Key residues in SARS-CoV-2 NSP3 hypervariable region are necessary to modulate early stress granule activity

Antagonism of the host responses that limits viral replication is critical to the success of infection. Recently, we identified that the hypervariable region (HVR) of SARS-CoV-2 NSP3 binds to FXR1 and disrupts stress granule formation during the early stages of infection. Despite variation across the rest of the HVR, a 20-amino acid region, highly conserved in the Sarbecovirus family, is required for NSP3-FXR1 binding, but the critical residues remained unresolved. In this study, we explore the individual residues in NSP3 driving FXR1 binding and determine their impact on viral replication, pathogenesis, and stress granule formation. Our results indicate that the tyrosine at position 138 (Y138) and a phenylalanine at position 145 (F145) are required for FXR1 binding and affinity. Using reverse genetics, we showed that mutating NSP3 Y138A/F145A (YF mutant) reduced viral replication in vitro and in vivo. Importantly, we demonstrate that attenuation is not due to differential type I interferon responses but rather loss of stress granule control by the NSP3 mutant as compared to wild type. Together, our findings demonstrate the importance of Y138 and F145 within the NSP3-HVR in regulating stress granule formation at the early times post-infection.IMPORTANCEStress granules play a key role in host-antiviral defenses, and viruses have developed strategies to antagonize their activity. For SARS-CoV-2, the virus has two proteins that antagonize stress granules, with NSP3 acting early and nucleocapsid acting at late times. Here, we show that key NSP3 residues Y138 and F145, conserved across the Sarbecovirus family, are necessary to bind FXR1 and disrupt its activity in stress granule formation. Mutating these residues results in attenuation of SARS-CoV-2 replication and induces stress granule formation at early times post-infection. These results show the importance of these NSP3 residues in disrupting stress granule formation early and highlight multiple approaches SARS-CoV-2 uses to antagonize stress granule activation.