Transcriptional kinetics of NADC34-like porcine reproductive and respiratory syndrome virus during cellular infection

Abstract NADC34-like porcine reproductive and respiratory syndrome virus (PRRSV) has evolved complicated strategies to synthesize subgenomic RNAs (sgRNAs), but their plasticity and temporal dynamics remain to be elucidated. Here, next-generation sequencing (NGS) presented the high-resolution landscapes of the PRRSV subgenome, uncovered a striking heterogeneity in temporal kinetics and transcriptional control, and revealed extensive coordination between TRS-dependent and TRS-independent sgRNAs. Moreover, our study conducted a comprehensive reannotation of transcription regulatory sequence (TRS) locations and clarified that its usage involves canonical, alternative, and non-canonical splicing events for annotated genes. These findings have led to the realization that the coding of genetic information held in viral genomes is far more intricate than previously anticipated. Collectively, the altered sgRNA phenotype offered distinctive insight into novel PRRSV variant infections and gave an additional impetus to mining the functional long-range RNA-RNA interactome at active viral replication sites.