Host microRNA interactions with the SARS-CoV-2 viral genome 3'-untranslated region

The 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. While the viral life cycle is well understood, most of the interactions at the virus-host interface remain elusive. Furthermore, the molecular mechanisms behind disease severity and immune evasion are still largely unknown. Conserved elements of the viral genome such as secondary structures within the 5- and 3-untranslated regions (UTRs) serve as attractive targets of interest and could prove crucial in furthering our understanding of virus-host interactions. It has been proposed that microRNA (miR) interactions with viral components could be used by both the virus and host for their own benefit. Analysis of the SARS-CoV-2 viral genome 3-UTR has revealed the potential for host cellular miR binding sites, providing sites for specific interactions with the virus. In this study, we demonstrate that the SARS-CoV-2 genome 3-UTR binds the host cellular miRNAs miR-760-3p, miR-34a-5p, and miR-34b-5p, which have been shown to influence translation of interleukin-6 (IL-6), the IL-6 receptor (IL-6R), as well as progranulin (PGRN), respectively, proteins that have roles in the host immune response and inflammatory pathways. Furthermore, recent work suggests the potential of miR-34a-5p and miR-34b-5p to target and inhibit translation of viral proteins. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3-UTR. Additionally, we investigated 2-fluoro-D-arabinonucleic acid (FANA) analogs of these miRNAs as competitive binding inhibitors for these miR binding interactions. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2 infection, and provide a potential molecular basis for cytokine release syndrome and immune evasion which could implicate the host-virus interface. Author SummarySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now plagued the world for over three years. In this time, scientific advancements have allowed for the development of mRNA vaccines and targeted antiviral drugs. However, many mechanisms of the viral life cycle, as well as the interactions at the host-virus interface, remain unknown. The host immune response is of particular interest in combating SARS-CoV-2 infection, with observed dysregulation in both severe and mild cases of infection. To uncover the link between SARS-CoV-2 infection and observed immune dysregulation, we investigated host microRNAs associated with the immune response, particularly miR-760-3p, miR-34a-5p, and miR-34b-5p and emphasize them as targets of binding by the viral genome 3-UTR. We utilized biophysical methods to characterize the interactions between these miRs and the SARS-CoV-2 viral genome 3-UTR. Lastly, we introduce 2-fluoro-D-arabinonucleic acid analogs of these microRNAs as disruptors of the binding interactions, with intent of therapeutic intervention.