Analyses of long non-coding RNAs and mRNA profiling through RNA sequencing of MDBK cells at different stages of bovine viral diarrhea virus infection

Background: Bovine viral diarrhea virus (BVDV) infection is a dynamic and complex process that leads to significant economic losses in the dairy and cattle industries. However, our understanding of the protective and pathological mechanism underlying host infection is limited. Methods: To determine whether BVDV regulates specific activities of the host cell, the expression of long non coding RNA (IncRNA) during BVDV NADL infection was studied by deep sequencing. Results: A total of 1236 lncRNA transcripts and 3261 mRNA transcripts were differentially regulated at 2 h, 6 h, and 18 h post-infection. The lncRNAs shared same characteristics with other mammals in terms of exon length, number, expression level, and conservation. The Gene Ontology (GO) enrichment and KEGG pathway analyses showed that lncRNAs regulate immune reaction during BVDV infection. Thirteen differentially expressed genes in 18 hpi were selected and independently validated by reverse-transcription qPCR. Conclusions: The present study is the first to provide insights into the biological connection of lncRNAs and BVDV, which can be further explored for the development of antiviral prevention strategies and in understanding persistent infection between viral and host components.