Abstract:[Objective] This study aims to obtain the miRNAs gene expression profiling of 3D4/21 cells infected with porcine circovirus type 2 (PCV2) and to explore the role of miRNA-98 in the replication of PCV2.[Methods] We used the porcine alveolar macrophage cell lines, 3D4/21 cells, as a cell model to analyze the different miRNAs of 3D4/21 cells infected or uninfected with PCV2. Combined with the results of bioinformatics and experiments, we screened the specific miRNAs related to virus replication and studied the role of miRNA-98 in PCV2 replication.[Results] Differential expression of miRNAs in the process of PCV2 infection was got by high-throughput sequencing technology and evaluated by qRT-RCR and preliminary study. The expression of miRNA-98 increased with the prolongation of PCV2 infection time, and the change trend of miRNA-98 was basically same as that of cap protein of PCV2. These results indicated that a significantly positive correlation between miRNA-98 expression and PCV2 replication. Overexpression of miRNA-98 significantly enhanced PCV2 replication and the expression of Cap. Further evidence supports a link between infection and the host immune regulatory cytokines, which is regulated by miRNA-98.[Conclusion] Overall, miRNA-98 can help PCV2 escape from immune surveillance by regulating the host immune system and enhance PCV2 replication. These results not only supply new insights about relationship between PCV2 infection and host but also provide a potential target for antiviral therapy against PCVAD (porcine circovirus-associated diseases).