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Relatively rapid evolution rates of SARS-CoV-2 spike gene at the primary stage of massive vaccination

Biosafety and Health 2022年第4期4卷 228-233页

作者： Jing Yang Min Han Liang Wang Likui Wang Tianrui Xu Linhuan Wu Juncai Ma Gary Wong Wenjun Liu George F.Gao Yuhai Bi CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyCenter for Influenza Research and Early-warning(CASCIRE)CAS-TWAS Center of Excellence for Emerging Infectious Diseases(CEEID)Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Department of Anatomy and Cell Biology McGill UniversityMontreal H3A0G4Canada Microbial Resource and Big Data Center Chinese National Microbiology Data Center(NMDC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institut Pasteur of Shanghai Chinese Academy of SciencesShanghai 200031China

A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic continues.Moreover,vaccination breakthrough infection and reinfection in convalescent coronavirus disease 2019(COVID-19)cases have been reported.Further,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants emerged with mutations in spike(S)gene,the target of most current vaccines.Importantly,the mutations exhibit a trend of immune escape from the vaccination.Herein the scientific question that if the vaccination drives genetic or antigenic drifts of SARS-CoV-2 remains elusive.We performed correlation analyses to uncover the impacts of wide vaccination on epidemiological characteristics of COVID-19.In addition,we investigated the evolutionary dynamics and genetic diversity of SARS-CoV-2 under immune pressure by utilizing the Bayesian phylodynamic inferences and the lineage entropy calculation respectively.We found that vaccination coverage was negatively related to the infections,severe cases,and deaths of COVID-19 respectively.With the increasing vaccination coverage,the lineage diversity of SARS-CoV-2 dampened,but the rapid mutation rates of the S gene were identified,and the vaccination could be one of the explanations for driving mutations in S gene.Moreover,new epidemics resurged in several countries with high vaccination coverage,questioning their current pandemic control strategies.Hence,integrated vaccination and non-pharmacological interventions are critical to control the pandemic.Furthermore,novel vaccine preparation should enhance its capabilities to curb both disease severity and infection possibility.

关键词： SARS-CoV-2 Vaccine Genetic evolution Genetic drift Antigenic drift lineage divergence Epidemiological characteristics

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