Reticuloendotheliosis virus (REV) is a gamma retrovirus that can cause immunosuppression, dwarf syndrome and acute reticulocytoma in poultry. The molecular mechanism by which REV infection leads to immunosuppression and tumorigenesis is poorly understood. In this study, we elucidated the regulatory network of miRNA-mRNA and the major signaling pathways involved in REV-SNV infection. Therefore, we used the spleen necrosis virus (SNV) model of REV to inoculate one-day-old specific pathogen-free (SPF) chickens and then performed global miRNA and mRNA expression profiling by conducting high-throughput sequencing of 18 bursa of Fabricius samples collected at 7, 14, and 21 dpi. In total, 213 differentially expressed miRNAs (DEMs) and 3311 differentially expressed genes (DEGs) were identified. In the miRNA-mRNA network constructed based on the association analysis of these DEMs and DEGs, 1376 negatively correlated miRNA-mRNA pairs were identified
among them, 82 pairs were identified at 7 dpi, 203 pairs were identified at 14 dpi, and 873 pairs were identified at 21 dpi. Moreover, the results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the mRNAs in the network revealed greater enrichment of immune-related pathways, such as the immune system, signal transduction, cell growth and death, and signaling molecules and interactions. We confirmed the selected immune-related DEMs and their DEGs by conducting quantitative RT-PCR (qRT-PCR) analysis. These findings increased our understanding of the interactions of miRNAs and their target genes during infection with REV-SNV, and contributed to the understanding of host-virus interactions.