Role of the Microbiota in the Evolution of the SARS-CoV-2 Disease,COVID-19, in Hospitalized Patients

Study Overview
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Brief Summary
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Patients hospitalized for COVID-19 may need intensive care (e.g. mechanical ventilation) during hospitalization. Some risk factors are already known but better targeting of such patients is still needed, at least because existing risk factors are not strong enough to provide an accurate prediction. Care organization would benefit for such a predictive tool. Oropharyngeal and gut microbiota could potentially fill a significant gap in predictive performances. The investigators therefore propose to sample 200 patients (oropharyngeal and rectal swab) admitted in infectious disease department at Bichat Hospital and at high risk of needing intensive care during hospitalization. The investigators plan to perform metagenomic sequencing and bioinformatic analysis of these samples to characterize the diversity of bacterial species present in the oropharynx and the gut and to identify new factors associated with the need for intensive care. Aside metagenomic analyses, The investigators will perform semi-quantitative cultures of the oropharyngeal and gut microbiota to identify and quantify pathogens in order to predict the risk of bacterial infections in COVD-19 patients. For patients transferred in intensive care unit, The investigators will to perform another series of samples to better characterize the evolution of microbiota during mechanical ventilation and identify factors associated with the risk of developing a ventilator-associated pneumonia. Microbiota data will be considered together with the host genotype, the viral sequence and a deep immunological profiling to identify the main determinants of the evolution toward severity of COVID-19.

Detailed Description
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Patients hospitalized for COVID-19 may need intensive care (e.g. mechanical ventilation) during hospitalization. Some risk factors are already known (e.g. sex, comorbidities, initial clinical presentation inflammatory cytokines), but better targeting of such patients is still needed, at least because existing risk factors are not strong enough to provide an accurate prediction. Care organization would benefit for such a predictive tool. Oropharyngeal and gut microbiota could fill a significant gap in predictive performances. The investigators therefore propose to take advantage of the French-COVID cohort and sample 200 patients (oropharyngeal and rectal swab) admitted in infectious disease department at Bichat Hospital and at high risk of needing intensive care during hospitalization. The investigators plan to perform metagenomic sequencing and bioinformatic analysis of these samples to characterize the diversity of bacterial species present in the oropharynx and the gut and to identify new factors associated with the need for intensive care. Aside metagenomic analyses, The investigators will perform semi-quantitative cultures of the oropharyngeal and gut microbiota to identify and quantify pathogens in order to predict the risk of bacterial infections in COVD-19 patients. The genetic determinants of the host (the patient) could also be predictive of the severity of the disease and so does the immunological response to the COVID-19. Likewise, it has been suggested that certain mutations (notably the D614G mutation) of the viral sequence could be associated with the infectivity of the virus. In addition to the direct role of the microbiota in the course of infection, the immune characteristics specific to the host, by themselves or in interaction with the microbiota, could play an important role in the progression of the disease. This project focuses on the clinical characterization of COVID-19 and its evolution, as well as disease management. The research focuses on 4 main areas: Characterization of the oropharyngeal and intestinal microbiota of patients with COVID-19 Characteristics of the host (genotype) Immune characteristics of the host Characteristics of the SARS-CoV-2 viral genome For patients transferred in intensive care unit, The investigators will to perform another series of samples to better characterize the evolution of microbiota during mechanical ventilation and identify factors associated with the risk of developing a ventilator-associated pneumonia.

Official Title
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Role of the Microbiota in the Evolution of the SARS-CoV-2 Disease in Hospitalized Patients

Conditions
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Covid19

Intervention / Treatment
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* Other: oropharyngeal and intestinal microbiota
* Other: host genotype
* Other: host immune factors
* Other: viral sequence


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Adult patient with documented SARS-CoV-2 infection requiring hospitalization. Exclusion Criteria: Lack of consent Patients hospitalized in an intensive care unit Patient under guardianship or curatorship

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 hospitalized for COVID-19<br> | Other: oropharyngeal and intestinal microbiota<br>* analysis of oropharyngeal and intestinal microbiota<br>Other: host genotype<br>* analysis of a part of host genotype<br>Other: host immune factors<br>* analysis of host immune factors<br>Other: viral sequence<br>* analysis of viral sequence<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Identify risk factors associated with severe forms of COVID-19 requiring transfer to ICU | The main endpoint is the indication of worsening of the general condition requiring transfer to ICU | day 14 | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Link between the composition of the gut microbiota and admission to intensive care | Composition of the gut microbiota on admission to intensive care to predict the outcome of severe COVID-19 in patients transferred to the ICU (subgroup analysis) | 3 months | 
| Predictive performance of semi-quantitative culture and rapid metagenomic evaluation | Predictive performance of semi-quantitative culture and rapid metagenomic evaluation of the oropharyngeal microbiota to predict the occurrence of VAP in patients admitted to an ICU and mechanically ventilated (subgroup analysis). | 3 months |