HARMONICOV

Context: Assessed by WHO as a pandemic on March 11, COVID-19 is caused by the SARS-CoV-2 coronavirus. The spectrum of its manifestations is strikingly broad and extends from mild disease (resembling an ordinary bout of flu or even asymptomatic) to pneumonia. The latter cases convey a high risk of evolution towards acute respiratory distress syndrome (ARDS), eventually fatal when worsening with cytokine storm and multiple organ failure or with superinfection and sepsis. In the absence of overt variations of the virus itself, its interactions with the host immune system are likely crucial. Clinical features of patients with severe forms of COVID-19 were reported, but immunological description of biomarkers for exacerbation and mortality vs recovery remains superficial. Globally decreased white blood cells, notably T-cells, suggest that CoV-2 might trigger or exploit an immune defect. This could correspond to gaps in immune cell subpopulations, kinetics of activation or repertoires. Immune failure would then be responsible for exacerbations and a poor outcome in intensive care unit (ICU) patients. Our objective is to characterize the kinetics of the immune response and of immune dysregulation in ARDS patients. In addition to studying severe ARDS patients, an inverse image of immune repertoires should appear in healed up patients, after they have reached an undetectable viral load and acquired protective antibodies (Abs). Humoral immunity mediated by specific anti-viral Abs was a key factor for recovery from SARS-CoV-1 infection, and this is also expected for CoV-2, making the Ig repertoire also of special interest for its inclusion of anti-viral neutralizing Abs (nAbs). Altogether, there is thus an urgent need for high-resolution characterization of the anti-CoV-2 immune response, correlating the dynamics of immune activation, cytokine production and immune repertoires with clinical evolution. In addition to providing biomarkers for prognosis evaluation and for monitoring innovative treatments, this will also participate to the urgent quest of as many possible mAb candidates for immunotherapy. Methods: In this prospective study, we will include 3 groups of 25 adult inpatients matched for age and sex from Rennes University Hospital. We will first concentrate on comparing either i) ICU patients with ARDS and laboratory-confirmed COVID-19, ii) COVID-19 patients without ARDS or undergoing rapid favorable evolution after their admission in the ICU, or iii) control ARDS patients without COVID-19. Clinical and laboratory data, including high-resolution immunomonitoring and serial samples for CoV-2 detection will be collected for all patients. Parameters collected will include complete analysis of blood lymphoid and myeloid subpopulations by Flow cytometry (FCM) and Mass cytometry (CyTOF), blood levels of inflammatory and regulatory cytokines, TCR and Ig repertoire evaluation by RepSeq, single-cell evaluation of gene expression. Specifically on blood samples from a fourth group of Covid-19 patients having recovered, presence of serum nAbs will be evaluated and EBV-transformed cell lines producing specific anti-CoV-2 mAbs will be grown and selected for the highest possible affinity and neutralizing ability. The project will thus pursue two complementary objectives, first determining biomarkers through high resolution immunomonitoring of critically ill patients without preexisting immune defect, hereby characterizing the breaches appearing in their immune defenses along COVID-19, and oppositely characterizing in healed-up patients potent nAbs the most representative of anti-CoV-2 immunity. Our ICU is used to research on sepsis, our labs are expert in biobanking, high-resolution immunomonitoring and immune repertoire studies. They are also fully operational during the COVID-19 outbreak within EFS and hospital premises despite the current confinement. This altogether warrants the unique feasibility and timeliness of the project.