Fig. 3: Association of the PBMC transcriptome and COVID-19 severity.

a PCA of the PBMC transcriptome. Each point represents a sample and is coloured by contemporaneous COVID-19 WHO severity (left) and overall clinical course (right). b The 30 GSVA transcriptomic pathway enrichment terms with the greatest RRA scores. All were significantly enriched in both Wave 1 and 2 cohorts (1% FDR). Terms are ordered and coloured by their effect size. Red=up-regulated in more severe COVID-19; blue=down-regulated. c Violin plots show gene expression values (Wave 1 cohort; n = 179 samples from 51 COVID-19 positive ESKD patients and 55 samples from COVID-19 negative ESKD patients) stratified by COVID-19 status and severity (at time of sample) for selected genes. Shaded areas indicate kernel density estimates. For boxplots, centre=median, upper bound=upper quartile (UQ), lower bound=lower quartile (LQ), upper whisker=largest value at most 1.5 * IQR (inter-quartile range) from the UQ, lower whisker=smallest value at most 1.5 * IQR from the LQ, points=samples outside of the range of the whiskers. All genes shown were significantly associated (1% FDR) with severity in both the Wave 1 and 2 cohorts. Genes are grouped by membership to pathways that were significantly enriched (1% FDR) in GSVA.