我国2020年下半年SARS-CoV-2病毒株的基因突变分析

Genetic mutation analysis of SARS-CoV-2 strains in the second half of 2020 in China

基于2020年6月1日—12月1日GISAID网站(http:∥platform.gisaid.org)公布的来自中国(不含台湾地区)的全部21条病毒基因组序列,以2019年12月公布的新型冠状病毒(SARS-CoV-2)参考株NC_045512和MN996528进行各基因组错义突变位点分析,计算突变频率,寻找各突变最早出现的时间和地点,GISAID网站内搜索相似病毒株.结果显示:我国2020年下半年公布的北京市、浙江省、辽宁省大连市、云南省、山东省青岛市五地全部21个病毒株中共有18处错义突变,集中分布于Spike(S)、ORF1ab和Nucleocapsid(N)基因.S蛋白的D614G突变和NSP12(RdRp)蛋白的P323L突变具有最高的突变频率;除北京市的病毒株中发现的一个新突变位点外,其他位点突变均主要出现于欧洲或北美洲.根据突变位点分类,病毒株均属于欧洲的G支系,其中云南省的病毒株属于GH支系,与来自于泰国等亚洲的病毒株相似;山东省青岛市、辽宁省大连市、浙江省、北京市的病毒株属于GR支系,与来自欧洲的病毒株相似.综上,2020年下半年我国SARS-CoV-2病毒株主要为外源输入病毒株,在新型冠状病毒肺炎(COVID-19)防控策略上要在各运输环节严防外源输入;病毒新突变在严格的防控措施下未发生扩散,进一步说明我国采取的防控措施非常有效.

Based on all the 21 SARS-CoV-2 genome sequences announced on GISAID website(http:∥platform.gisaid.org)that was collected from June 1st to December 1st,2020 in China(excluding Taiwan region),and using NC_045512 and MN996528 strains as reference strains,we found the missense mutation sites of each strain,calculated the mutation frequency,found the earliest occurrence time and location of each mutation,and searched for similar virus strains on GISAID.Results showed that there were 18 missense mutations in all 21 strains,mainly located in Spike(S),ORF1ab and Nucleocapsid(N)genes.D614G mutation in S protein and P323L mutation in NSP12(RdRp)protein had the highest mutation frequency.Except for a new missense mutation in the strain from Beijing,the other mutations were mainly distributed in the strains from Europe or North America.According to the classification of mutation sites,all the virus strains belonged to G clade,among which Yunnan virus strains belonged to GH subclade,similar to those strains from other Asia countries such as Thailand.The strains from Qingdao,Dalian,Zhejiang and Beijing belonged to GR subclade,which were similar to those strains from Europe.Taken together,the SARS-CoV-2 strains collected from China in the second half of 2020 were mainly imported from other countries.In terms of prevention and control strategy,we should prevent the importation of foreign source virus strains via all transportation links.The strain containing a novel mutation did not spread to other places,which further indicated the effectiveness of prevention and control measures of COVID-19 adopted in China.