In silico identification of microRNAs from the giant freshwater prawn Macrobrachium rosenbergii targeting white tail disease-associated viruses (MrNV and XSV).

White tail disease (WTD), caused by co-infection with Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV), is a major viral disease affecting the giant freshwater prawn and is associated with severe mortality during early developmental stages. MicroRNAs (miRNAs) have emerged as important regulators of antiviral responses in invertebrates, yet their potential interactions with WTD-associated viral genomes remain poorly understood. In this study, host-derived miRNAs previously shown to be upregulated following polyinosinic:polycytidylic acid (Poly I:C) stimulation were analyzed for predicted interactions with MrNV and XSV genomes using an integrative computational approach. High-confidence miRNA-virus interactions were identified through consensus prediction, structural and thermodynamic analysis, seed-region classification, and conservation assessment across viral isolates. Several conserved miRNA response elements (MREs) were identified within viral genes encoding essential proteins, including the RNA-dependent RNA polymerase (RdRP) and capsid proteins. The conservation and functional importance of these viral genes suggest that host miRNAs may interact with critical components of the viral life cycle. Identification of such candidate interactions provides a basis for improving understanding of host-virus molecular relationships and may help identify candidate miRNAs for future investigation of antiviral defense. This study provides a foundation for future functional investigations and contributes to understanding molecular mechanisms underlying viral infection and host antiviral responses in crustaceans.