SARS-CoV-2 antigen persistence links to postacute sequelae of COVID-19. (A) Patients were stratified based on viral qPCR positivity in any gut segment. Patients without evident mucosal viral RNA by PCR (negative [neg.]) were compared with patients with detectable viral RNA (positive [pos.]). Proportion of patients who reported symptoms compatible with postacute COVID-19 syndrome is shown in red. Note that 0/14 patients without detectable mucosal viral RNA (based on qPCR in any gut segment) reported symptoms, whereas postacute COVID-19 symptoms were reported from 21/32 patients with detectable RNA (with specific symptoms listed). Statistical significance was calculated using the Fisher exact test. (B) Patients were stratified according to nucleocapsid immunoreactivity as assessed using immunofluorescence and data is depicted equivalent to (A). (C) Proportion of patients without IBD medication, with 5-aminosalycilates, and with immunosuppressive therapy (ie, azathioprine, anti-TNF therapy, or vedolizumab) in both groups (defined using qPCR positivity). (D) Quantification of fecal calprotectin concentrations in both groups (defined using qPCR positivity) using ELISA. (E) Quantification of SARS-CoV-2 nucleocapsid specific T-cell responses defined using IGRA (according to qPCR positivity). (F) Proportion of patients with positive, borderline, and negative nucleocapsid IgG in both groups (defined using qPCR positivity). Borderline and negative results were pooled, and statistical significance was calculated using the Fisher exact test. (G) Relative quantification of indicated cytokines defined using ICFC of T cells from patients with or without anti-TNF therapy after exposure to peptides of the SARS-CoV-2 nucleocapsid (n = 5). Boxplots represent median percentages of cytokine-positive CD4+ and CD8+ cells. Differences between groups were calculated using the Fisher exact test (A and B), 2-tailed Student t tests (D, E, and F), and 2-way analysis of variance (ANOVA) with Sidak multiple comparison post-hoc test (G). Boxplots represent values as median (bold horizontal line), interquartile range (IQR) (box), and 1.5 x IQR (whiskers). Bars represent the mean and whiskers the standard deviation.