Diagnostic and pathological characterization of senecavirus A-associated epidemic transient neonatal losses in swine

Senecavirus A (SVA) has emerged as a significant viral pathogen of swine, traditionally associated with idiopathic vesicular disease but more recently linked to epidemic transient neonatal losses (ETNL), a syndrome characterized by increased mortality in piglets without consistent vesicular lesions. The mechanisms underlying SVA-associated neonatal mortality remain unclear due to the lack of specific clinical signs, frequent co-infections, and limited tissue characterization. This retrospective study analyzed 186 neonatal submissions (<24 days old) that were tested for SVA by RT-qPCR at the Iowa State University Veterinary Diagnostic Laboratory to elucidate the pathological, molecular, and microbial features associated with SVA infection. Clinical, histopathological, and microbiological data were compared between SVA-positive (n = 71) and SVA-negative (n = 253) cases, and selected tissues were analyzed by RNAscope® in situ hybridization (ISH) and immunohistochemistry (IHC) to localize viral RNA and assess co-infections with Rotavirus A and C. SVA was detected in 21.9% of cases, most frequently in feces, serum, and spleen with significantly lower Ct values on spleen (p < 0.05), indicating a higher viral load and suggesting preferential replication in lymphoid tissues. RNAscope® analysis confirmed SVA RNA localization in spleen, lymph node, and within lymphoid aggregates of the lamina propria of the small intestine and colon, supporting a lymphoid tropism and possible immune cell replication. Clinically, diarrhea and increased mortality were the most frequent findings and were strongly associated with SVA detection (p < 0.001). The occurrence of co-infections was common; 28.2% of SVA-positive animals had co-infection with Rotavirus A, while Rotavirus C and bacterial agents, such as Clostridium perfringens, E. coli, and Salmonella spp., were detected across both groups. Notably, respiratory pathogens including Streptococcus suis, Actinobacillus suis, and Streptococcus equisimilis were significantly more frequent in SVA-positive animals (p < 0.01), suggesting immunosuppression. Despite SVA's short viremic phase, its persistence in lymphoid tissues and association with mortality indicate a potential immunomodulatory role. These findings highlight SVA as a contributor to multifactorial neonatal disease, emphasizing the need for integrated molecular, histopathological, and epidemiological approaches to improve diagnosis and understanding of SVA pathogenesis.