Fig. 7: Host response to CoV strains are similar to other respiratory viruses.

a Box plots revealing a strong and equivalent upregulation of summary (eigengene [E_g]) expression for the interferon response network among ORV- and CoV-infected GALA II subjects (n = 22, 9 respectively), compared to uninfected subjects (n = 582). Differential expression analysis between infected and uninfected groups was performed with a two-sided t-test. b Box plots revealing a strong and equivalent upregulation of summary (eigengene [E_g]) expression for the cytotoxic immune response network among ORV- and CoV-infected GALA II subjects (n = 22, 9 respectively), compared to uninfected subjects (n = 582). Differential expression analysis between infected and uninfected groups was performed with a two-sided t-test. c Scatterplot showing the similarity in log₂FC differential expression of genes in ORV (x axis) and CoV (y axis) infected individuals relative to uninfected subjects. The color of the points corresponds to the group in which each gene was identified as significant (FDR < 0.05, absolute log₂FC > 0.5). The Pearson correlation coefficient of the significant genes (excluding the “Neither” category) is 0.95. Top enrichment terms for genes that were significantly differentially expressed in both virus infections (blue) are shown. d Top upstream regulators predicted by Ingenuity Pathway Analysis to be regulating the genes that were upregulated in CoV. Enrichment values for these CoV regulators, using the ORV upregulated genes are also shown. Enrichment p-values were obtained from IPA. No multiple comparison adjustment was performed. e Box plots revealing upregulation of IL6 expression in virus-infected individuals (n: CoV⁺ = 9, ORV⁺ = 22, non-infected = 582). Differential expression analysis was performed with limma. Benjamini–Hochberg correction was used to control for false discovery rate. f Box plots revealing upregulation of ACE2 expression in virus-infected individuals (n: CoV⁺ = 9, ORV⁺ = 22, non-infected=582). Differential expression analysis was performed with limma. Benjamini–Hochberg correction was used to control for false discovery rate. Box centers give the median, upper and lower box bounds correspond to first and third quartiles and the upper/lower whiskers extend from the upper/lower bounds up to/down from the largest/smallest value, no further than 1.5 × IQR from the upper/lower bound (where IQR is the inter-quartile range). Data beyond the end of whiskers are plotted individually.