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The study investigators hypothesize that SARS-Cov2 infection alters the composition of the digestive microbiota and its functionality, resulting in changes in intestinal permeability and consequently in microbial digestive translocation. These changes may correlate with the magnitude of the SARS-CoV-2 viral load in the gastrointestinal tract and may have an impact on the clinical manifestations and evolvability of COVID-19.
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| Label | Type | Description | Intervention Names |
|---|---|---|---|
| Patients with high viral load of SARS-CoV-2 in feces |
| ||
| Patients with low viral load of SARS-CoV-2 in feces |
|
| Name | Type | Description | Arm Group Labels | Other Names |
|---|---|---|---|---|
| Fecal sample | Other | Fecal sample taken to investigate intestinal microbiota |
|
| Measure | Description | Time Frame |
|---|---|---|
| Number of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) | RT-qPCR of SARS-CoV-2 to calculate copies/mg | Day 0 |
| Measure | Description | Time Frame |
|---|---|---|
| Age of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | Age in years | Day 0 |
| Sex of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) |
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Inclusion Criteria:
Exclusion Criteria:
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All adult patients hospitalized in the Nimes University Hoptial with SARS-CoV-2 infection confirmed by RT-PCR
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| Name | Affiliation | Role |
|---|---|---|
| Albert Sotto | CHU Nimes | Principal Investigator |
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| CHU de Nimes | Nîmes | France |
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| ID | Term |
|---|---|
| D000086382 | COVID-19 |
| ID | Term |
|---|---|
| D011024 | Pneumonia, Viral |
| D011014 | Pneumonia |
| D012141 | Respiratory Tract Infections |
| D007239 | Infections |
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Fecal and blood samples taken for a biobank
Male/female
| Day 0 |
| Clinical features of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | Date of start of symptoms, current therapeutics, antibiotic therapy, blood pressure, heart rate, respiration rate, oxygen saturation, symptoms, Covid stage (ordinal 8 stage scale) | Day 0 |
| Total blood count of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | lymphocyte count, eosinophil count | Day 0 |
| C-reactive protein level biological data of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | concentration | Day 0 |
| Fibrinogen level of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | concentration | Day 0 |
| Lactate Dehydrogenase of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | concentration | Day 0 |
| D-dimer level of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | concentration | Day 0 |
| Ferritin levels, of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | Concentration | Day 0 |
| Albumin levels of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | concentration | Day 0 |
| Calcium levels of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | concentration | Day 0 |
| Glomerular filtration rate of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | volume per time | Day 0 |
| Liver function tests of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | Day 0 |
| Cytobacteriological urine exam of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | Day 0 |
| Blood cultures of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | Day 0 |
| Other infectious samples (other than SARS-CoV-2) of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) if tested | Day 0 |
| Taxonomic features of intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | Number of Operational Taxonomic Unit | Day 0 |
| Percentage of Operational Taxonomic Units in intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | % | Day 0 |
| Diversity of intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | Shannon Index | Day 0 |
| Diversity of intestinal microbiota of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | Bray Curtis Index | Day 0 |
| LPS-binding Protein concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | pg/ml ELISA | Day 0 |
| soluble CD14 concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | ng/ml ELISA | Day 0 |
| RNA16s concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | PCR and sequencing | Day 0 |
| RNA18 concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | PCR and sequencing | Day 0 |
| I-FAB concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | ng/ml:ELISA | Day 0 |
| Claudin 3 concentration of patients with high viral load of SARS-CoV-2 in feces (>50 copies/mg) versus low viral load (≤50 copies/mg) | ng/ml:ELISA | Day 0 |
| D014777 |
| Virus Diseases |
| D018352 | Coronavirus Infections |
| D003333 | Coronaviridae Infections |
| D030341 | Nidovirales Infections |
| D012327 | RNA Virus Infections |
| D008171 | Lung Diseases |
| D012140 | Respiratory Tract Diseases |