Defective viral genomes of porcine reproductive and respiratory syndrome virus type 2: Generation, characterization and interference effects on viral replication

Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) is a major swine pathogen that causes substantial economic losses worldwide. Defective viral genomes (DVGs) are important regulators of viral replication, persistence, and evolution in many RNA viruses. However, the characteristics and functions of DVGs generated during PRRSV-2 infection remain unknown. Here, we systematically analyzed publicly available high-throughput sequencing datasets and characterized DVGs generated during both in vitro and in vivo PRRSV-2 infection. We found that PRRSV-2 preferentially generates large deletion DVGs, particularly in porcine alveolar macrophages (PAMs), and that DVG formation is associated with microhomology sequences, RNA secondary structure and AU-rich sequences. Break positions were enriched in the GP5/M genomic region, whereas rejoin positions clustered predominantly within the nsp1/nsp2 genomic region of the PRRSV-2 genome. Notably, the deletion events within the same gene were highly enriched in the nsp2 region, where multiple naturally occurring nsp2 deletion sites overlapped with DVG junction sites. These findings suggest that DVG-associated recombination may contribute to the formation of PRRSV-2 nsp2 deletion variants. Functionally, PRRSV-2-derived DVGs exhibited potent broad-spectrum antiviral activity against multiple prevalent PRRSV-2 lineage strains and PRRSV-1. Overall, our findings provide the first systematic characterization of PRRSV-2 DVGs, reveal a potential evolutionary link between DVGs and nsp2 deletion variants, and highlight the antiviral potential of PRRSV-2 DVGs.