Viral-host RNA-RNA interactions in SARS-CoV-2: Study of miR-34a-5p binding interactions within the genome 3'-untranslated region.

Abstract

SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, has contributed to 615 million cases and over 6.5 million deaths worldwide. COVID-19 has a higher death rate (1.1%) than other respiratory viruses, and while the implementation of vaccines has shown to be effective in mitigating disease spread, a lack of therapeutic options still exists. Further, the mechanisms behind COVID-19 disease severity are not well understood. Sequence analysis of SARS-CoV-2 has revealed that host miRNA miR-34a-5p can interact with the genome 3’-UTR, providing a potential mechanism of viral hijacking. MiR-34a-5p has been shown to indirectly regulate interleukin-6 (IL-6), a key cytokine in cytokine release syndrome (CRS). Viral hijacking of miR-34a-5p could contribute to CRS through IL-6 dysregulation and increase severity of COVID-19 cases. This study demonstrates that the viral genome 3’-UTR binds miR-34a-5p, and that these interactions are mediated by viral genome and miRNA secondary structures. Further, this study aims to elucidate disruption of the proposed interactions through intervention with competitive, complementary nucleic acid analogs. Native gel electrophoresis, 1H NMR spectroscopy, and fluorescence spectroscopy were used to characterize binding interactions of miR-34a-5p to the 3’-UTR at its predicted binding site, and in the context of the entire genome 3’-UTR. The molecular mechanisms detailed by this study have the potential to drive the development of antiviral treatments for severe SARS-CoV-2 infections with CRS and may provide a systematic approach to be replicated for the study of other RNA viruses with binding affinity for host cellular miRNAs.