Abstract

Co-circulation of multiple viruses within a host can produce pathological outcomes distinct from those of single-virus infections. Over 700 million documented severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during the coronavirus disease 2019 (COVID-19) pandemic indicate frequent co-circulation of SARS-CoV-2 with other human viruses. However, how SARS-CoV-2 infection influences other viral infections remains unclear. In this study, we investigated how the proteolytic activity of SARS-CoV-2 papain-like protease (PLpro) influences infection by other human viruses. In silico analysis identified candidate PLpro cleavage sites across numerous viral proteins, and biochemical assays confirmed that PLpro catalyzes the degradation of Epstein–Barr virus (EBV) nuclear antigen 1 (EBNA1) in a manner requiring its protease activity. Both ectopic PLpro expression and SARS-CoV-2 infection reduced EBNA1 abundance, leading to reactivation of latent EBV. Given the essential role of EBNA1 in maintaining EBV-associated tumorigenesis, SARS-CoV-2 and PLpro-mediated degradation of EBNA1 can be translated into an inhibitory effect on EBV-driven tumor proliferation. These findings establish a molecular mechanism by which SARS-CoV-2 PLpro disrupts EBV latency and suppresses EBV-associated tumorigenesis, positioning EBNA1 as a potential therapeutic target in EBV-related malignancies.