Deciphering immune features and cellular heterogeneity in PRRSV infection via single-cell RNA sequencing

Porcine reproductive and respiratory syndrome virus (PRRSV), a major immunosuppressive pathogen, inflicts substantial economic losses on the global swine industry. Despite extensive research into PRRSV pathogenesis, the mechanisms by which PRRSV induces immune dysfunction <i>in vivo</i> remain incompletely understood. Here, we performed single-cell RNA sequencing on cells isolated from the lung of PRRSV-infected piglets, generating transcriptomic profiles for 46,922 single cells encompassing 15 major cell types. We observed a significant reduction in the number of macrophages in lung tissues, which was primarily attributed to the extensive apoptosis of macrophages induced by PRRSV infection. PRRSV infection triggered aberrant differentiation of macrophage, and the SPP1^high macrophage subpopulation was identified as the primary target cells for PRRSV infection. Cell-cell communication analysis revealed that PRRSV infection enhanced ligand-receptor interactions between macrophages and other cell types, associated with inflammatory responses, activation of T cells and B cells, and cell adhesion. In addition, monocytes exhibited a tendency to differentiate into macrophages, potentially compensating for the depletion of macrophages caused by PRRSV infection. Moreover, PRRSV infection caused abnormal development of B cells and incomplete activation of cytotoxic T lymphocytes in the lungs. This study provides a comprehensive characterization of how PRRSV perturbs pulmonary immune cell populations, offering valuable insights into the mechanisms underlying PRRSV-induced lung injury.IMPORTANCEPorcine reproductive and respiratory syndrome virus (PRRSV) has consistently posed a significant and enduring threat to the swine industry. However, the virus-host interactions during <i>in vivo</i> infection <i>in vivo</i> remain poorly understood. In this study, we applied single-cell RNA sequencing to characterize the cellular heterogeneity of lung tissues from PRRSV-infected piglets. Through intracellular viral RNA tracking, we identified SPP1^high macrophages as the primary reservoir of PRRSV. Furthermore, we analyzed the cell-cell communication between macrophages and other cell types and investigated the immune responses and heterogeneity of monocytes, T cells, and B cells upon PRRSV infection. Our findings provide a comprehensive single-cell landscape of the complex host-pathogen interplay during PRRSV infection.