Fig. 5: Gene expression alteration of hamster lungs upon infection with Omicron subvariants.

A mRNA of the lung tissues obtained at day 2 post-infection was used to measure expression levels of inflammatory genes (Cxcl10, Il-6, Isg15, and Mx-1) with normalization using the housekeeping gene Rpl18. B Similarity of gene expression alteration upon infection with the Omicron subvariants and the ancestral B.1.1 lineage. Spearman’s correlation of the log 2-fold change (FC) value [infected versus uninfected hamsters] was calculated between pairs of variants. Results for 2 d.p.i. (left) and 5 d.p.i. (right) are shown. C Heatmap showing gene expression alteration caused by the respective variants at 2 d.p.i. The scaled fold change (FC) values for 438 genes that were differentially expressed between uninfected and infected hamsters and among the variants are shown. Genes were categorized into six clusters. Information on the clusters is summarized in Supplementary Data 1. D GO enrichment analysis for genes in the clusters. Of the significantly enriched GO terms, the top 3 terms are shown. The full list of GO terms is summarized in Supplementary Data 2. E Expression dynamics of genes in clusters 1 and 6 from 2 d.p.i. to 5 d.p.i. Gene expression levels were normalized as Z scores, and the mean values among replicates are shown. The black line indicates the mean dynamics. Genes associated with the GO terms “cell division” (for cluster 1) and “innate immune response” (for cluster 6) are colored. In A, each dot indicates the result from an individual hamster. The statistical significance of differences among Omicron subvariants was tested by Tukey’s multiplicity correction (*P < 0.05).