Nanopore direct RNA sequencing reveals transmissible gastroenteritis virus epitranscriptomic and transcriptomic landscapes modulated by gene 7

Viral non-structural proteins are key mediators of host-virus interplay, including RNA modification dynamics. The function of the transmissible gastroenteritis virus (TGEV) gene 7, which encodes a non-structural protein, remains poorly understood. Using Oxford Nanopore direct RNA sequencing, we explored the host and viral RNA landscapes modulated by TGEV gene 7 in Swine testis cells. Deletion of the TGEV gene 7 halved viral RNA replication yet significantly increased m6A modification levels on both the viral genome and host mRNAs. This epitranscriptomic rewiring was accompanied by reciprocal shifts in the m6A regulators FTO (eraser) and RBM15 (writer). Despite comparable bulk transcriptome changes, gene 7 deletion introduced additional differentially expressed genes, showing stronger enrichment of antiviral and chemokine pathways, indicating heightened innate immunity. PolyA analysis uncovered a gene 7-dependent extension of viral, but not host, polyA tails. These findings highlight RNA-modification machinery as a potential target for coronavirus control and provide a framework for vaccine strategies exploiting gene 7 attenuation.