In order to establish an in vivo correlation with the observed loss of the epithelial barrier function in our in vitro super-infection model (Supplementary Fig. 5 and Fig. 2), we validated the downregulation of ZO-1 in the lung following viral infection (Supplementary Fig. 8f) and the increases in S. aureus invasion in the lung (Supplementary Fig. 10g and Fig. 5f) and bacteremia during super-infection (Supplementary Fig. 10h and Fig. 5g). The gene discussed is TJP1; the disease is infection.