The aim of the study is to characterize and to quantify SARS-CoV-2 strains in stools, in comparison with the viral strains in respiratory samples, from patients hospitalized for COVID-19. The methods will be standard ddPCR quantifying SARS-CoV-2 RNA and next generation sequencing-whole genome sequencing. The expected results will allow us to better understand SARS-CoV-2 dynamics and compartmentalization, both in the respiratory tract and in digestive-related tissues, according to the evolution of SARS-CoV-2 variants.

Inclusion Criteria:

• Age: men or women of 18 years-old or more
• Clinical signs: hospitalised patient for SARS-CoV-2 infection, nasopharyngeal PCR-confirmed (or any other sample) (in: Infectious diseases department, Intensive care unit), whatever the severity of the clinical form.
• The subject gave his/her informed and writen consent, after complete explanations on the research schedule.
• Compulsory affiliation to a social security scheme.
• Previous medical examination, when a patient is admitted to the hospital, according to good clinical practices.

Exclusion Criteria:

• Subject corresponding to articles L. 1121-5, L. 1121-7 and L1121-8 of the French Public health code:

  • pregnant woman, parturient or breastfeeding woman
  • Minor person
  • Person of full age under guardianship, curatorship, safeguard of justice

• Woman who wants to be pregnant during the study period

• Person in psychiatric care - articles L. 3212-1 and L. 3213-1 who do not fall under the article L. 1121-8 (without consent hospitalisation)

Hospitalised patient for SARS-CoV-2 infection, nasopharyngeal PCR-confirmed (or any other sample) in Infectious diseases department and Intensive care unit, whatever the severity of the clinical form.

n=30

Sampling dates:

COVID-19 diagnostics day (d0), day-2, day-4, day-end of hospitalization, day-post hospitalization