Flaviviridae RdRp exploits NSUN2-driven m5C methylation to establish persistent infection

Flaviviridae viruses constitute formidable zoonotic agents with substantial global health and economic ramifications, attributable to their adeptness at circumventing host immune surveillance and establishing persistent infections across human and animal populations. Despite their pervasive impact, broadly effective antiviral strategies remain elusive. Emerging studies underscore the pivotal role of RNA modifications, particularly 5-methylcytosine (m5C), in fine-tuning host-pathogen interactions. Expanding upon prior evidence linking NSUN2-mediated m5C deposition to Classical swine fever virus (CSFV, Pestivirus of Flaviviridae) persistence, the present study demonstrates that Japanese encephalitis virus (JEV, Flavivirus of Flaviviridae) similarly commandeers host epitranscriptomic machinery. Specifically, JEV-encoded RNA-dependent RNA polymerase (RdRp) engages the SAE1 to induce SUMO3/4-mediated stabilization of NSUN2. Elevated NSUN2 promotes m5C methylation of Cebpd mRNA, expediting transcript degradation and dampening cGAS-STING-driven antiviral signaling. This regulatory cascade facilitates viral replication and persistence. This regulatory axis supports sustained viral replication and persistence. Notably, a homologous mechanism is operative in Orthomyxoviridae infection, indicating evolutionary convergence on NSUN2 as a proviral effector. Overall, these unprecedented findings define a conserved RdRp-SAE1-NSUN2-CEBPD axis as a key epitranscriptomic immune evasion strategy and nominate m5C methyltransferases as tractable targets for host-directed, broad-spectrum antiviral therapy.