Epidemiological Characteristics Of The Genetic Evolution And Asymptomatic Infection Of SARS-CoV-2

ObjectiveSince early November,2019,the infection with SARS-Co V-2 has been emerging in the world including Eroupe,America,and Asia.The pandemic of novel coronavirus disease(COVID-19)has been continuously causing a worldwide public health crisis.Up to now,SARS-Co V-2 keeps pandemic.It evolves fast and often appears as novel variants that facilitate the transmission in humans and possibly weaken the pathogenicity.This might lead to the increase in the proportion of asymptomatic infection.However,the origination and evolution of the novel coronavirus SARS-Co V-2 remain largely unknown.There are still many problems regarding this novel coronavirus such as prevention and control,pathogen evolution tracing and clinical diagnosis and treatment that need to be further clarified.Virus sequences in public databases can provide valuable information to understand and clarify virus characteristics.In order to understand the pathogenesis and transmission mechanism of SARS-Co V-2,it is of great importance to further study the recombination mode of this virus and its sequence characteristics in different regions.In this study,we performed bioinformatics analysis to trace possible recombination events of SARS-Co V-2,and describe the process of global transmission,and assess the impact of SARS-Co V-2 mutations using all available sequences in the public databases.Meanwhile,cell experiments were carried out to observe the infection ability of the mutant strains.In addition,the epidemiological characteristics,virus clearance time and antibody dynamic conversion data between asymptomatic SARS-Co V-2 carriers and confirmed COVID-19 patients were analyzed.The current study aims to provide basic data for the prevention and control of COVID-19 and will shed light on the next stage of preventing COVID-19 and other emergining infectious diseases.MethodsPart 1We conducted recombination analysis to detect potential recombination events using available public databases.Transmission tree was constructed and performed to depict the evolutionary process of SARS-Co V-2.Changes in the affinity were predicted to assess the effect of viral mutations occurring in receptor-bind region of the spike protein of SARS-Co V-2.Viral infectivity and antigenicity related to predicted changes were tested through pseudovirus transfection and neutralizing antibody test in HEK293T-ACE2 cells.Part 2We enrolled 193 subjects tested positive for SARS-Co V-2 genomic RNA in Ningbo and Zhoushan,Zhejiang,China,from January 21 to March 6,2020.All subjects were followed up to monitor the dynamics of serum antibody immunoglobulin M(Ig M)and Ig G against SARS-Co V-2 using enzyme-linked immunosorbent assays.ResultsPart 1Two potential recombination events associated with SARS-Co V-2-like viruses were identified in coronaviruses from nature.Transmission-related phylogenetic analyses indicated that worldwide identified SARS-Co V-2 strains were grouped into clusters.The bioinformatics analysis found that,the SARS-Co V-2 has been changing constantly in nucleotide and amino acid levels,leading to a high level of diversity during global transmission,especially in India and Japan.SARS-Co V-2 in China mainly concentrated in a single type.The SARS-Co V-2 in the United States is not directly from China’s mainland.The European viral strains are closer to the North American counterparts on the transmission network.SARS-Co V-2 appears in Europe and America was earlier than that in China.There were a total of 38 mutations at the receptor binding domain of the spike protein,which increased the receptor-binding affinity of SARS-Co V-2.Two viral mutations,V367 F and N354 D,were screened out and proved to enhance the infectivity of SARS-Co V-2 pseudovirus.V367 F mutant is more sensitive to the neutralizing antibody than the wild-type pseudovirus.Part 2Among the 193 subjects,31 were asymptomatic SARS-Co V-2 carriers,149 were symptomatic COVID-19 patients,and 14 were in incubation period.Compared to the symptomatic COVID-19 patients,asymptomatic carriers were younger and had higher levels of white blood cell and lymphocyte,but lower level of C-reactive protein and shorter viral shedding duration.Conversion of Ig M from positive to negative was shorter in asymptomatic carriers than in COVID-19 patients(7.5 days vs.25.5 days,P=0.030).The proportion of those persistently seropositive for Ig G against SARS-Co V-2 was higher in COVID-19 patients than in asymptomatic carriers(66.1% vs.33.3%,P=0.037).Viral load was higher in symptomatic patients than patients in incubation period(P=0.003)and asymptomatic carriers(P=0.004).Viral shedding duration was longer of patients in incubation period than those asymptomatic carriers(48.0 vs.24.0 days,P=0.002).Compared to COVID-19 patients,asymptomatic carriers were more likely to be infected by familial transmission(61.0% vs.89.0%,P=0.028).Of the four SARS-Co V-2 families,the asymptomatic carriers were mainly children and young adults,while severe COVID-19 was mainly seen in family members over 60 years of age and with basic diseases.ConclusionRecombination among viruses may lead to the emergence of viruses with similarity to SARS-Co V-2.So far,all the evidence does not support the notion that the virus first emerged from China.Mutant strains might facilitate the transmission of SARS-Co V-2.The antiviral immunity of asymptomatic carriers to SARS-Co V-2 clearance may be higher than that of symptomatic COVID-19 patients,and this antiviral immunity should not be contributed to humoral immunity.The early severity of COVID-19 is associated with older age and basic diseases like hypertensionin and so on.