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

Nilsson-Payant, Benjamin E; Uhl, Skyler; Grimont, Adrien; Doane, Ashley S; Cohen, Phillip; Patel, Roosheel S; Higgins, Christina A; Acklin, Joshua A; Bram, Yaron; Chandar, Vasuretha; Blanco-Melo, Daniel; Panis, Maryline; Lim, Jean K; Elemento, Olivier; Schwartz, Robert E; Rosenberg, Brad R; Chandwani, Rohit; tenOever, Benjamin R

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. IMPORTANCE The COVID-19 pandemic has caused significant mortality and morbidity around the world. Although effective vaccines have been developed, large parts of the world remain unvaccinated while new SARS-CoV-2 strains keep emerging. Furthermore, despite extensive efforts and large-scale drug screenings, no fully effective antiviral treatment options have been discovered yet. Therefore, it is of the utmost importance to gain a better understanding of essential factors driving SARS-CoV-2 replication in order to be able to develop novel approaches to target SARS-CoV-2 biology.