Raw data of "Single-cell RNA sequencing analysis revealed a novel porcine alveolar macrophage subtype with high SLMAF7 expression promoting PRRSV infection"

Porcine reproductive and respiratory syndrome virus (PRRSV), a major swine pathogen, causes a highly contagious disease that severely impacts the global pork industry. Typically, porcine alveolar macrophage (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. Herein, using single-cell RNA sequencing (scRNA-seq), significant differences were found in PAMs between culture in vitro and freshly isolated. Inflammation, apoptosis, autophagy, and TNF signal pathway were activated both in vivo and in vitro, however, partially GO terms and KEGG pathways were coincidence. Notably, PRRSV genomes were detected in T and B cells in vivo, indicating the potential effect of PRRSV on T and B cells function. We also found that although PRRSV infection triggered robust inflammation, only a minority of PAMs were infected. Interestingly, bystander cells in displayed similar inflammatory responses to those in PRRSV-infected cells, suggesting a role for bystander cells in the inflammatory response. Through scRNA-seq analysis, transcriptomic profiling of cells pre- and post-PRRSV infection revealed several distinct subclusters (S1–S8 and SS1–SS7), with the S6 subpopulation exhibiting the highest PRRSV infected rate and the SS7 subpopulation showing the fastest PRRSV replication rate. The SLMAF7 emerged as a key gene in these two subpopulations for PRRSV infection. Knockdown of SLMAF7 significantly reduced PRRSV infection and suppressed PRRSV-induced inflammation. Collectively, our findings provide insights into the host response to PRRSV infection and identify SLAMF7 as a novel potential therapeutic target tackling PRRSV infection.