CIHR-CORONABIO DATASET

Title

CIHR - CORONABIO Project Dataset

Description

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.

Dataset

ID: Number of patient

WARD_patients: Patients hospitalized to pneumology, infectious diseases or internal medicine wards (0=No; 1=Yes)

ICU_patients: Patients admitted to the ICU (0=No; 1=Yes)

HC0_OU1_W2_ICU3: Healthy Controls; outpatients; ward patients; ICU patients (Healthy controls=0; Outpatients=1; ward patients=2; ICU patients=3)

Hospital_admission_yes_no: Patients hospitalized (0=No; 1=Yes)

Hospital_admission_date: Date of hospital admission 

Hospital_discharge_date: Date of hospital discharge

ICU_admission_date: Date of ICU admission

ICU_discharge_date: Date of ICU discharge

Date_Emergency_HOSP_ICU_Admission: Date of admission to the emergency room, to the ward or to the ICU

Date_sample_extraction: Date of blood sample extraction

Exitus: Exitus lethalis during hospital stay (0=No; 1=Yes)

Exitus_date: Date of exitus

Causes_of_mortality: Causes of hospital mortality

Date_hosp_discharge_or_exitus: Date of hospital discharge or date of exitus

Symptoms_onset_date : Date of symptoms onset

 

 

SARSCOV2_N1_copies_mL_plasma: Copies of SARS-CoV-2 N1 per ml of plasma (dPCR)

SARSCOV2_N2_copias_mL_plasma: Copies of SARS-CoV-2 N2 per ml of plasma (dPCR)

RNAemia_SARSCOV2_plasma: Presence of SARS-CoV-2 RNA in plasma (0=No; 1=Yes)

Rnase_P_copias_mL_plasma: Copies of human ribonuclease (Rnase) P per ml of plasma

IgG_anti_SARS_CoV2: Presence of anti-SARS-CoV-2 IgG (0=No; 1=Yes)

 

Age: Age (years)

Sex: Sex (0=Female; 1=Male)

Current_smoker: Current smoker (0=No; 1=Yes)

Alcoholism: Alcoholism (0=No; 1=Yes)

Drugs_abuse: Drugs abuse (0=No; 1=Yes)

Obesity : Obesity, BMI > 30 (0=No; 1=Yes)

Hypertension: Hypertension (0=No; 1=Yes)

Diabetes_type1: Diabetes type I (0=No; 1=Yes)

Diabetes_type2: Diabetes type II (0=No; 1=Yes)

Dyslipidemia: Dyslipidemia (0=No; 1=Yes)

Chronic_cardiac_disease: Chronic cardiac disease (0=No; 1=Yes)

Peripheral_vascular_disease: Peripheral vascular disease (0=No; 1=Yes)

Ictus: Ictus (0=No; 1=Yes)

Chronic_neurological_disease: Chronic neurological disease (0=No; 1=Yes)

Chronic_pulmonary_disease: Chronic pulmonary disease (0=No; 1=Yes)

Asthma: Asthma 0=No; 1=Yes)

Chronic_kidney_disease: Chronic kidney disease (0=No; 1=Yes)

Dialysis: Dialysis (0=No; 1=Yes)

Cancer: Active cancer (0=No; 1=Yes)

Hemiplegia_paraplegia: Hemiplegia or paraplegia (0=No; 1=Yes)

Inflammatory_bowel_disease: Inflammatory bowel disease (0=No; 1=Yes)

Chronic_liver_disease: Chronic liver disease (0=No; 1=Yes)

HIV: Human immunodeficiency virus infection (0=No; 1=Yes)

Autoimmune_disease: Autoimmune disease (0=No; 1=Yes)

Splenectomy: Splenectomized patient (0=No; 1=Yes)

Inhaled_corticosteroids_treatment: Inhaled corticosteroids treatment within 3 months before (0=No; 1=Yes)

Oral_corticosteroids_treatment: Oral corticosteroids treatment within 3 months before (0=No; 1=Yes)

Chemotherapy: Chemotherapy treatment (0=No; 1=Yes)

Radiotherapy: Radiotherapy treatment (0=No; 1=Yes)

Pregnancy: Pregnancy at the time of admission (0=No; 1=Yes)

 

Temperature: Temperature in ºC

Systolic_pressure_mmHg: Arterial systolic pressure in mmHg

Oxygen_saturation: Oxygen saturation %

Bilateral_pulmonary_infiltrate: Presence of bilateral pulmonary infiltrate (0=No; 1=Yes)

PaO2_FiO2: PaO2/FiO2

 

CURB65_score: CURB65 score

APACHE_score: Acute Physiology And Chronic Health Evaluation II

SOFA_score: Sepsis related Organ Failure Assessment Score

 

Complications: Complications during hospital stay (0=No; 1=Yes)

ARDS: Acute respiratory distress syndrome (0=No; 1=Yes)

Sepsis: Sepsis (0=No; 1=Yes)

Septic_shocK: Hypotension, administration of vasopressors (MAP of 65 mmHg) and lactate > 2mmol/L (0=No; 1=Yes)

Pulmonary_thromboembolism: Pulmonary thromboembolism (0=No; 1=Yes)

Deep_vein_thrombosis: Deep vein thrombosis (0=No; 1=Yes)

Ictus_c: Ictus (0=No; 1=Yes)

Myocardial_infarction: Myocardial infarction (0=No; 1=Yes)

Acute_arrhythmia: Acute arrhythmia (0=No; 1=Yes)

Heart_failure: Heart failure (0=No; 1=Yes)

Myocarditis: Myocarditis (0=No; 1=Yes)

DIC: Disseminated intravascular coagulation (0=No; 1=Yes)

Secondary_infections: Secondary infections (0=No; 1=Yes)

Microorganisms: Results of microorganisms culture

Hydroxychloroquine: Hydroxychloroquine (0=No; 1=Yes)

Chloroquine: Chloroquine treatment (0=No; 1=Yes)

Corticoids: Corticoids treatment (0=No; 1=Yes)

Azithromycin: Azithromycin treatment (0=No; 1=Yes)

Other_antibiotics: Other antibiotics treatment (0=No; 1=Yes)

Antibiotics_oral0_IV1: Oral or intravenous antibiotics (0=Oral; 1=Intravenous)

Antipyretic_analgesics: Antipyretics analgesics (0=No; 1=Yes)

Antipyretic_analgesics_oral0_IV1: Oral or intravenous antipyretic analgesics (0=Oral; 1=Intravenous)

Remdesivir_treatment: Remdesivir treatment (0=No; 1=Yes)

Tocilizumab_treatment : Tocilizumab treatment (0=No; 1=Yes)

Lopinavir_treatment: Lopinavir treatment (0=No; 1=Yes)

Interferon_alpha_treatment: Interferon alpha treatment (0=No; 1=Yes)

Interferon_beta_treatment: Interferon beta treatment (0=No; 1=Yes)

Fluid_therapy: Fluid therapy (0=No; 1=Yes)

Other_treatments: Other treatments (0=No; 1=Yes)

CT_scan: Computed tomography scan (0=No; 1=Yes)

CT_scan_findings: Findings of computed tomography scan

Oxygen_therapy: Oxygen therapy (0=No; 1=Yes)

Non_invasive_mechanical_ventilation: Non invasive mechanical ventilation (0=No; 1=Yes)

Invasive_mechanical_ventilation: Invasive mechanical ventilation (0=No; 1=Yes)

Vasopressors: Vasopressors (0=No; 1=Yes)

 

Date_blood_analysis: Date of blood analysis

Lymphocytes_cells_mm3: Lymphocytes count (cells/mm^3)

Monocytes_cells_mm3 : Monocytes count (cells/mm^3)

Neutrophils_cells_mm3 : Neutrophils count (cells/mm^3)

CRP_mg_dl: C-Reactive Protein (mg/dl)

Creatinine_mg_dl: Creatinine (mg/dl)

Glucose_mg_dl: Glucose (mg/dl)

Na_mEq_L: Na (mEq/L)

K_mEq_L: K (mEq/L)

Platelets_x103_uL: Platelets count (cells x 10³/uL)

INR: International normalized prothrombin ratio (INR)

LDH_UI_L: Lactate dehydrogenase (UI/L)

GPT_UI_L: Glutamic pyruvic transaminase (GPT) (UI/L)

WBC_cells_mm3: White Blood Cells (cells/mm^3)

Eosinophils_cells_mm3: Eosinophils count (cells/mm^3)

Basophils_cells_mm3: Basophils count (cells/mm^3)

Procalcitonin_ug_L: Procalcitonin (ug/L)

Fibrinogen_mg_dl: Fibrinogen (mg/dl)

TTPA_seg: Activated partial thromboplastin time

D_Dimer_ng_ml: D Dimer (ng/ml)

Ferritin_ug_L: Ferritin (ug/L)

CPK_UI_L: Creatine phospho kinase (UI/L)

Bilirrubin_mg_dl: Bilirrubin (mg/dl)

GOT_UI_L: Glutamic oxaloacetic transaminase (UI/L)

Blood_total_proteins_g_dl: Blood total proteins (g/dl)

Albumin_g_dl: Albumin (g/dl)

Troponin_T_ng_L: Troponin T (ng/L)

Troponin_T_high_sensitivity_test: Troponin T high sensitivity test

Troponin_I_ng_L: Troponin I (ng/L)

Troponin_I_high_sensitivity_test: Troponin I high sensitivity test

Arterial_lactate_mmol_L: Arterial lactate (mmol/L)

Arterial_pH: Arterial pH

Arterial_bicarbonate: Arterial bicarbonate

Arterial_PaO2: Arterial partial pressure of oxygen

Arterial_PaCO2: Arterial partial pressure of carbon dioxide

 

ICAM_pg_ml_plasma: Intercellular adhesion molecule 1(pg/ml plasma)

LIPO_pg_ml_plasma: Lipocalin-2 (pg/ml plasma)

MPO_pg_ml_plasma: Myeloperoxidase (pg/ml plasma)

VCAM1_pg_ml_plasma : Vascular Cell Adhesion Molecule 1 (pg/ml plasma)

PDL1_pg_ml_plasma: Programmed death-ligand 1 (pg/ml plasma)

GCSF_pg_ml_plasma: Granulocyte colony-stimulating factor (pg/ml plasma)

IL1b_pg_ml_plasma: Interleukin (IL)-1β (pg/ml plasma)

VEGFC_pg_ml_plasma: Vascular endothelial growth factor (pg/ml plasma)

DDIMER_pg_ml_plasma: DDIMER (pg/ml plasma)

ESELECTIN_pg_ml_plasma: ESELECTIN (pg/ml plasma)

FERRITIN_pg_ml_plasma: FERRITIN (pg/ml plasma)

SPD_pg_ml_plasma: Surfactant protein D (pg/ml plasma)

IL10_pg_ml_plasma: Interleukin 10 (pg/ml plasma)

IL17A_pg_ml_plasma: Interleukin-17A (pg/ml plasma)

GMCSF_pg_ml_plasma : Granulocyte Macrophage Colony-Stimulating Factor (GM-CSF) (pg/ml plasma)

IL7_pg_ml_plasma: Interleukin 7 (pg/ml plasma)

CXCL10_pg_ml_plasma : C-X-C motif chemokine ligand 10 (CXCL10) (pg/ml plasma)

ANGIOPOIETIN2_pg_ml_plasma: ANGIOPOIETIN2 (pg/ml plasma)

IL1_ra_pg_ml_plasma: Interleukin-1 receptor antagonist (IL-1Ra) (pg/ml plasma)

IL6_pg_ml_plasma: Interleukin 6 (IL-6) (pg/ml plasma)

CCL2_pg_ml_plasma: C-C motif chemokine ligand 2 (CCL2) (pg/ml plasma)

IL12p70_pg_ml_plasma: Interleukin-12p70 (IL-12) (pg/ml plasma)

IL2_pg_ml_plasma: Interleukin 2 (pg/ml plasma)

IL4_pg_ml_plasma: Interleukin 4 (pg/ml plasma)

IL15_pg_ml_plasma: Interleukin 15 (pg/ml plasma)

GRANZYMEB_pg_ml_plasma: GRANZYME B (pg/ml plasma)

IFNg_pg_ml_plasma: IFN-gamma (interferon-gamma) (pg/ml plasma)

TNFa_pg‎_ml_plasma: Tumour Necrosis factor alpha (TNF-alpha) (pg‎/ml plasma)