苏州市2019新型冠状病毒全基因组序列特征的分析

Genomic characteristics of 2019 novel coronavirus in Suzhou City

目的了解苏州市2019新型冠状病毒感染病例的病毒分子变异及宿主适应性情况。方法采集苏州市9例本土2019新型冠状病毒感染病例和6例境外输入2019新型冠状病毒感染病例的咽拭子样本,提取病毒核酸进行病毒全基因组测序。以武汉株Wuhan-Hu-1为参考序列进行比对分析。采用MEGA 7.0软件构建病毒全基因组序列系统进化树。结果15条2019新型冠状病毒基因组序列分别按照中国分型法、Nextstrain分型法、Pangolin分型法和全球共享流感数据倡议组织(Global Initiative on Sharing All Influenza Data,GISAID)分型法可分为7个型、6个型、8个型和5个亚型/谱系。与Wuhan-Hu-1参考株相比,基于核苷酸翻译的氨基酸序列突变位点中位数为3个,范围为0~12个。6条境外输入病毒株刺突蛋白均检出可导致传播力增强的D614G突变。输入病例的基因序列中未发现可导致病毒传播力明显增强的阿尔法变异株、贝塔变异株和伽马变异株。15条序列核苷酸突变位点中位数为8个,范围为3~23个。结论2019新型冠状病毒在不断变异,已衍生出多种进化谱系/基因型。苏州市境外输入病毒株均携带可致传染性增强的突变。

Objective To investigate the viral molecular mutations of 2019 novel coronavirus(2019-nCoV)and host adaptability in Suzhou City.Methods The throat swab specimens from nine local cases and six imported cases with 2019-nCoV viral nucleic acid test positive in Suzhou City were sequenced for the whole genome of the virus,and the Wuhan-Hu-1 strain was used as the reference sequence for alignment and analysis.The phylogenetic tree of the viral whole genome sequence was constructed by MEGA 7.0 software.Results According to the Chinese typing method,Nextstrain typing method,Pangolin classification method and Global Initiative on Sharing All Influenza Data(GISAID)typing method,the 152019-nCoV genome sequences could be divided into seven types,six types,eight types and five subtypes,respectively.Compared with Wuhan-Hu-1 strain,the median number of amino acid sequence mutation sites based on nucleotide translation was three(ranging from 0 to 12).D614G mutation of spike protein was identified from all six imported viral strains,which could enhance the transmissibility.No Alpha,Beta,or Gamma mutants,which also could enhance the transmissibility,was found in the genomic sequences of the imported cases.The median number of nucleotide mutation sites in 15 sequences was eight(ranging from three to 23).Conclusions 2019-nCoV is constantly mutating,and a variety of evolutionary lineages/genotypes have been derived.All imported viruses in Suzhou City carry mutations that can increase infectivity.