Fig. 2: Genetic programs preferentially activated in vaccinated COVID-19 hospitalized patients compared to unvaccinated ones.

a Canonical pathway analysis of significantly enriched genes in clusters for innate immune-related biological processes, including OAS antiviral response. b Relative mRNA levels of 20 genes that are induced in vaccinated patients as compared to unvaccinated ones and enriched in IFN signaling are presented by bar graphs. A p value by the Wald statistic from DESeq2 were listed in Supplementary Data 2. *p < 0.05, ***p < 0.0001, ****p < 0.00001. c–f Relative normalized expression of OASs gene from unvaccinated and vaccinated patients in longitudinal analysis (c–e) as well as Day 0 and Days 7–10 of naïve volunteers receiving the first dose of the BNT162b2 vaccine (f). A two-tailed unpaired t-test with Welch’s correction was used to evaluate the statistical significance between two groups as well as two time points. *p < 0.05, **p < 0.001, ***p < 0.0001, ****p < 0.00001. g OAS1-3 mRNA levels from primary bronchial cells untreated or treated with different IFNs were measured by RNA-seq. Results are shown as the means ± s.e.m. of independent biological replicates (n = 3). Two-way ANOVA followed by Tukey’s multiple comparisons test was used to evaluate the statistical significance of differences. h ChIP-seq for STAT transcription factors, the histone marks H3K27ac and H3K4me3, and Pol II was conducted in primary bronchial cells at the absence and presence of IFNβ¹². i Relative mRNA levels of three genes that are induced in vaccinated patients as compared to unvaccinated ones and enriched in p53 regulated cell cycle arrest are presented by bar graphs. A p value by the Wald statistic from DESeq2 were listed in Supplementary Data 2. *p < 0.05.