Project description:Porcine deltacoronavirus (PDCoV) is a newly emerging and special delta coronavirus, which infect mammals such as pigs, cattle and humans, as well as chickens and birds. Exploring RNA structures in the viral genome benefits the understanding of the role of RNA in the lifecycle of viruses. In this study, vRIC-seq is employed to analyze the RNA-RNA interaction in the whole genome structure of PDCoV in virions. About 12.87 and 13.52 million paired reads are obtained in two biological replicates, respectively, with 17.9% and 14.8% of them are identified as valid chimeric reads. These are employed to predict the RNA secondary structure, which is compact and highly structured. A twisted-cyclized conformation is observed in the RNA-RNA interaction map of PDCoV for the first time. 77 multi-way junctions are evenly distributed in the PDCoV genome. Our work provides fundamental structural insights that are essential for understanding the genomic structure and function, genetic evolution, and packaging characteristics of PDCoV.
Project description:mircoRNAs (miRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of miRNAs in ST cells uninfected or infected by PDCoV by high-throughput sequencing
Project description:Circular RNAs (circRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of circRNAs in swine testicular (ST) cells uninfected or infected by PDCoV by high-throughput sequencing.
Project description:Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that causes acute diarrhea, vomiting, dehydration, and even death in piglets, resulting in serious economic losses to the pork industry worldwide. PDCoV has received much attention owing to its broad host range, including humans, posing a potential threat to public health. However, the prevalence, characteristics, and host cellular gene expression of PDCoV remain poorly understood. In this study, a new PDCoV strain (CHN/SX-Y/2023, GenBank number PQ373831) was successfully isolated, identified, and subjected to phylogenetic tree and transcriptome analyses in human hepatoma (Huh7) cells following PDCoV infection. The results showed that the CHN/SX-Y/2023 strain belongs to the Chinese lineage and causes cytopathic effects in the cells of various species. Based on transcriptome analysis, 1799 differentially expressed genes (DEGs) were upregulated and 771 were downregulated during PDCoV infection. Among the upregulated genes, FCGR1A, VSIG1, TNFRSF9, and PLCXD3 are associated with immunity, inflammation, and lipid catabolism. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the upregulated DEGs were significantly enriched in the MAPK, TNF, and NF-κB signaling pathways and viral protein interactions with cytokines and cytokine receptors. Protein-protein interaction networks showed that the upregulated genes CXCL8, DUSP1, PTGS2, and IL15 were associated with inflammation and immunity. In addition, the protein levels of ACSL4, LC3-II, and p-IRF3 increased, suggesting that PDCoV infection in Huh7 cells induces an intrinsic immune response, cellular autophagy, and ferroptosis. Collectively, our findings provide new insights into the characteristics and mechanisms of PDCoV infection.
Project description:Long noncoding RNAs (lncRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of lncRNAs and mRNAs in the PDCoV-infected cells by high-throughput sequencing