Statistical analysis

The data were assessed for normal distribution using the Shapiro–Wilk test and for the assumption of homogeneity of variance through Levene's test. Non-parametric analyses were conducted when the assumption of normality or homogeneity of variance was violated. Statistical analysis was performed using the one-way ANOVA with Dunnett's post hoc analysis, the Wilcoxon matched-pairs signed rank test, the Signed test, the paired t-test, the unpaired t-test or Pearson correlation as appropriate based on the results of assessing normality and a symmetrical distribution of differences using GraphPad Prism 10.01 or SAS. The sample size calculations for the experiments of assessing different levels of IL-1R1 expression by CD4⁺ T cell subsets incubated with S protein and the effect of IL-1β on cytokine expression by S protein-specific CD4⁺ T cells were done based on our previous work which assessed IL-1R1 expression by CD4⁺ T cells and the effects of IL-1β on IL-17 production by IL-1R1⁺CD4⁺ T cells stimulated with anti-CD3/CD28 antibodies.³ The calculations were done using PASS software (Power Analysis and Sample Size, NCSS and PASS). Given the nature of single cell RNA-seq and CyTOF analyses, the sample sizes for these analyses were determined based on our published study which used the same analytic tools.¹⁰ For the experiment of investigating the effect of the anti-IL-1R1 blocking antibody treatment in mice, the sample size calculation was done based on previously published studies in mice and humans.^3,12 The additional details on the sample size calculations were provided in the Supplementary Methods.