Interaction and co-phase separation of SARS-CoV-2 nucleocapsid protein and human hnRNPA1 and its implications for viral life cycle

The nucleocapsid (N) protein of SARS-CoV-2 is central to viral assembly and replication. It binds viral RNA to form a helical nucleocapsid and enabling genome packaging and release into host cells. Human hnRNPA1, one of the most abundant RNA-binding proteins in eukaryotes, regulates key aspects of RNA metabolism, including splicing, transcription, localisation, and transport. Here, we report a direct physical interaction between SARS-CoV-2 N protein and hnRNPA1 with moderate affinity (Kd ∼ 0.18 μM), primarily mediated through their intrinsically disordered regions. Furthermore, we found that these proteins co-phase separate in vitro and co-localise within stress granules in cells. In vivo studies reveal that hnRNPA1 suppresses viral replication, suggesting that the N protein – hnRNPA1 interaction plays an important role in modulating the viral life cycle.