Fig. 6: Upper airway host gene expression and the nasal microbiome differ between SOT recipients and controls.

a Gene set enrichment analysis (GSEA) highlighting pathways differentially enriched in solid organ transplant (SOT) recipients (yellow, n = 63) versus controls (blue, n = 125) in the upper respiratory tract (without adjustment for SARS-CoV-2 viral reads per million (rpM)). b Differences in the longitudinal dynamics of signaling pathways. A positive normalized enrichment score (NES) value indicates that the pathway was enriched over time in SOT. A negative NES value indicates that the pathway was enriched over time in controls. c Longitudinal plots highlighting changes in normalized expression of representative immune signaling pathways that showed significantly different dynamics in SOT recipients versus controls. The ribbons indicate the 95% confidence interval of the linear mixed-effects model fits. P values were calculated with a a linear model or b, c a linear mixed-effects model with Benjamini–Hochberg correction. d Box plot demonstrating differences in upper airway bacterial microbiome alpha diversity in SOT recipients (n = 86) versus controls (n = 172). Boxes show the median and interquartile range (IQR), whiskers were calculated as the 25th percentile minus 1.5 times the IQR and the 75th percentile plus 1.5 times the IQR. P values were calculated with the two-sided Wilcoxon rank-sum test. e Robust regression with 95% confidence intervals highlighting the longitudinal changes in upper airway alpha diversity following hospitalization. f Radial plot highlighting differential abundance from genus (inner most ring) to phylum (outer most ring) and phylogenetic relatedness (inner tree) of taxa differentially enriched in SOT recipients versus controls. P values in (e, f) were calculated with a linear mixed-effects model and f Benjamini–Hochberg correction). The number of patients sampled at each time point is depicted graphically below the X axis of (c, e).