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Numerous ncRNAs have been implicated in infections caused by viruses such as HCV, DENV and SARS-CoV. This review highlights the biogenesis and multifaceted functions of both host-encoded and virus-encoded ncRNAs in shaping host-pathogen interactions. It also examines their potential as novel biomarkers and therapeutic agents for viral infections. We discuss translational applications such as Miravirsen, a miRNA inhibitor that reached clinical trials for Hepatitis C Virus (HCV) and diagnostic relevance of lncRNA NEAT1 in SARS-CoV-2 infection. 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