Intestinal Microbiota of Patients Hospitalized With Sars-CoV-2

Study Overview
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Brief Summary
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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.

Official Title
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Intestinal Microbiota of Patients Hospitalized With Sars-CoV-2

Conditions
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COVID-19

Intervention / Treatment
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* Other: Fecal sample


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: patient hospitalized at in Nimes University hospital Infection with SARS-CoV-2 confirmed by RT-PCR The patient must have signed the consent form The patient must be a member or beneficiary of a health insurance plan Exclusion Criteria: The subject is participating in an interventional study susceptible to modify the intestinal microbiota, or is in a period of exclusion determined by a previous study It is impossible to give the subject informed information The patient is under safeguard of justice or state guardianship Patient with a chronic digestive pathology or having been operated in the previous year or having enteral nutrition or having had bariatric surgery Patient is pregnant, parturient or breastfeeding

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Patients with high viral load of SARS-CoV-2 in feces<br> | Other: Fecal sample<br>* Fecal sample taken to investigate intestinal microbiota<br>|
| Patients with low viral load of SARS-CoV-2 in feces<br> | Other: Fecal sample<br>* Fecal sample taken to investigate intestinal microbiota<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | 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 | 

Secondary Outcome Measures

| Outcome Measure | 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) | 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 | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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microbiota, gastrointestinal microbiome, translocation