Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ

Hayn, Manuel; Hirschenberger, Maximilian; Koepke, Lennart; Straub, Jan H; Nchioua, Rayhane; Christensen, Maria H; Klute, Susanne; Bozzo, Caterina Prelli; Aftab, Wasim; Zech, Fabian; Conzelmann, Carina; Müller, Janis A; Badarinarayan, Smitha Srinivasachar; Stürzel, Christina M; Forne, Ignasi; Stenger, Steffen; Conzelmann, Karl-Klaus; Münch, Jan; Sauter, Daniel; Schmidt, Florian I; Imhof, Axel; Kirchhoff, Frank; Sparrer, Konstantin MJ

The innate immune system constitutes a powerful barrier against viral infections. However, it may fail because successful emerging pathogens, like SARS-CoV-2, evolved strategies to counteract it. Here, we systematically assessed the impact of 29 SARS-CoV-2 proteins on viral sensing, type I, II and III interferon (IFN) signaling, autophagy and inflammasome formation. Mechanistic analyses show that autophagy and type I IFN responses are effectively counteracted at different levels. For example, Nsp14 induces loss of the IFN receptor, whereas ORF3a disturbs autophagy at the Golgi/endosome interface. Comparative analyses revealed that antagonism of type I IFN and autophagy is largely conserved, except that SARS-CoV-1 Nsp15 is more potent in counteracting type I IFN than its SARS-CoV-2 ortholog. Altogether, however, SARS-CoV-2 counteracts type I IFN responses and autophagy much more efficiently than type II and III IFN signaling. Consequently, the virus is relatively resistant against exogenous IFN-α/β and autophagy modulation but remains highly vulnerable towards IFN-γ and -λ treatment. In combination, IFN-γ and -λ act synergistically, and drastically reduce SARS-CoV-2 replication at exceedingly low doses. Our results identify ineffective type I and II antagonism as weakness of SARS-CoV-2 that may allow to devise safe and effective anti-viral therapies based on targeted innate immune activation.