Distinct cell-type-specific gene expression programs associated with persistence versus clearance of arterivirus infection

ABSTRACT This study aims to identify cellular markers correlated to persistent viral infection by a comprehensive comparison of blood immune transcriptomes and cell composition from acute and long-term stages of infection using a porcine arterivirus as the model. We applied single-cell RNA sequencing (scRNA-seq) to characterize blood mononuclear cells collected at 14 (acute) and 84 (long-term) days post-infection (DPI) with porcine reproductive and respiratory syndrome virus (PRRSV). Pigs were grouped as persistently infected (PI, n = 5 at 14 DPI; n = 10 at 84 DPI) or virus-extinct (VE, n = 2) phenotypes based on detection of viral RNA in blood collected weekly and tissue samples collected at either 14 or 84 DPI. Monocytes emerged as the primary cellular drivers of infection outcome, with divergence driven mainly by cell-type-specific transcriptional programs rather than differences in immune cell compositions. At 14 DPI, genes expressed at higher levels in monocytes from VE pigs, which were enriched for activation of antiviral and interferon responses, and subsequently transitioned toward a homeostatic profile by 84 DPI. In contrast, monocytes from PI pigs were characterized by metabolic dysregulation at 14 DPI, followed by a chronic inflammation profile at 84 DPI. Temporal analysis revealed the “when and how” rather than the intensity of immune activation as a critical determinant of outcome, with PI pigs failing to mount early, effective antiviral responses. Collectively, these findings identified early monocyte transcriptional programs associated with PRRSV persistence, offering a potential application in the selection of biomarkers for disease surveillance and outbreak management in swine production. IMPORTANCE Persistent viral infection remains a critical challenge in human health, as well as livestock disease management, yet the viral-host immune mechanisms that determine whether infection resolves or persists remain poorly understood. This study used a swine arterivirus persistent infection model system along with advanced single-cell RNA sequencing (scRNA-seq) technology to address a broad biological significance question—how circulating immune cell-type-specific transcriptional programs at early stages of infection determine long-term viral outcomes in the host. This work generated the first scRNA-seq data set for porcine reproductive and respiratory syndrome virus (PRRSV) persistent infection and provides a framework for mining cell-type-resolved blood transcriptomes, which could assist in developing therapeutic strategies to manipulate host immune responses toward viral extinction pathways during infection.