大连市一起由境外输入引起的本土新冠肺炎关联病例的病毒基因组特征分析

了解引起大连市本土新型冠状病毒肺炎（COVID-19）的新型冠状病毒（SARS-CoV-2）流行株的基因组特征和变异情况，追溯SARS-CoV-2来源。

选取2022年8月20日—9月14日97例由境外输入引起的COVID-19关联病例的样本。采用SARS-CoV-2全基因组靶向扩增结合高通量测序技术（Ion Torrent测序平台）进行全基因组测序。分析SARS-CoV-2的基因组特征、核苷酸和氨基酸突变位点和基因分型。构建进化树，结合病例的流行病学资料，溯源SARS-CoV-2流行株。

共获得97例SARS-CoV-2全基因组序列，基因组全长29 735～29 741 bp，平均测序深度1 457×～50 485×，测序覆盖率范围95.9%～100.0%。同NCBI数据库中的SARS-CoV-2参考基因组（NC_045512）序列相比，97例SARS-CoV-2全基因组序列共享75个核苷酸突变位点，22例在此基础上新增1～3个突变位点。75个共享突变位点类型包括：4个非编码区和7个基因编码区，其中基因编码区的70个突变位点，来自基因ORF1ab、S、ORF3a、E、M、ORF8、N。共享的氨基酸突变类型包括15个同义突变和51个非同义突变。97例SARS-CoV-2全基因组序列，Pangolin分型为BA.5.2.1.21 （BF.21进化分支）型，Nextstrain分型为22B型，GISAID分型为GRA型。经与大连SARS-CoV-2基因库的序列比对，与8月9日境外输入的编号20220809-1和20220809-2病例共享75个核苷酸突变位点，高度同源。进化分析结果显示，此次SARS-CoV-2流行株与同时期日本大阪SARS-CoV-2流行株共同处于BF.21进化分支上，与病例20220809-1和20220809-2流行病学调查中的来源国日本一致。

此次SARS-CoV-2流行株属于Omicron变异株（BF.21进化分支），来源于日本。

Viral genomic characteristics of an overseas-imported locally associated COVID-19 case in Dalian

Objective To monitor the genomic characteristics and variation of the SARS-CoV-2 epidemic strain causing COVID-19 pneumonia in Dalian and to trace the source of SARS-CoV-2. Methods Samples were collected from 97 cases of COVID-19 associated with overseas-imported cases from August 20, 2022 to September 14, 2022. The whole genome sequencing of SARS-CoV-2 genome-wide targeted amplification combined with high-throughput sequencing (Ion Torrent) was used to analyze the genomic characteristics, nucleotide and amino acid mutation sites and genotyping of SARS-CoV-2. The origin of SARS-CoV-2 was confirmed by constructing the phylogenetic tree and combining with the epidemiological data of the cases. Results The whole genome sequence of SARS-CoV-2 was successfully obtained from the 97 cases of COVID-19. The whole genome was from 29 735 bp to 29 741 bp in length, with average sequencing depth from 1 457× to 50 485×, and cover ages from 95.9% to 100.0%. Compared with the SARS-CoV-2 reference genome sequences (NC_045512) in the NCBI database, the 97 cases shared 75 nucleotide mutations, among which 22 cases had 1 to 3 more new nucleotide mutations. The 75 shared mutation sites included four non-coding regions and seven coding regions, among which 70 mutation sites in the coding region were derived from ORF1ab, S, ORF3a, E, M, ORF8 and N. The amino acid mutations included 15 synonymous mutations and 51 non-synonymous mutations. The 97 genome sequences were located in the BA.5.2.1.21 (BF.21) evolutionary branch of Pangolin lineage. The Nextstrain was classified as 22B (Omicron). GISAID was classified as GRA. By sequence comparison with SARS-CoV-2 gene pool in Dalian, the 75 nucleotide mutation sites were shared with two samples ( 20220809-1 and 20220809-2) from Japan on August 9, which was highly homologous. The results of evolutionary analysis showed that both the SARS-CoV-2 epidemic strain and the one in Osaka, Japan at the same time were in the BF.21 evolutionary branch. It was consistent with the country of origin of the epidemiological investigation information for cases 20220809-1 and 20220809-2 in Japan. Conclusion The SARS-CoV-2 epidemic strain belongs to Omicron variant (BF. 21 evolutionary branch) and originated from Japan.