Between March and May 2020, critically ill patients admitted to three ICUs from academic hospital (Hospices Civils de Lyon, Lyon, France) who presented with pulmonary infection with SARS-CoV-2 confirmed by RT-PCR testing were prospectively included in the study. A flowchart describing the patient datasets used for the different analyses is provided in Additional file 1: Figure S1. Preliminary results from a subgroup of the cohort were published previously [9]. This project was part of an ongoing prospective observational clinical study (RICO, REA-IMMUNO-COVID). It was approved by ethics committee (Comité de Protection des Personnes Ile de France 1 - N°IRB/IORG #: IORG0009918) under agreement number 2020-A01079-30. This clinical study was registered at (NCT04392401). The committee waived the need for written informed consent because the study was observational, with a low risk to patients, and no specific procedure, other than routine blood sampling, was required. Oral information and non-opposition to inclusion in the study were mandatory and were systematically obtained before any blood sample was drawn. This was recorded in patients’ clinical files. If a patient was unable to consent directly, non-opposition was obtained from the patient’s legally authorized representative and reconfirmed from the patient at the earliest opportunity. Inclusion criteria were: patients aged > 18 years, diagnosis of COVID-19 confirmed by RT-PCR testing in one respiratory sample. Inclusion criteria were (1) man or woman aged 18 or over, (2) hospitalization in ICU for SARS-CoV-2 pneumopathy, (3) first hospitalization in ICU, (4) positive diagnosis of SARS-CoV2 infection carried out by PCR or by another approved method in at least one respiratory sample, (5) sampling in the first 24 h after admission to ICU (D0) feasible and (6) patient or next of kin who has been informed of the terms of the study and has not objected to participating. Exclusion criteria were pregnancy, institutionalized patients, inability to obtain informed consent.

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