Systemic pathogenesis and complete genome characterization of encephalomyocarditis virus in naturally infected pigs during high‑mortality outbreaks in Brazil

Abstract Encephalomyocarditis virus (EMCV) is an emerging cardiovirus associated with high mortality in swine, but natural infections in South America have been poorly characterized. We investigated outbreaks of sudden death in growing–finishing pigs from three commercial farms in Brazil using an integrated clinical, pathological, molecular, and genomic approach. Affected herds experienced mortality peaks of up to 19% and necropsies revealed multifocal myocardial necrosis with IBA1⁺ macrophage-predominant inflammation, mineralization, and reparative changes, as well as concentric left ventricular hypertrophy suggestive of viral-induced remodeling. In situ hybridization confirmed active viral replication in cardiomyocytes, macrophages, splenic germinal centers, renal tubular epithelium, and pulmonary inflammatory cells, indicating systemic dissemination and supporting urinary shedding as a possible transmission route. PCR detected EMCV in cardiac and lymphoid tissues, and full-genome sequencing of a cardiac isolate identified a 7.5-kb Cardiovirus A1 strain with > 99% VP1 identity to contemporary Brazilian rodent and swine strains, suggesting sustained circulation at the rodent–swine interface. This study provides the first complete genomic characterization of EMCV in Brazil and South America, expands the recognition of tissue tropism and highlights the need for enhanced surveillance and control strategies in intensive pork production systems.