Analysis Of RNA Expression In The Early Stage Of SARS-CoV-2 Infection

Coronaviruses are highly diverse RNA viruses with a wide range of hosts,and it is known to infect mammals such as human,mice,swine as well as cat,causing respiratory,digestive,or neurological diseases ranging from mild to severe.In the past two decades,three kinds of animal beta coronaviruses caused by cross infection with humans have generated serious outbreaks.They are SARS-CoV,MERS-CoV and SARS-CoV-2.SARS-CoV-2 has 79% genome homology with SARS-CoV and50% with MERS-CoV.Although SARS-CoV-2 also belongs to the coronavirus,the impact caused by SARS-CoV-2 is far more serious than the other two viruses.SARSCoV-2 mainly damages the respiratory system,and complications of other systems such as the cardiovascular system,nervous system,kidney and other organs are also causes of death.The symptoms of infected individuals include asymptomatic infection,mild infection,moderate infection and severe infection.SARS-CoV-2belongs to single strand RNA,which is prone to base mismatch to produce different mutations in the replication process.It is extremely difficult to design targeted drugs or vaccines,and no specific medicine for SARS-CoV-2 has been exploited yet.The purpose of this study is to provide data information for the prevention and treatment of SARS-CoV-2 from the perspective of gene regulation by taking the early response genes in host cells of viral infection.In the early stage of viral infection,the host cells respond to the invasion of the virus and undergo a series of changes at the gene level.GEO(Gene Expression Omnibus)is a database which contains expression of genes for various,and it can provide amount of data of progression in disease.In this paper,we selected two data sets of host cell gene expression at different time points after early infection with SARS-CoV from GEO database,and carried out statistical analysis of differential genes at each time point.The gene expression data sets of other types of coronaviruses such as H1N1,H5N1 and MERS-CoV were used as controls to analyze the gene expression data.Seven genes in the intersection of the two datasets were primarily found to be differentially expressed 7 hours after infection with SARS-CoV: Linc01093,EDAR,HHIP,PAEP,PNPLA5,PRNT,and IGKV320.What’s more,the seven genes were highly expressed in SARS-CoV infection in cells but not significantly changed in H1N1,H5N1 and MERS-CoV infection.We also discovered two potential pan-viral regulatory genes: HCP5 and MIR155 HG.Besides,the GEO data analysis also suggested that NSP16,one of the viral components,might be associated with the high expression of Linc01093.Due to the high homology of SARS-CoV-2 and SARS-CoV,we speculate that genes changed early in host cells after infection with SARS-CoV may also have similar effects in SARS-CoV-2 infection.We further analyzed the effects of each protein component of SARS-CoV-2 virus on the early differential genes of virus infection.The results show that some proteins of SARS-CoV-2 caused expression changes among screening genes.For instance,overexpression of NSP14,NSP15 and NSP16 of SARS-CoV in cells leads to up-regulation of Linc01093 gene,overexpression of NSP1,NSP6,NSP9,NSP11,ORF8 and N leads to down-regulation of IGKV320,etc.Besides,we found that NSP16 was involved in several gene regulatory processes among all the viral proteins that cause gene upregulation,and the highest expression level of Linc01093 was to about 80 times after overexpressing NSP16,which is far more than the expression of other changed genes.In order to explore the relationship between the regulatory pathway of Linc01093 and NSP16,we overexpressed both NSP16 and Linc01093 in cells.Transcriptomic sequencing analysis was conducted on the two groups of overexpressed cells,and it was found that intersection genes of the two groups were involved in several reported diseaserelated pathways,such as NOD-like receptor signaling pathway(NLRP),Coronavirus disease COVID-19,Epstein-Barrvirus infection,Human immunodeficiency virus 1infection,Apoptosis,Human T-cell leukemia virus 1 infection,Viral carcinogenesis,Influenza A,Viral life cycle of HIV-1,PD-L1/ PD-1 checkpoint in cancer,T cell receptor signaling pathway(TCR),p53 signaling pathway,Toll-like receptor signaling pathway(TLR),etc.These disease-related pathways suggest that Linc01093 may play a significant role in the process of virus infection.At present,there are many studies on the prevention and treatment of SARSCoV-2,while most of them are based on the principle of reducing viral titers or blocking viral replication.However,few studies pay attention to the change of gene expression in cells when viral components produced in the early stage of SARS-CoV-2 infection.Gene expression in host cells includes coding region and non-coding region.Currently,the coding region has been extensively studied,while the noncoding region has been not.In conclusion,this study focuses on the expression of intracellular differential genes and the changes of non-coding genes in the early stage of viral infection,providing new possibilities for the prevention and treatment of SARS-CoV-2.