摘要
As severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)continues to disperse globally with worrisome speed,identifying amino acid variations in the virus could help to understand the characteristics of it.Here,we studied 489 SARS-CoV-2 genomes obtained from 32 countries from the Nextstrain database and performed phylogenetic tree analysis by clade,country,and genotype of the surface spike glycoprotein(S protein)at site 614.We found that virus strains from China's Mainland were mostly distributed in Clade B and Clade undefined in the phylogenetic tree,with very few found in Clade A.In contrast,Clades A2(one case)and A2a(112 cases)predominantly contained strains from European regions.Moreover,Clades A2 and A2a differed significantly from those of China's Mainland in age of infected population(P Z 0.0071,mean age 40.24 to 46.66),although such differences did not exist between the US and China's Mainland.Further analysis demonstrated that the variation of the Sprotein at site 614(QHD43416.1:p.614D>G)was a characteristic of stains in Clades A2 and A2a.Importantly,this variation was predicted to have neutral or benign effects on the function of the S protein.In addition,global quality estimates and 3D protein structures tended to be different between the two S proteins.In summary,we identified different genomic epidemiology among SARS-CoV-2 strains in different clades,especially in an amino acid variation of the S protein at 614,revealing potential viral genome divergence in SARS-CoV-2 strains.
基金
This work was supported by the research-oriented clinician funding program of Tongji Medical College,Huazhong University of Science and Technology.The mentioned funding institutions played no role in the study design,data collection,and analysis,decision to publish,or preparation of the manuscript.We are grateful for the computational analysis tools of Nextstrain,SWISS-MODEL,PROVEAN(v1.1)and PolyPhen-2.We sincerely thank the work done by all anti-epidemic personnel.
