Since 2010, porcine epidemic diarrhea virus (PEDV) has received global attention with the emergence of variant strains characterized with high pathogenicity. The pathogen–host interaction after PEDV infection is still unclear. To investigate this issue, high-throughput-based sequencing technology is one of the optimal choices. In this study, we used in vitro transcription sequencing alternative polyadenylation sites (IVT-SAPAS) method, which allowed accurate profiling of gene expression and alternative polyadenylation (APA) sites to profile APA switching genes and differentially expressed genes (DEGs) in IPEC-J2 cells during PEDV variant strain infection. We found 804 APA switching genes, including switching in tandem 3′ UTRs and switching between coding region and 3′ UTR, and 1,677 DEGs in host after PEDV challenge. These genes participated in variety of biological processes such as cellular process, metabolism and immunity reactions. Moreover, 413 genes, most of which are the “focus” genes in interaction networks, were found to be involved in both APA switching genes and DEGs, suggesting these genes were synchronously regulated by different mechanisms. In summary, our results gave a relatively comprehensive insight into dynamic host–pathogen interactions in the regulation of host gene transcripts during PEDV infection.

自2010年以来，猪流行性腹泻病毒（PEDV）随着高致病性变异株的出现而受到全球关注。PEDV感染后的病原体-宿主相互作用仍不清楚。为了研究这个问题，基于高通量的测序技术是最佳选择之一。在本研究中，我们使用体外转录测序替代多聚腺苷酸化位点 (IVT-SAPAS) 方法，该方法可以准确分析基因表达和替代多聚腺苷酸化 (APA) 位点，以分析 IPEC-J2 中的 APA 转换基因和差异表达基因 (DEG) PEDV 变异株感染期间的细胞。我们在PEDV攻击后发现了804个APA转换基因，包括串联3'UTR的转换以及编码区和3'UTR之间的转换，以及1,677个DEGs。这些基因参与了多种生物过程，例如细胞过程、新陈代谢和免疫反应。此外，发现413个基因，其中大部分是相互作用网络中的“焦点”基因，被发现参与APA转换基因和DEGs，表明这些基因受到不同机制的同步调控。总之，我们的结果对 PEDV 感染期间宿主基因转录物调控中的动态宿主 - 病原体相互作用提供了相对全面的见解。