SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production.

The SARS-CoV-2 genome encodes 16 nonstructural proteins (Nsps), with Nsp2 being the least conserved and understood. This study highlights a crucial role for Nsp2 in the early phase of the viral life cycle, particularly its interaction with GIGYF2, which relocates near double-membrane vesicles (DMVs) and enhances viral protein production. Deletion of the Nsp2-coding region from the viral genome led to a drastic reduction in viral RNA synthesis early in infection (3-4 h after infection). Interactome analysis in virus-infected cells identified GIGYF2, a host-encoded translational regulation protein, as a key Nsp2 partner. This interaction was confirmed for both SARS-CoV-1 and SARS-CoV-2. Depletion of GIGYF2 or its cofactor ZNF598 phenocopied the replication defects observed with Nsp2 deletion, suggesting their critical roles in viral reproduction. Upon infection, GIGYF2 and ZNF598 relocate to areas near DMVs, viral replication sites. This relocation does not occur with the Nsp2-deleted virus, indicating Nsp2's role in directing GIGYF2 to DMVs. Formaldehyde crosslinking and immunoprecipitation sequencing (fCLIP-seq) identified regions within viral RNAs that potentially interact with GIGYF2, including those encoding M and Orf6. Depletion of GIGYF2 resulted in decreased protein expression of M and Orf6. Our findings reveal the function of Nsp2 in supporting viral protein production by exploiting GIGYF2 as a host factor.