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

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.

Application of multiplex PCR combined with invasive reaction and chromogenic reaction catalyzed by gold nanoparticles in detection of encephalitis and meningitis virus / 中国人兽共患病学报

We developed a method for detecting encephalitis and meningitis virus by using multiplex PCR combined with invasive reaction and a chromogenic reaction catalyzed by gold nanoparticles.Primers were designed based on the conservative regions of encephalitis and meningitis virus (Eastern equine encephalitis virus,EEEV;Western equine encephalomyelitis virus,WEEV;West Nile virus,WNV;Nipah virus,NiPA;Japanese encephalitis virus,JEV).Multiplex PCR system,invasive reaction and a chromogenic reaction catalyzed by gold nanoparticles were established to detect different encephalitis and meningitis virus in one reaction.Tick-borne encephalitis virus (TBEV),St Louis encephalitis virus (StLEV),Chikungunya virus (CHIKV) and Dengue virus(DV) were used to test its specificity.Quantitative RNA transcribed in vitro and PCR fragments were used to assess its sensitivity.Clinical specimens collected from JEV patients were detected by this method.A method for detecting encephalitis and meningitis virus by using multiplex PCR,invasive reaction and a chromogenic reaction catalyzed by gold nanoparticles were successfully established.This method can detect targeted pathogens specifically,and it has no cross reaction with TBEV,StLEV,CHIKV and DV.The detecting limitation for different targets was 103 copies/μL.Clinical samples were positive for JEV nucleic acids for above assay.The method presented here has characteristic of high specificity,sensitivity and throughput.The results can be observed by visual inspection.This method has broad application prospects in pathogen detection.