French COVID Cohort

Study Overview
=================
Brief Summary
-----------------
Infectious disease is the single biggest cause of death worldwide. New infectious agents, such as the SARS, MERS and other novel coronavirus, novel influenza viruses, viruses causing viral haemorrhagic fever (e.g. Ebola), and viruses that affect the central nervous system (CNS) such as TBEV & Nipah require investigation to understand pathogen biology and pathogenesis in the host. Even for known infections, resistance to antimicrobial therapies is widespread, and treatments to control potentially deleterious host responses are lacking. In order to develop a mechanistic understanding of disease processes, such that risk factors for severe illness can be identified and treatments can be developed, it is necessary to understand pathogen characteristics associated with virulence, the replication dynamics and in-host evolution of the pathogen, the dynamics of the host response, the pharmacology of antimicrobial or host-directed therapies, the transmission dynamics, and factors underlying individual susceptibility. The work proposed here may require sampling that will not immediately benefit the participants. It may also require analysis of the host genome, which may reveal other information about disease susceptibility or other aspects of health status.

Official Title
-----------------
Clinical Characterisation Protocol for Severe Emerging Infections

Conditions
-----------------
Coronavirus Infections

Participation Criteria
=================
Eligibility Criteria
-----------------
Inclusion Criteria: - Any patient admitted to a health care facility, with an infection confirmed by SARS-CoV-2 (virologically confirmed diagnosis by PCR). Non inclusion criteria: Subject deprived of freedom, subject under a legal protective measure Refusal by participant, parent or appropriate representative. Exclusion Criteria: - Confirmed diagnosis of another pathogen than SARS-CoV-2 and no indication or likelihood of co-infection with SARS-CoV-2.
Sexes Eligible for Study
-----------------
All

Accepts Healthy Volunteers
-----------------
No

Study Plan
=================
How is the study designed?
-----------------
What is the study measuring?
-----------------
Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Clinical features | Describe the clinical features of the illness or syndrome (cardio-respiratory signs or symptoms, and laboratory results) and complications, and determinants of severity. Assessment daily for 15 days, then weekly until max 100 days, then 3 and 6 months. | 18 months | 
| Response to treatment | Describe the response to treatments (including supportive care and novel therapeutics) by clinical, biological, radiological and virological assessments. Assessment daily for 15 days, then weekly until max 100 days, then 3 and 6 months. | 18 months | 
| Pathogen replication, excretion and evolution, within the host | high-throughput sequencing of pathogen genomes obtained from respiratory tract, blood, urine, stool, CSF and other samples. Assessment on Day 1, Day 2, Day 3, Day 5, Day 7, Day 9, Day 11, Day 13, Day 15 then weekly until max 100 days, then 3 and 6 months. | 18 months | 
| Immune host responses to infection and therapy | Characterise the innate and acquired immune responses, circulating levels of immune signalling molecules and gene expression profiling in peripheral blood. Assessment on Day 1, Day 2, Day 3, Day 5, Day 7, Day 9, Day 11, Day 13, Day 15 then weekly until max 100 days, then 3 and 6 months. | 18 months | 
| Host genetic variants | Identify host genetic variants associated with disease progression or severity | Day 1 | 

 Terms related to the study
=================
Keywords Provided by Centre Hospitalier Valida
-----------------
SARS-CoV-2, Coronavirus, 2019-nCoV, COVID-19, Cohort