Bioinformatics-driven genome-wide identification of viral miRNAs in high spillover bat coronaviruses and their target genes in human.

Zoonotic spillover, driven by interspecies pathogen transmission, poses a significant global health threat. Recent studies highlight farmed fur animals as reservoirs for diverse coronaviruses, particularly Pipistrellus bat coronavirus HKU5 (Pi-Bat-CoV HKU5), which demonstrates high spillover potential. Additionally, the genetically distinct Pipistrellus bat coronavirus HKU5-CoV-2 (Pi-Bat HKU5-CoV-2), capable of utilizing the ACE2 receptor for entry into mammalian cells, further underscores the risk of bat-origin viruses infecting mammalian hosts. MicroRNAs (miRNAs) are small, endogenous non-coding RNAs that regulate post-transcriptional expression of mRNA. In this study, we utilized Vmir to predict pre-miRNAs for three bat coronaviruses, which were validated using a consensus-based approach using iMcRNA-PseSSC, iMcRNA-ExPseSSC, and iMiRNA-PseDPC. We identified 28, 34, and 40 pre-miRNAs for Pi-Bat-CoV HKU5, Pi-Bat HKU5-CoV-2, and Ty-Bat-CoV HKU4, respectively, exhibiting unique profiles distinct from SARS-CoV-2. Mature miRNAs were predicted with the MatureBayes server, and 549, 680, and 800 target genes corresponding to the Pi-Bat-CoV HKU5, Pi-Bat HKU5-CoV-2, and Ty-Bat-CoV HKU4 were identified using the miRDB database. Gene Ontology (GO) enrichment analysis was performed using Enrichr to explore associated biological functions. The enriched target genes were found to be involved in critical pathways such as serotonergic synapse, RNA degradation, Wnt signaling, and cell cycle regulation. Furthermore, the network analysis revealed important targeted hub genes such as SOX2, ESR1, FGF2, SMAD4, YWHAZ, PRKACB, MAPK1, EP300, and GSK3β, which have been implicated in the repression of viral replication and host defense against viral infection. The findings provide a framework for genomic surveillance of v-miRNA repertoires, offering insights into viral adaptation and spillover, but future in vitro and in vivo studies will be essential to validate these findings.