The Immune Escape Of SARS-CoV-2 Main Protease And Characterization Of Cytokines And Antibodies In COVID-19 Patients

Severe acute respiratory syndrome coronavirus 2（SARS-CoV-2）,which causes coronavirus disease 2019（COVID-19）,constitutes a global pandemic.After infecting the host,it will lead to a series of innate immune responses,such as the production of interferon and inflammatory cytokines.The innate immune response further stimulates and coordinates the adaptive immune response,resulting in the secretion of antibodies,thereby forming effective antiviral immunity.However,to efficient replication and production in the host,viruses often evolve strategies to antagonize the host’s innate immunity,especially against innate effectors,such as interferon and interferon-induced factors.A critical role in protecting the host against invading pathogens is carried out by interferon-stimulated genes（ISGs）,the primary effectors of the type Ⅰ interferon（IFN）response.All coronaviruses studied thus far have to first overcome the inhibitory effects of the IFN/ISG system before establishing efficient viral replication.In addition,cytokines and antibodies also play an important role in the occurrence,development and defense of COVID-19.In this work,we mainly discuss the SARS-CoV-2-host interactions from two aspects:the immune escape strategies of the main protease(M^pro)of SARS-CoV-2,the levels of cytokines and antibodies in asymptomatic and re-positive patients.The main protease of coronaviruses,commonly associated with viral polyprotein precursors processing,is essential to antagonize intracellular antiviral defenses.Here,we show that the main protease of SARS-CoV-2 significantly suppresses the expression and transcription of downstream ISGs driven by IFN-stimulated response elements（ISREs）in a dose-dependent manner,and similar negative regulations were observed in two mammalian epithelial cell lines（simian Vero E6 and human A549）.To inhibit the ISG production,M^pro cleaves histone deacetylases（HDACs）rather than directly targeting IFN signal transducers.In addition,M^proselectively abolishes the antiviral activity of ISG effector mRNA-decapping enzyme 1a（DCP1A）by cleaving it at residue Q343.Moreover,M^pro from different genera of coronaviruses has the protease activity to cleave both HDAC2 and DCP1A,even though the alphacoronaviruse M^pro exhibits weaker catalytic activity in cleaving HDAC2.M^pro suppresses IFN response,from ISG induction to ISG activity,thus providing new insights into the pathogenesis and transmission of SARS-CoV-2.The asymptomatic infections and re-positive patients are special cases in COVID-19patients.Despite a positive SARS-CoV-2 RNA test,asymptomatic patients did not develop concomitant clinical symptoms,whereas patients who were re-positive showed only asymptomatic or mild symptoms,so there is a lack of a corresponding scientific basis for the diagnosis and treatment of these patients.To better understand the immunological characterization of these patients,we investigated the cytokines and antibodies for SARS-CoV-2 asymptomatic infection and re-positive patients in two cohorts established in the early COVID-19 outbreak in Wuhan.We found that the IgG levels in asymptomatic infections were approximately half those in patients recovering from symptomatic infections,whereas the IgG levels in re-positive patients showed no significant difference with recovered patients;Moreover,the inflammatory cytokines in these two types of patients differed significantly from those in the healthy group,but the overall cytokine levels are still within the healthy reference range.Based on our findings and the research content of other members,we concluded that both innate and adaptive immunity were activated in asymptomatic infection but clearly showed dysregulation and provided only partial immune protection,which may lead to delayed viral clearance.However,the adaptive immunity in re-positive patients is relatively normal,and innate immunity also plays a protective role.In this study,we discovered two new immune escape strategies based on the main protease of SARS-CoV-2.We show that the viral main proteases lead to the in-vivo proteolytic cleavage of four important proteins of the host immune response:HDAC1,HDAC2,HDAC3 and DCP1A.These results not only show the exquisite specificity of the viral proteases,but also suggest SARS-CoV-2 uses its protease to further impact the host innate immune signaling.In addition,this study mainly investigated the cytokines and antibodies in asymptomatic and re-positive patients,which will further provide valuable information for the diagnosis,treatment and vaccine of these special cases.