Transcriptomic analysis of small intestinal mucosa from porcine epidemic diarrhea virus infected piglets

Abstract

A B S T R A C TCaused by porcine epidemic diarrhea virus (PEDV), porcine epidemic diarrhea (PED) is an acute infectious disease which causes damage to the intestine including intestinal villus atrophy and shedding, leading to serious economic losses to the pig industry worldwide. In order to obtain detailed information about the pathogenesis and host immune response in a PEDV-infected host for first In vivo study we used high-throughput sequencing to analyze the gene expression differences of the small intestinal mucosa after infection with PEDV. Transcripts obtained were over 65,525,000 clean reads after reassembly were 22,605 genes detected, of which 22,248 were known genes and 371 new genes were predicted. Moreover, 3168 genes expression was up-regulated and 3876 genes down-regulated. (Gene Ontology) GO annotation and functional enrichment analysis indicated that all of the DEGs (differentially expressed genes) were annotated into biological process, cellular component and molecular function. Most of these unigenes are annotated in cellular processes, the cell and binding. KEGG analysis of the DEGs showed that a total of 7044 DEGs unigenes were annotated into 323 pathways classified into 6 main categories. Most of these unigenes are annotated were related to immune system response to the infectious diseases pathways. In addition, 20 DEGs were verified by quantitative real-time PCR. As the first, in vivo, RNAseq analysis of piglets and PEDV infection, our study provides knowledge about the transcriptomics of intestinal mucosa in PEDV-infected piglets, from which a complex molecular pathways and pathogenesis-related biological processes are involved in PEDV interaction with piglet intestinal mucosa.

Microarray analysis reveals the inhibition of intestinal expression of nutrient transporters in piglets infected with porcine epidemic diarrhea virus

“…There is very little information available on the regulation of intestinal transporters in piglets by PEDV infection 22–25 . Schweer 26 found that PEDV infection decreased the GLUT2 mRNA level but increased the SLC6A14 level in the piglet jejunum.…”

“…Regarding the omic studies with PEDV-infected pigs, Sun et al . 22 found that PEDV infection enhanced the expression of 7044 genes and most of them were related to the immune response to infectious disease pathways. Of note, based on the KEGG analysis, 374 of the differentially expressed genes (DEGs) are related to nutrient transport and catabolism, and this result is in good agreement with that of our present study.…”

RNA-Seq-Based Whole Transcriptome Analysis of IPEC-J2 Cells During Swine Acute Diarrhea Syndrome Coronavirus Infection

“…Most viruses attempt to change host cellular processes and organism systems to improve the efficiency of virus infection, and, on the other hand, the cells employ multiple mechanisms in responses to generating an antiviral state (13,14). As reported, CoV infection can cause alterations in the transcription and translation patterns, cell cycle, cytoskeleton, and apoptosis pathways of host cells (15)(16)(17)(18)(19)(20)(21)(22). With traditional approaches, it is difficult to explore the intricate and mass interactions between viruses and hosts/cells.…”

“…Next-generation' sequencing (NGS) technology has provided a powerful tool for the studies of emerging and re-emerging human and animal pathogens/diseases. NGS technology, including whole genome sequencing, RNA-Seq, and single cell sequencing, has been extensively applied in genome sequencing, gene expression profiling analysis, and pathogen detection ( 15 , 23 – 25 ).…”

Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells

“…This reliable platform with a high-throughput and powerful tool guarantees the enormous gene study. Across all RNA species, RNA-seq has revolutionized and become a widely used approach to study quantitative aspects of transcriptome profiling in the virus-infected cells Sun et al, 2014Sun et al, , 2019Zhou et al, 2017). In the current study, we have explored the miRNA milieu in CRFK cells infected with CPV-2c Laotian isolates (Puentes et al, 2012).…”