Nanopore direct-RNA sequencing reveals TGEV epitranscriptomic and transcriptomic landscapes modulated by gene 7

Viral non-structural proteins have gained increasing attention for their roles in regulating host-virus interplay and reported to act as a key mediator of host and virus RNA modification dynamics. Transmissible gastroenteritis virus (TGEV) gene 7 has been implicated in virulence, but its other molecular functions remain unclear.

Here, we compared wild-type TGEV (TGEV-wt) with a recombinant strain lacking gene 7 (TGEV-Δ7) in swine testis cells using Oxford Nanopore direct RNA sequencing. High-coverage datasets enabled simultaneous profiling of the full-length transcriptome, N6-methyladenosine (m6A) modifications, and polyA tail length.

Deletion of TGEV gene 7 halved viral RNA replication yet increased m6A modification by ∼32 % across the viral genome, and elevated host m6A levels by ∼17 %, accompanied by reciprocal shifts in the m6A regulators FTO (eraser) and RBM15 (writer). Despite bulk transcriptome changes were comparable between strains, gene 7 deletion introduced additional DEGs beyond WT infection, showing stronger enrichment of antiviral and chemokine pathways, indicating heightened innate immunity. PolyA analysis uncovered the polyA features of TGEV gRNA and sgRNAs, and revealed a gene 7 dependent extension of viral by 7 nt, 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.