Grass carp hemorrhagic disease is a fatal disease caused by the grass carp reovirus (GCRV). The aberrant regulation of transcripts has been implicated in many types of diseases. In the present study, we characterized mRNA and miRNA transcriptomes of different virulent GCRVs using RNA sequencing (RNA-Seq). One hundred eighteen miRNAs were identified as being differentially expressed between different virulent viruses in grass carp fibroblasts. Eight miRNAs were selected to verify the RNA-Seq results using RT-PCR and mRNA methods. In total, 996 differentially expressed mRNA genes were identified in grass carp fibroblasts, while 901 miRNA-mRNA target pairs were observed to be inversely regulated in grass carp fibroblasts. Integrated mRNA/miRNA expression profiling analysis results showed that the most influenced processes were the immune response and cell death. Three miRNAs were shown to exhibit the same expression patterns when two different methods were used and had important functions during viral infection. These results provide insights into the miRNA-mediated regulation of mRNA and valuable resources on transcript variation and regulation during GCRV infection, which are potentially useful for mechanistic and drug studies.

草鱼出血病是由草鱼呼肠孤病毒（GCRV）引起的致命疾病。转录本的异常调节与多种疾病有关。在本研究中，我们使用 RNA 测序 (RNA-Seq) 表征了不同毒力 GCRV 的 mRNA 和 miRNA 转录组。118 个 miRNA 被鉴定为在草鱼成纤维细胞中不同毒力病毒之间差异表达。使用 RT-PCR 和 mRNA 方法选择了 8 个 miRNA 来验证 RNA-Seq 结果。总共在草鱼成纤维细胞中鉴定了 996 个差异表达的 mRNA 基因，而在草鱼成纤维细胞中观察到 901 个 miRNA-mRNA 靶标对被反向调节。综合 mRNA/miRNA 表达谱分析结果表明，受影响最大的过程是免疫反应和细胞死亡。当使用两种不同的方法时，三种 miRNA 显示出相同的表达模式，并且在病毒感染期间具有重要功能。这些结果为 miRNA 介导的 mRNA 调控提供了见解，并提供了有关 GCRV 感染期间转录本变异和调控的宝贵资源，这对机制和药物研究可能有用。