The rise of SARS-CoV2 coronavirus infections since January 2020 has changed the global health landscape. The spectrum of clinical manifestations caused by this virus (COVID-19) is surprisingly broad and ranges from mild illness (even sometimes asymptomatic) to pneumonia. The latter cases carry a high risk of progressing to acute respiratory distress syndrome (ARDS), which can be fatal if it worsens and leads to multi-organ failure due to secondary infections (bacterial, fungal or viral).

Pathophysiology of SARS-CoV2 infections

The penetration of this coronavirus in the respiratory tract through its surface protein Spike which binds to the ACE2 receptors of the host cells (Grupta et al. Nat Med 2021) will first of all allow the virus to replicate itself by using the cellular machinery of the host cell. The maturation of these new virions also has a direct toxic effect on these cells responsible for cell death, tissue damage and local inflammation involving a myriad of immune responses.


In most cases, the host immune system will be able to contain the spread of these virions. Nevertheless, in some patients (especially in case of defective innate responses involving type I interferons), viral replication is too important (and/or the defective immune system does not allow to fight effectively against this pathogen). This leads to the spread of the virus throughout the respiratory tract and the occurrence of extensive tissue damage. An exacerbated inflammatory reaction (also called "cytokine storm") will then occur, the consequences of which can be fatal. The main clinical manifestations of these severe infectious states include the initial onset of fever and cough, progressing to respiratory failure due to alveolar damage. Extra-respiratory manifestations may also occur in the context of COVID-19, essentially involving neurological (stroke, encephalopathy, anosmia, etc.), renal, digestive, cardiac (myocarditis, myocardial infarction, etc.) or vascular (venous thrombosis and pulmonary embolism) disorders. As with bacterial infections, all of these manifestations are intimately linked to interactions between the virus, the endothelium and the host immune system where the propagation of the pathogen as well as the occurrence of organ failure will depend on the host's reaction and the use of antimicrobials capable of preventing superinfections. However, unlike bacterial infections, to date there are few treatments that effectively combat this virus (except in the early phase, where therapeutic antibodies and the recent paxlovid can slow down the infection) and, in patients already in the severe infection phase, viral clearance will therefore rely primarily on the host immune system.

From susceptibility to severe forms of COVID-19 to susceptibility to secondary infections

The first descriptions of patients with SARS-CoV2 infections have made it possible to easily draw a picture of the clinical and biological manifestations of these infections but also to identify the risk factors associated with the occurrence of severe forms. Even if the mechanisms responsible are not all elucidated, elderly patients or patients with comorbidities such as diabetes, overweight, hypertension or the presence of an immunosuppression have been identified early as more frequently suffering from severe COVID-19.

On the other hand, in some patients without these comorbidities, the occurrence of these severe forms seems more difficult to explain at first sight. The biological characteristics of the patients concerned have nevertheless allowed the demonstration of particular phenotypes including an overall decrease in white blood cells, in particular T cells, suggesting that SARS-CoV-2 could trigger or exploit an immune defect responsible for a persistent sustained inflammation linked and/or responsible for viral clearance defects. The immunological mechanisms involved involve both the innate (cytokine toxicity) and adaptive (T cell exhaustion) immune systems and result in a state of acquired immunosuppression. Beyond the persistence of the COVID-19 clinical manifestations (essentially respiratory), this state of immunosuppression is responsible for an increased risk of acquiring secondary infections (essentially bacterial but also fungal or viral reactivations). The occurrence of these nosocomial infections seems to be the cornerstone of delayed morbidity and mortality and makes it essential to better characterize and understand the mechanisms leading to this state of post-COVID-19 immunodepression.

Characterization of the immune response during COVID-19 & SITI

What immune flaws does the SARS-CoV-2 virus exploit in patients who develop severe forms of Covid-19? Teachers, researchers, doctors and engineers from Rennes have been mobilized very quickly to produce a high resolution description of the immune response to this coronavirus. Objectives: to reveal the flaws exploited by the virus in these patients, to isolate biomarkers useful to physicians for prognosis, and to describe the antibodies most representative of immunity to SARS-CoV-2 to prepare the therapeutic response.

Lymphopenia and COVID-19

The first explorations of biological abnormalities observed during severe SARS-CoV2 infections revealed a profound lymphopenia whose persistence is associated with a poor prognosis. This T-cell deficiency could disrupt the immune response in some patients, altering specific populations of immune cells in the activation dynamics of the response to infection, and in the immune repertoire that our organism uses and continuously enriches to defend itself.

The exploration of the mechanisms responsible for the occurrence of lymphopenia was the first research axis of the different teams during the COAL project (COVID-19 Associated Lymphopenia). This project was supported by CFTR2 (COVID-19 Fast Track Research Rennes) funding from the University Hospital of Rennes.

The April 2021 publication in the Journal of Clinical Immunology shows a correlation between the appearance of a B and T lymphocyte deficiency on the one hand, and the variation in the number of two categories of immune cells (increase in myeloid suppressor cells, associated with a decrease in CD8pos T lymphocytes) on the other. In addition, a reduction in the proliferative capacity of T lymphocytes was observed in vitro and could be corrected by arginine supplementation.

This work is at the origin of the CACOLAC clinical trial currently underway at the University Hospital of Rennes (NCT04404426), initiated by Prof. Jean Marc Tadié and his team, which consists in providing citrulline (arginine precursor) supplementation in an attempt to improve immune responses in intensive care patients.

Immunological signature of severe SARS-CoV2 infections

Scientists and clinicians from Rennes then mobilized around a second research axis whose objective was to evaluate and compare the immune response and its dysfunctions between three groups of patients all requiring admission to a medical resuscitation service:

  • 25 patients suffering from COVID-19 associated acute respiratory distress syndrome (ARDS);
  • 25 patients who tested positive for the SARS-CoV2 virus but without respiratory distress, or who had a favorable and rapid evolution after admission to the intensive care unit;
  • 25 patients withARDS not caused by SARS-CoV-2 (control group).

Clinical and analytical data were collected for all patients, including immunological monitoring by new approaches allowing fine characterization of phenotypic changes in cells, as well as viral load monitoring by regular collection of samples. The objective is to identify biomarkers that will allow physicians to

  • Anticipate the evolution of the disease in critically ill patients with no previous history of immune deficiency ;
  • Adapt care accordingly ;
  • Monitor the effect of new SARS-CoV-2 treatments currently being tested.

The May 2021 article in Cell Reports Medicine presenting the results of this project is based on an analysis using innovative mass cytometry techniques, linked to artificial intelligence allowing the identification of an "immune signature" common to COVID-19 patients, whether or not they are affected by an ARDS, including the expansion of atypical circulating monocytes.

This approach, carried out by Prof. Mikael Roussel, has been patented (Roussel, Tadié, Tarte). It will lead to applications for the biological monitoring of patients in intensive care.

Humoral immunity and COVID-19                                                                                                                                                               

The third research axis of the teachers/researchers, doctors and engineers from Rennes mobilized on this project within the MICMAC research unit (University of Rennes 1/Inserm/EFS), the University Hospital of Rennes and the French Blood Establishment was the exploration of the humoral response during these infections within the framework of the HARMONICOV project financed by the National Research Agency (projects "Flash COVID-19").

The study of the immune repertoire of patients cured of a COVID-19 will allow us to better understand the dynamics of the modifications of the adaptive immune system. Finally, blood samples collected from a group of patients 4 months after the occurrence of Covid-19 will allow to evaluate the antibodies present in their serum. From these samples, the researchers are cultivating modified cell lines in the laboratory, capable of producing antibodies against SARS-CoV-2. These will be selected according to their affinity for the virus and their ability to neutralize it.

In contrast, the immune repertoire in patients in remission is expected to be the reverse, once the viral load in these patients has fallen to undetectable levels and they have acquired protective antibodies. During the SARS-CoV-1 epidemic in 2003, specific antiviral antibodies played a crucial role in the recovery of patients. The same is expected for SARS-CoV-2, with a major role played by immunoglobulins.

The intention is to contribute to the urgent search for antibody candidates to develop immunotherapy treatments against SARS-CoV-2.

These different projects involve :

  • A clinical team, led by Jean-Marc Tadié, professor at the University of Rennes 1 and head of the medical resuscitation department at the University Hospital of Rennes, particularly involved in research on the immunological mechanisms of sepsis ;
  • The translational platform SITI of the MICMAC unit from the University Hospital of Rennes, directed by Professor Karin Tarte;
  • The PFBI platform of the EFS Bretagne, under the scientific direction of Professor Michel Cogné, coordinator of the whole project.

SARS-CoV-2 induced ARDS associates MDSC expansion and lymphocyte dysfunction due to arginine shortage
Reizine F, Lesouhaitier M, Gregoire M, Pinceaux K, Gacouin A, Maamar A, Painvin B, Camus C, Le Tulzo Y, Tattevin P, Revest L, Le Bot A, Ballerie4 A, Cador- Rousseau B, Lederlin M, Lebouvier T, Launey Y, Latour M, Verdy C, Rossille D, Le Gallou S, Dulong J, Moreau C, Bendavid C, Roussel M, Cogne M, Tarte K, Tadié JM
J. Clin.
Immunol. 2021 Apr;41(3):515-525. doi: 10.1007/s10875-020-00920-5

Comparative immune profiling of acute respiratory distress syndrome patients with or without SARS-CoV2 infection
Roussel M, Ferrant J, Reizine F, Le Gallou S, Dulong J, Carl S, Lesouhaitier M, Gregoire M, Bescher N, Verdy C, Latour M, Bézier I, Cornic M, Vinit A, Monvoisin C, Sawitzki B, Leonard S, Paul S, Feuillard J, Jeannet R, Daix T, Tiwari VK, Tadié JM, Cogné M.*,Tarte K* (*co-senior authors)
Cell Reports Medicine 2021, May 6:100291. doi: 10.1016/j.xcrm.2021.100291

Michel COGNE : professor of immunology - Université RENNES 1 et CHU RENNES