输入病毒导致的十起本土疫情首例病例新冠病毒基因特征分析

SARS-CoV-2 Genetic Characterization of Imported from First Case in Ten Local Outbreaks of China

2020年4月中国阻断湖北省武汉市新冠肺炎疫情传播后,中国国内报道了多起由境外输入导致的本土聚集性新冠肺炎疫情。为分析引起聚集性疫情的输入性新型冠状病毒(SARS-CoV-2)的基因组特征,本研究对2020年4-11月份十起输入相关本土疫情首例病例的SARS-CoV-2全基因组基因特征进行分析,系统阐述了相关SARS-CoV-2的全基因组和氨基酸变异特征。结果显示,与武汉参考株相比,十起本土聚集性疫情首例病例的SARS-CoV-2核苷酸突变中位数为10个(8个-26个),氨基酸突变的中位数为6个(4个-16个),且刺突(spike,S)蛋白只有D614G一个氨基酸发生突变。除分支位点外,10条SARS-CoV-2全基因组序列的65个核苷酸突变位点以及35个氨基酸突变仅出现1-2次,呈现随机性。全基因组分析表明,这十起本土疫情的首例病例基因组按照中国分型法可划分为4个型,按照Pangolin分型法可划分为7个型,与我国2020年1-3月份武汉流行的毒株属于不同基因型,不是本土SARS-CoV-2的持续传播。与2020年9-12月英国和南非变异株属于不同基因型,无相关性。本文系统分析了2020年由输入病毒导致的十起本土疫情首例病例的SARS-CoV-2核苷酸与氨基酸变异特征,为我国新冠防控策略的制定以及后续新冠疫情的溯源提供了参考依据。

Many cases of local COVID-19 outbreaks induced by imported viruses were reported in China after the local transmission of the SARS-CoV-2 had been interrupted in Wuhan,Hubei Province on April 2020.To investigate the genomics characteristics of imported SARS-CoV-2 that caused local outbreaks,the SARS-CoV-2 strains from first case of ten local outbreaks from April to November in 2020 were used to perform whole genome sequencing,and genomics and amino acid variation analyses.The results showed that the median(minimum to maximum)of nucleotide mutation was 10(8 to 26)and the median(minimum to maximum)of amino acid mutation was 6(4 to 16)in 10 strains when compared with the Wuhan reference strain.In addition,spike(S)protein only had D614 G mutation.There were 65 nucleotide sites and 35 amino acid mutations occurred only once or twice in ten strains except the sites defining branches,which indicated the random mutation.Whole genome analysis showed that the ten strains were divided into 4 genotypes according to the Chinese lineage typing method or 7 genotypes according to the Pangolin lineage typing method.All of the ten strains were different from the one prevalent in Wuhan,Hubei Province from January to March in 2020 that means no persistent transmissions of local SARS-CoV-2.In addition,all of the ten strains had low similarity with the United Kingdom or South African variants.Our study clarified the characteristics of SARS-CoV-2 nucleotide and amino acid variation from first case of ten local outbreaks caused by importation,which provided reference for the making of prevention and control strategies and the tracing the source of new outbreaks.