Small RNA transcriptome profiling reveals an essential role for miR-133b-3p_3 and miR-146b_1 in spring viraemia of carp virus infection in common carp (Cyprinus carpio L.).

MicroRNAs (miRNAs), a class of evolutionarily conserved non-coding short RNAs, play a crucial role in antiviral responses through modulating the expression of targeted genes. However, the functional roles of miRNAs in common carp (Cyprinus carpio L.) during viral infection remain poorly characterized. In the present study, small RNA sequencing analysis identified 1062 miRNAs, among which 111 were differentially expressed (DEmiRs) following spring viremia of carp virus (SVCV) infections. GO and KEGG analyses revealed that the putative target genes of these DEmiRs were predominantly associated with immune-related processes. In addition, the immune-related miRNA-mRNA interaction network was constructed to delineate potential regulatory relationships. The further functional analysis revealed that miR-133b-3p_3 promoted SVCV replication by targeting p62. Additionally, miR-146b_1 was found to facilitate SVCV proliferation through regulating TLR9 expression. Collectively, these findings indicate that SVCV infection alters the expression of specific immune-related miRNAs in the common carp, implicating their involvement in host-pathogen interactions. Our findings reveal a novel mechanism of the host's immunological response to SVCV and suggest potential strategies to prevent infection in common carp.