Abstract

Senecavirus A ( SVA ) is a newly emerged picornavirus causing swine idiopathic vesicular disease and epidemic transient neonatal losses, leading to considerable economic losses to global swine industry. While SVA transmission occurs through direct contact and vertically from sows to piglets, the risk posed by semen remains poorly characterized. This study investigated SVA prevalence in clinically healthy boar semen samples, and genetically characterized a novel recombinant SVA isolate from boar semen with low viral loads. The results of qRT-PCR revealed that 8.45% (18/213) of fresh semen samples were positive, with high Ct values, indicating subclinical SVA circulation and low viral loads shedding in the semen of partial Chinese boars. From five fresh semen samples from boars of no SVA shedding in body fluids and secretions, a novel semen-derived SVA/China/seHN-3–2/2024 was successfully isolated and identified with virus titers of 1 × 10 7.0 TCID 50 /100 μL in PK-15 cells. Complete genome sequencing and analysis revealed that SVA/China/seHN-3–2/2024 contains three special nucleotide mutations, and shared highest identity of 99.31% with GD06/2017, and the lowest identity of 91.78% with USA/MN88–36695/1988. Phylogenetic analysis indicated that the isolate was clustered within the traditional USA lineage alongside GD06/2017 and SVA/CHN/08/2017, and Chinese SVA strains have been constantly evolving toward more diversity and complexity. Recombination analysis demonstrated that the isolate likely originated from recombination between USA lineage USA/IA09–34037/2009 and Canadian lineage SVA/Canada/MB/NCFAD-104–9/2015, with the breakpoints in the VP3-VP1–2A-2B region. These findings first confirmed subclinical SVA shedding in Chinese boar semen and demonstrated that semen with low viral titers can harbor infectious virus, highlighting semen as a potential risk for inter-farm transmission, and providing a basis for SVA surveillance in global breeding stock and semen trad