The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, packages its large single-stranded RNA genome through a precise yet not fully revealed mechanism. Previous studies have indicated the presence of packaging signal (PS) within the viral genome that facilitate the assembly of new viral particles. In this study, we utilized an infectious virus-like particles (iVLPs) model to investigate the impact of untranslated regions (UTRs) on viral packaging and the content of N protein within. Also, we employed proximity ligation data to map the RNA interactome associated with PS9. We report the role of the 5' and 3' UTRs in packaging signal (PS)-mediated genome packaging. Through proximity ligation analysis, we demonstrated direct interactions between the UTRs and the PS9 element within the SARS-CoV-2 genome. We also found that the presence of UTRs enhances the packaging efficiency of iVLPs and recruits more nucleocapsid (N) protein, indicating that UTRs play a critical role in genome compaction and packaging. Subsequent analysis of SPLASH data allowed us to identify core sequences within the UTRs that interact with PS9, which are essential for initiating the packaging process. Furthermore, through multiple sequence alignment, we discovered that these sequences are highly conserved among different coronaviruses, particularly those causing severe outbreaks. This study provides new insights into the regulatory mechanisms of SARS-CoV-2 genome packaging, offering new targets for antiviral therapy. Also, these findings may contribute to a broader understanding of coronavirus assembly mechanisms.
 

mRNA,UTR,SARS-CoV-2,genome