte Macrophage Colony-Stimulating Factor (GM-CSF) (pg/ml plasma) <strong>IL7_pg_ml_plasma: </strong>Interleukin 7 (pg/ml plasma) <strong>CXCL10_pg_ml_plasma : </strong>C-X-C motif chemokine ligand 10 (CXCL10) (pg/ml plasma) <strong>ANGIOPOIETIN2_pg_ml_plasma: </strong>ANGIOPOIETIN2 (pg/ml plasma) <strong>IL1_ra_pg_ml_plasma: </strong>Interleukin-1 receptor antagonist (IL-1Ra) (pg/ml plasma) <strong>IL6_pg_ml_plasma:</strong> Interleukin 6 (IL-6) (pg/ml plasma) <strong>CCL2_pg_ml_plasma: </strong>C-C motif chemokine ligand 2 (CCL2) (pg/ml plasma) <strong>IL12p70_pg_ml_plasma:</strong> Interleukin-12p70 (IL-12) (pg/ml plasma) <strong>IL2_pg_ml_plasma: </strong>Interleukin 2 (pg/ml plasma) <strong>IL4_pg_ml_plasma: </strong>Interleukin 4 (pg/ml plasma) <strong>IL15_pg_ml_plasma:</strong> Interleukin 15 (pg/ml plasma) <strong>GRANZYMEB_pg_ml_plasma: </strong>GRANZYME B (pg/ml plasma) <strong>IFNg_pg_ml_plasma: </strong>IFN-gamma (interferon-gamma) (pg/ml plasma) <strong>TNFa_pg‎_ml_plasma: </strong>Tumour Necrosis factor alpha (TNF-alpha) (pg‎/ml plasma)