Verification of SARS-CoV-2-Encoded small RNAs and contribution to Infection-Associated lung inflammation

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. SARS-CoV-2 is a positive-stranded RNA virus belongs to Coronaviridae family. The viral genome of SARS-CoV-2 contains around 29.8 kilobase with a 5′-cap structure and 3′-poly-A tail, and shows 79.2% nucleotide identity with human SARS-CoV-1, which caused the 2002-2004 SARS outbreak. As the successor to SARS-CoV-1, SARS-CoV-2 now has circulated across the globe. There is a growing understanding of SARS-CoV-2 in virology, epidemiology, and clinical management strategies. In this study, we verified the existence of two 18-22 nt small viral RNAs (svRNAs) derived from the same precursor in human specimens infected with SARS-CoV-2, including nasopharyngeal swabs and formalin-fixed paraffin-embedded (FFPE) explanted lungs from lung transplantation of COVID-19 patients. We then simulated and confirmed the formation of these two SARS-CoV-2-Encoded small RNAs in human lung epithelial cells. And the potential pro-inflammatory effects of the splicing and maturation process of these two svRNAs in human lung epithelial cells were also explored. By screening cytokine storm genes and the characteristic expression profiling of COVID-19 in the explanted lung tissues and the svRNAs precursor transfected human lung epithelial cells, we found that the maturation of these two small viral RNAs contributed significantly to the infection associated lung inflammation, mainly via the activation of the CXCL8, CXCL11 and type I interferon signaling pathway. Taken together, we discovered two SARS-CoV-2-Encoded small RNAs and investigated the pro-inflammatory effects during their maturation in human lung epithelial cells, which might provide new insight into the pathogenesis and possible treatment options for COVID-19.

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

“…1B). This number is in agreement with similar studies of svRNAs in other RNA viruses (10)(11)(12). SARS-CoV-2 infection resulted in minimal alteration of some host miRNA levels, but no miRNA displayed a uniformly significant change across all three cell lines (red and blue dots in Figs.…”

“…2 (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.…”

“…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.…”

“…Viruses can produce their own miRNAs, often via non-canonical biogenesis pathways; especially cytoplasmic viruses have devised multiple strategies to bypass the requirement for nuclear Drosha (4, 9). 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).…”

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

“…that coronaviruses, SARS-CoV and SARS-CoV-2, produce small viral RNAs (svRNAs) involved in viral pathogenesis independent of the RNAi pathway (10,11). Recent studies suggested the existence of miRNA-like RNAs produced by SARS-CoV-2, which might regulate inflammation and interferon (IFN) signaling (12,13).…”