【摘要】 目的 对经福州海关关区输入的境外新型冠状病毒感染者标本进行全基因组测序，了解关区范围内输入性新型冠状病毒全基因组特征及变异情况，为新冠疫情防控中的新冠病毒溯源提供参考。方法 采用靶向扩增方法结合二代测序技术获得新型冠状病毒全基因组，应用在线分析平台及序列分析软件，判断病毒型别，分析病毒突变位点；构建系统发育树，并结合病例流行病学资料进一步证实病毒的来源。结果 获得30株2021年5月至2022年4月期间输入性新型冠状病毒感染者的SARS-CoV-2全基因组序列。Pangolin分型显示30株病毒分别属于R.1进化分支、Alpha变异株(B.1.1.7)、Beta变异株(B.1.351)、Delta变异株(B.1.617.2)和Omicron变异株(B.1.1.529),2022年1月之后的毒株均为Omicron变异株，分别属于BA.1和BA.2两种进化分支。全基因组核苷酸突变位点分析显示，与武汉参考株(NC＿045512.2)相比30个SARS-CoV-2基因组序列核苷酸突变为24～71个，核苷酸突变位点在全基因组中分布不一致，突变位点数较多的分别是S基因、ORF1a基因、ORF1b基因和N基因。在氨基酸水平上，30株病毒S蛋白存在8个非特征性突变位点，其余突变位点均为相应谱系的特征性突变位点(75%以上同谱系流行株共有的突变位点)。核苷酸系统进化树分析显示，输入性病毒与来源地区流行毒株相似度较高。结论 对福州海关关区输入的新冠肺炎感染者标本进行病毒全基因组测序，获得30个SARS-CoV-2序列。分析表明输入病毒株存在多种不同谱系，核苷酸突变差异导致了氨基酸的特征性突变和非特征性突变，可以为新冠疫情防控中的病毒溯源提供了依据。更多还原

【Abstract】 Objective To investigate the genomic characteristics and mutations of imported SARS-CoV-2 strains, provide the genomics evidence to trace the potential source of SARS-CoV-2 viruses in the later work of COVID-19 epidemic prevention and control, the viral genomes from COVID-19 cases imported via the Fuzhou customs district were sequenced. Methods Throat swab specimens from 209 COVID-19 cases imported via the Fuzhou customs district were collected and rechecked by SARS-CoV-2 real-time RT-PCR before sequencing. The targeted genome amplification method was combined with Ion Torrent S5 next-generation sequencing(NGS) technology to perform the whole genome sequencing. This study used online analysis platforms and sequence analysis software to classify the viruses, analyze mutation sites in the genome and construct the phylogenetic tree. Combined with the epidemiological data of the cases, the analysis results of the sequences could further verify the source of the viruses. Results Thirty genome sequences of SARS-CoV-2 were successfully obtained from imported cases via the Fuzhou customs district from May 2021 to April 2022. The complete genomes of the viruses were 29 633-29 886 bp in length, with coverage of 98.54%-99.98% and a nucleotide mutations number of 24-71 compared with the Wuhan reference strain(NC＿045512.2). The results of Pangolin classification showed the sequenced genomes belong to R.1 lineage(1/30),Alpha variants(B.1.1.7,3/30),Beta variants(B.1.351,2/30),Delta variants(B.1.617.2,3/30) and Omicron variants(B.1.1.529,21/30) respectively, after January 2022 the sequenced genomes were all Omicron variants and classified as BA.1 or BA.2 subvariants. Nucleotide mutation sites were distributed inconsistently throughout the whole genome, and more mutation sites in the S gene(4-31),ORF1a gene(3-19),ORF1b gene(3-8),and N gene(1-7). This study found eight non-characteristic amino acid mutation sites in the spike protein; the remaining mutation sites were all characteristic mutation sites(Mutations with > 75% prevalence in one lineage). The analysis of the nucleotide phylogenetic tree showed the sequences of imported viruses were similar to the circulating strains in the region of origin. Conclusion In this study, the whole genomes of SARS-CoV-2 from thirty COVID-19 cases imported through the Fuzhou customs district were sequenced. These imported SARS-CoV-2 strains had different nucleotide mutations among different lineages, resulting in characteristic and non-characteristic amino acid mutations. It could provide the genomics evidence to trace the potential source of the SARS-CoV-2 virus for the prevention and control of the COVID-19 epidemic.更多还原