Single-cell RNA sequencing analysis reveals a novel porcine alveolar macrophage subtype with high SLAMF7 expression promoting PRRSV infection

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major and highly contagious swine pathogen that severely impacts the global pork industry. Typically, porcine alveolar macrophages (PAM) isolated from pigs and infected with PRRSV are used to analyze viral pathogenesis, although it remains unclear whether it accurately reflects the in vivo disease process. In this study, scRNA-seq analysis revealed distinct transcriptional profiles between in vitro-cultured and freshly isolated PAMs. Inflammation, apoptosis, autophagy, and the TNF signal pathway were activated both in vivo and in vitro, however, only partial enriched GO terms and KEGG pathways were coincidental. Notably, PRRSV genomes were detected in the T and B cells in vivo, indicating a potential effect of PRRSV on T and B cell function. Results also showed that although PRRSV infection triggered robust inflammation, only a minority of PAMs were infected. Interestingly, bystander cells displayed similar inflammatory responses to those of PRRSV-infected cells, hinting at the role bystander cells play in the inflammatory response. Through scRNA-seq analysis, transcriptomic profiling of cells pre- and post-PRRSV infection revealed several distinct subclusters (S0-S7 and SS0-SS6), with the S5 subpopulation exhibiting the highest PRRSV infection rate and the SS6 subpopulation showing the fastest PRRSV replication rate. The <i>SLAMF7</i> gene emerged as a key gene in these two subpopulations infected with PRRSV. Knockdown of SLAMF7 significantly reduced PRRSV infection and suppressed PRRSV-induced inflammation, while its overexpression promoted replication of PRRSV and inflammation induced by PRRSV.