Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells

Abstract

MicroRNAs (miRNAs) are critical regulators of gene expression that may be used to identify the pathological pathways influenced by disease and cellular interactions. Viral miRNAs (v-miRNAs) encoded by both DNA and RNA viruses induce immune dysregulation, virus production, and disease pathogenesis. Given the absence of effective treatment and the prevalence of highly infective SARS-CoV-2 strains, improved understanding of viral-associated miRNAs could provide novel mechanistic insights into the pathogenesis of COVID-19. In this study, SARS-CoV-2 v-miRNAs were identified by deep sequencing in infected Calu-3 and Vero E6 cell lines. Among the ~0.1% small RNA sequences mapped to the SARS-CoV-2 genome, the top ten SARS-CoV-2 v-miRNAs (including three encoded by the N gene; v-miRNA-N) were selected. After initial screening of conserved v-miRNA-N-28612, which was identified in both SARS-CoV and SARS-CoV-2, its expression was shown to be positively associated with viral load in COVID-19 patients. Further in silico analysis and synthetic-mimic transfection of validated SARS-CoV-2 v-miRNAs revealed novel functional targets and associations with mechanisms of cellular metabolism and biosynthesis. Our findings support the development of v-miRNA-based biomarkers and therapeutic strategies based on improved understanding of the pathophysiology of COVID-19.

SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

“…As compared to other studies of SARS-CoV-2, we did not detect svRNAs derived from the N gene (10, 12), which suggests that the functions of those is not related to RNAi pathway. Interestingly, vmiR-5p was also detected by Meng and colleagues, but was not selected for further validation (12).…”

“…There are multiple examples of svRNAs expressed by RNA viruses, such as influenza (42), enterovirus 71 (43), Hepatitis C (44), hepatitis A (45), Polio (44), Dengue (44, 46), Vesicular Stomatitis (44), West Nile (44, 47), coronaviruses (10-12) and retroviruses (48, 49). It has been suggested that some svRNAs function through the host-cell RNAi pathway (12, 44, 45), but most proposed roles are independent of this machinery (10, 11, 42, 43, 50). As compared to other studies of SARS-CoV-2, we did not detect svRNAs derived from the N gene (10, 12), which suggests that the functions of those is not related to RNAi pathway.…”

“…It has been suggested that some svRNAs function through the host-cell RNAi pathway (12, 44, 45), but most proposed roles are independent of this machinery (10, 11, 42, 43, 50). As compared to other studies of SARS-CoV-2, we did not detect svRNAs derived from the N gene (10, 12), which suggests that the functions of those is not related to RNAi pathway. Interestingly, vmiR-5p was also detected by Meng and colleagues, but was not selected for further validation (12).…”

“…It has been proposed that coronaviruses, SARS-CoV and SARS-CoV-2, produce small viral RNAs (svRNAs) involved in viral pathogenesis independently of RNAi pathway (10, 11). One recent study suggested the existence of miRNA-like RNAs produced by SARS-CoV-2, which might contribute to inflammation and type I interferon (IFN) signaling (12).…”

Non-Coding RNAs in COVID-19: Emerging Insights and Current Questions

“…These concepts were explored in a study in which the authors started by infecting cultured cell lines with SARS-CoV-2 [ 99 ]. RNA sequencing was then used to identify a swathe of virus-derived small RNAs.…”