Figure 3.

Shared CDR3 in the IgH and TRD cell subsets differentiate mild and severe subjects. (a) IgH-TRD Jaccard overlap matrix. Both IgH and TRD matrices were median normalized against each other. Positive values represent a greater proportion of shared IgH clones and negative values represent a greater proportion of shared TRD clones. (b) Logistic regression was used to model the odds ratio of non-zero vs zero overlap between pairs of samples from the IgH Jaccard overlap matrix. The model comprised different COVID-19 severity groups, and compared them against a healthy-healthy baseline as indicated by the vertical dashed line. As disease severity increases, the odds of finding shared IgH clones also increases between COVID-19 individual pairs. (c) Logistic regression comparing the odds ratio of non-zero vs zero overlap between pairs of samples from the TRD Jaccard overlap matrix, for COVID-19 severity groups compared against healthy-healthy background. As disease severity increases, the odds of finding shared TRD clones decreases between COVID-19 individual pairs. (d) McFadden's adjusted pseudo-R² for different models in terms of the association of COVID-19 clinical status (healthy, mild or severe) with sample covariates describing IgH-, TRB- and TRD- specific cell counts and clonal overlaps. In forest plots depicting logistic regression results (Figure 3B and C), the open circles are point estimates of odds ratios. The horizontal bars flanking them mark 95% confidence intervals of odds ratios.