Fig. 4: Prolonged viral shedding is associated with T-cell exhaustion.

A Spearman correlation matrix focusing on the most significant immune variables and serum analytes monitored within the first 20 days of symptoms in patients diagnosed with COVID-19 in the Cancer_FR1_TR cohort. Stars indicate significant values (P < 0.05) for positive (red) or negative (blue) correlations. B Percentages of PD-1 expressing cells within the non-naive CD8⁺CD3⁺ population (B, upper panel), monitoring in various phases of COVID-19 presentation (no virus infection (Ctls, gray dots), asymptomatic viral infection (Asym, light blue dots), symptomatic viral infection examined in the first 20 days (≤20 d) or after 20 days (>20 d) of symptoms with those experiencing short-term viral RNA shedding (SVS, orange dots) or long-term viral RNA shedding (LVS, purple dots) and RT-qPCR-negative COVID-19 patients in the convalescent phase (recovery, green dots or circled dots) among Cancer_FR1_TR (B, middle panel) and Spearman correlation with the duration of SARS-CoV-2 RT-qPCR positivity measured within the first 20 days of symptoms (B, lower panel). C Percentages of subsets co-expressing PD-1 and Granzyme B (C, left panel) or Granzyme B and FasL (C, right panel) in non-naive CD8⁺. D Percentage of PD-1⁺ and Granzyme B⁺ within the non-naive CD8⁺ expressing Eomes^highTCF-1^high gate (D, left panel) and Spearman correlation between this ratio measured within the first 20 days of symptoms with the duration of SARS-CoV-2 RT-qPCR positivity (D, right panel). Box plots display a group of numerical data through their 3rd and 1st quartiles (box), mean (central band), minimum, and maximum (whiskers). Each dot represents one sample, each patient being drawn one to three times. Statistical analyses used one-way ANOVA with Kenward–Roger method to take into account the number of specimen/patients: *P < 0.05, **P < 0.01, ***P < 0.001. Each line and dot represents one patient and one sample, respectively (B, middle panel).