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.

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.

This study will enrol eligible patients (children and adults) with confirmed infection with SARS-CoV-2. Recruitment of patients with Day 1 (enrolment) data is the priority.

The patient's follow-up will be done strictly within the management adapted to his infection. No visits will be made specifically for research purposes. The organisation of convalescence visits is left to the discretion of each centre according to its post-hospitalisation patient follow-up procedures.

Additional biological samples will be collected when samples are taken in the context of care in order to meet the research objectives, with the exception of certain blood samples for pharmacokinetic analyses.