Immune Alterations in a Patient with SARS-CoV-2-Related Acute Respiratory Distress Syndrome

Abstract

We report a longitudinal analysis of the immune response associated with a fatal case of COVID-19 in Europe. This patient exhibited a rapid evolution towards multiorgan failure. SARS-CoV-2 was detected in multiple nasopharyngeal, blood, and pleural samples, despite antiviral and immunomodulator treatment. Clinical evolution in the blood was marked by an increase (2-3-fold) in differentiated effector T cells expressing exhaustion (PD-1) and senescence (CD57) markers, an expansion of antibody-secreting cells, a 15-fold increase in γδ T cell and proliferating NK-cell populations, and the total disappearance of monocytes, suggesting lung trafficking. In the serum, waves of a pro-inflammatory cytokine storm, Th1 and Th2 activation, and markers of T cell exhaustion, apoptosis, cell cytotoxicity, and endothelial activation were observed until the fatal outcome. This case underscores the need for well-designed studies to investigate complementary approaches to control viral replication, the source of the hyperinflammatory status, and immunomodulation to target the pathophysiological response. The investigation was conducted as part of an overall French clinical cohort assessing patients with COVID-19 and registered in clinicaltrials.gov under the following number: NCT04262921.

Keywords: COVID-19; T cells; cytokines; immune dysfunction.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1

Timeline from arrival in Europe to death in the ICU. Upper panels summarize the clinical, biological (leucocyte and lymphocyte counts), and radiological data of the patient. Lower panels indicate the support, anti-infectious, and immunomodulatory treatments received by the patient throughout his hospitalization. The timing of immunological evaluations is indicated by the red arrows. TA, tracheal aspirate; SOFA, sepsis-related organ failure assessment; CAP, community acquired-pneumonia; MV, mechanical ventilation; NO, nitric oxide; REM, remdesivir; HSCH, hydrocortisone hemisuccinate; IT, immunoglobulin therapy; IFN β1a, interferon β1a

Fig. 2

Kinetics and activation status of immune-cell subsets throughout the infection. a–c Frequency (left set of plots) of CD4 and CD8 T cell subsets (CD45RA+CCR7+: naïve (N), CD45RA+CCR7−: central memory (CM), CD45RA−CCR7−: effector memory (EM), CD45RA+CCR7−: terminal effector (TE)) (a), activated CD38+HLADR+ (b), and exhausted PD1+CD57+ CD4 and CD8 T cells (c). d Frequency of γδ T cells (gated on CD3+ T cells) and CD16 and NKG2A expression (gated on γδ CD3 T cells). e Frequency of B cell subsets (CD21+CD27−: naïve, CD21+CD27+: resting memory (RM), CD21−CD27+: activated memory (AM), CD21−CD27−: exhausted (Ex)) and plasmablasts (CD38++CD27+) gated on CD19+ B cells. f–h Frequency of NK-cell subsets (gated on CD3−) (CD56 Bright: CD56++CD16+, CD56dim: CD56+CD16+) (f), differentiated Ki67+ NK cells (gated on CD56dimCD57+ NK cells) (g) and inhibitor receptor NKG2A (gated on NK cells) (h). i Monocyte subsets (gated CD3−CD56−) (classical monocytes: CD14+CD16−, intermediate monocytes: CD16+CD14+, non-classical monocytes: CD14−CD16+) detected by flow cytometry of blood collected at days 14–20 following symptom onset from the patient and healthy donors (n = 5, median with interquartile range); gating examples shown to the right

Fig. 2

Kinetics and activation status of immune-cell subsets throughout the infection. a–c Frequency (left set of plots) of CD4 and CD8 T cell subsets (CD45RA+CCR7+: naïve (N), CD45RA+CCR7−: central memory (CM), CD45RA−CCR7−: effector memory (EM), CD45RA+CCR7−: terminal effector (TE)) (a), activated CD38+HLADR+ (b), and exhausted PD1+CD57+ CD4 and CD8 T cells (c). d Frequency of γδ T cells (gated on CD3+ T cells) and CD16 and NKG2A expression (gated on γδ CD3 T cells). e Frequency of B cell subsets (CD21+CD27−: naïve, CD21+CD27+: resting memory (RM), CD21−CD27+: activated memory (AM), CD21−CD27−: exhausted (Ex)) and plasmablasts (CD38++CD27+) gated on CD19+ B cells. f–h Frequency of NK-cell subsets (gated on CD3−) (CD56 Bright: CD56++CD16+, CD56dim: CD56+CD16+) (f), differentiated Ki67+ NK cells (gated on CD56dimCD57+ NK cells) (g) and inhibitor receptor NKG2A (gated on NK cells) (h). i Monocyte subsets (gated CD3−CD56−) (classical monocytes: CD14+CD16−, intermediate monocytes: CD16+CD14+, non-classical monocytes: CD14−CD16+) detected by flow cytometry of blood collected at days 14–20 following symptom onset from the patient and healthy donors (n = 5, median with interquartile range); gating examples shown to the right

Fig. 2

Kinetics and activation status of immune-cell subsets throughout the infection. a–c Frequency (left set of plots) of CD4 and CD8 T cell subsets (CD45RA+CCR7+: naïve (N), CD45RA+CCR7−: central memory (CM), CD45RA−CCR7−: effector memory (EM), CD45RA+CCR7−: terminal effector (TE)) (a), activated CD38+HLADR+ (b), and exhausted PD1+CD57+ CD4 and CD8 T cells (c). d Frequency of γδ T cells (gated on CD3+ T cells) and CD16 and NKG2A expression (gated on γδ CD3 T cells). e Frequency of B cell subsets (CD21+CD27−: naïve, CD21+CD27+: resting memory (RM), CD21−CD27+: activated memory (AM), CD21−CD27−: exhausted (Ex)) and plasmablasts (CD38++CD27+) gated on CD19+ B cells. f–h Frequency of NK-cell subsets (gated on CD3−) (CD56 Bright: CD56++CD16+, CD56dim: CD56+CD16+) (f), differentiated Ki67+ NK cells (gated on CD56dimCD57+ NK cells) (g) and inhibitor receptor NKG2A (gated on NK cells) (h). i Monocyte subsets (gated CD3−CD56−) (classical monocytes: CD14+CD16−, intermediate monocytes: CD16+CD14+, non-classical monocytes: CD14−CD16+) detected by flow cytometry of blood collected at days 14–20 following symptom onset from the patient and healthy donors (n = 5, median with interquartile range); gating examples shown to the right

Fig. 2

Kinetics and activation status of immune-cell subsets throughout the infection. a–c Frequency (left set of plots) of CD4 and CD8 T cell subsets (CD45RA+CCR7+: naïve (N), CD45RA+CCR7−: central memory (CM), CD45RA−CCR7−: effector memory (EM), CD45RA+CCR7−: terminal effector (TE)) (a), activated CD38+HLADR+ (b), and exhausted PD1+CD57+ CD4 and CD8 T cells (c). d Frequency of γδ T cells (gated on CD3+ T cells) and CD16 and NKG2A expression (gated on γδ CD3 T cells). e Frequency of B cell subsets (CD21+CD27−: naïve, CD21+CD27+: resting memory (RM), CD21−CD27+: activated memory (AM), CD21−CD27−: exhausted (Ex)) and plasmablasts (CD38++CD27+) gated on CD19+ B cells. f–h Frequency of NK-cell subsets (gated on CD3−) (CD56 Bright: CD56++CD16+, CD56dim: CD56+CD16+) (f), differentiated Ki67+ NK cells (gated on CD56dimCD57+ NK cells) (g) and inhibitor receptor NKG2A (gated on NK cells) (h). i Monocyte subsets (gated CD3−CD56−) (classical monocytes: CD14+CD16−, intermediate monocytes: CD16+CD14+, non-classical monocytes: CD14−CD16+) detected by flow cytometry of blood collected at days 14–20 following symptom onset from the patient and healthy donors (n = 5, median with interquartile range); gating examples shown to the right

Fig. 3

Heatmap of standardized biomarker expression in serum throughout the infection. The colors represent standardized expression values centered around the mean, with variance equal to 1. Biomarker hierarchical clustering was computed using the Euclidean distance and Ward’s method [11]. HD, healthy donors (n = 5); SS, septic shock (n = 5)