The NF-κB transcriptional footprint is essential for SARS-CoV-2 replication

SARS-CoV-2, the etiological agent of COVID-19, is characterized by a delay in Type I interferon (IFN-I)-mediated antiviral defenses alongside robust cytokine production. Here we investigate the underlying molecular basis for this imbalance and implicate virus-mediated activation of NF-κB in the absence of other canonical IFN-I-related transcription factors. Epigenetic and single cell transcriptomic analyses show a selective NF-κB signature that was most prominent in infected cells. Disruption of NF-κB signaling through the silencing of the NF-κB transcription factors p65 or p50 resulted in loss of virus replication that was rescued upon reconstitution. These findings could be further corroborated with the use of NF-κB inhibitors, which reduced SARS-CoV-2 replication in vitro. These data suggest that the robust cytokine production in response to SARS-CoV-2, despite a diminished IFN-I response, is the product of a dependency on NF-κB for viral replication. (1) Independent biological triplicates of transformed lung alveolar (A549) cells transduced with a vector expressing human ACE2 infected with SARS-CoV-2 (USA-WA1/2020, MOI: 2) for 2/4/6/9/12/18/24 hours. Samples were examined by mRNA-seq. (2) Independent biological triplicates of transformed lung alveolar (A549) cells transduced with a vector expressing human ACE2 infected with SARS-CoV-2 (USA-WA1/2020, MOI: 0.01) for 24 hours. Samples were examined by scRNA-seq. (3) Independent biological triplicates of transformed lung alveolar (A549) cells transduced with a vector expressing human ACE2 infected with SARS-CoV-2 (USA-WA1/2020, MOI: 0.1) for 24 hours. Samples were examined by ATAC-seq.