Early acute infection and A549 infected cells shared 150 upregulated genes including ATF3 (Figure 3D), a stress induced transcription factor, as well as other genes involved in the innate immune response such as MX1, DDX58/RIG-I, IFIT1, IFIT2, DHX58/MDA5, and OASL (Supplementary Tables S3 and S5). Here, IFIT1 is linked to infection.