Upregulated gene expression at the site of infection in the URT (Table 2) shows that of the nine upregulated genes (gene expression >1 over mock challenged) on D3 post-challenge (MCP-1, CXCL10, TGFB1, STAT1, STAT2, STAT3, RIG-I, SOCS3, and TSLP), seven genes (MCP-1, CXCL10, STAT1, STAT2, STAT3, RIG-I, and SOCS3) showed greatest fold-increase following IAV (either CA or KS) infection, whereas only two genes (TGFB1 and TSLP) were highest following IBV (PH) infection. Here, TGFB1 is linked to infection.