Evolutionary Dynamics and Transboundary Spread of Senecavirus A: The Role of Recombination and Global Swine Trade.

Senecavirus A (SVA) is an emerging swine pathogen associated with vesicular disease and neonatal mortality, posing significant challenges to global swine health. Here, we report the isolation and identification of two contemporary SVA strains, JS01 and JS02, from clinically suspected cases in China. Both isolates demonstrated high replication competence and clustered within Clade Ib, the dominant globally circulating swine-associated lineage, showing close genetic ties to strains from southeastern China. Phylogenetic and recombination analyses identified multiple putative recombination events within nonstructural genomic regions, suggesting that recombination drives SVA diversification. Spatiotemporal analysis revealed uneven sequence availability over time and across regions, with sampling concentrated in Asia and the Americas during 2015-2018. Phylogeographic reconstruction indicated supported geographic transition connecting Brazil to China, the United States, and Canada. Notably, the inferred dispersal pattern visually overlapped with global live-swine trade networks, pointing to a potential possible link with animal trade. Furthermore, our analysis uncovered a divergent, marine-associated lineage (Clade II) comprising Senecavirus-like sequences from dolphins, which represents a distinct sister clade to terrestrial swine-associated viruses. These findings highlight the evolutionary complexity of SVA and emphasize the importance of genomic surveillance for investigating viral dispersal and its relationship with animal movements.