Emergence of a novel triple - lineage recombinant PRRSV with twelve complex hotspots in China

In recent years, the co-circulation of multiple porcine reproductive and respiratory syndrome virus (PRRSV) lineages in China has markedly increased viral diversity through frequent recombination events. In this study, we report the isolation and characterization of a novel PRRSV strain, designated N1, obtained during a severe outbreak with high mortality in a vaccinated pig farm in Hebei province in 2024. Genomic analysis reveals that the N1 strain (15,016 nt in length) represents a complex triple-lineage recombinant. Its genome backbone is primarily derived from Lineage 8.3 (JXA1-like), with significant segments acquired from Lineage 1.8 (NADC30-like) and Lineage 3 (QYYZ-like). Recombination analysis, confirmed by both SimPlot and RDP4, identified 12 distinct breakpoints, partitioning the genome into 13 regions and highlighting hotspots within Nsp1, Nsp2, Nsp3, Nsp4, Nsp7, Nsp9, Nsp12, ORF3, and ORF5. Pathogenicity assessment in 6-week-old piglets demonstrated that the N1 strain induces significant clinical disease, characterized by persistent high fever, reduced average daily gain, prolonged viremia, and severe lung pathology including interstitial pneumonia. These findings underscore the role of multi-lineage co-infection in driving the emergence of novel, pathogenic recombinant strains. The study highlights the critical need for enhanced surveillance of such complex recombinants and the development of updated vaccines and control strategies to mitigate their impact on the swine industry.