Transcriptome analysis revealed inhibition of lipid metabolism in 2-D porcine enteroids by infection with porcine epidemic diarrhea virus

Porcine epidemic diarrhea virus (PEDV) is a swine enterovirus that causes huge economic losses to the swine industry. It is of great interest to understand the gene expression patterns of host responses to PEDV infection and the mechanistic insights. Here, we report the differences of gene expression profiles by RNA-seq in the porcine small intestinal 2-D enteroids cells infected with low-passage (16 passages, P16) and high-passage (120 passages, P120) PEDV strains for 12, 24 and 36 h. Of the 57 genes differentially expressed in P16 PEDV infected enteroids, 49 were upregulated and 7 downregulated at all time points. There were 247 genes with different patterns of expression in the enteroids infected with P120 PEDV: upregulation seen with 105 genes and downregulation with the remaining majority at all time points. Infection of both P16 and P120 PEDV strains led to significant upregulation of ISGs, such as ISG15, MX1 and RSAD2. In particular, P120 PEDV infection inhibited transcription of genes related to lipid metabolism, including those involved in lipid decomposition, absorption, bile secretion and cholesterol metabolism. Treatment of the infected enteroids with palmitic acid resulted in marked reduction of replication of both P16 and P120 PEDV strains. These results indicate that PEDV might manipulate lipid metabolism of the host to benefit its replication. Further research is warranted to study the mechanisms how palmitic acid inhibits PEDV replication.