TNF and infection: To better understand the differences in the immune response induced by different SARS-CoV-2 variants, we performed lung mRNA cytokine profiling on days 2, 5, and 7 post infection (Fig. 3). We investigated differential gene expression of pro-inflammatory cytokines (IL-1α, IL-1β, CCL2, CCL3, CXCL9, CXCL10, IRF-1, TNF-α) and anti-inflammatory cytokines (COX2, IL-10, IL-4, IL-6, and TGF-β, Type II IFN: IFN-γ; and type III IFN response: IFN- λ) in infected lung tissues (Fig. 3A–D).