摘　要：为了进一步准确筛查、鉴定新型冠状病毒SARS-CoV-2，寻找可能与传播能力和症状强弱相关的变异位点，对12例意大利和西班牙国外输入浙江省的病例和7例国内病例引起的新冠肺炎临床标本进行了高通量宏转录组（metatranscriptomic）测序和基于杂交捕获的病毒基因组测序。结果表明，与宏转录组测序相比，捕获测序样本具有一致的准确突变检测结果，且所需数据量仅为宏转录组测序的1/10或更少，是一种更适合于低病毒载量样本的检测方法。SARS-CoV-2参考基因组（EPI_ISL_402119）突变分析表明，国内样本大部分都是ORF8:L84S突变株，国外样本主要是S:D614G突变株，其余样本在病毒基因ORF1a发现2种突变型，分别是ORF1a:C409S和ORF1a:P1207H。变异分析表明，在中国及意大利的新型冠状病毒肺炎患者中检测到的SARS-CoV-2病毒基因组均存在不一样的变异类群。同时，样本间检测具有差异的单核苷酸变异（SNVs），表明了SARS-CoV-2病毒变异的多态性。对同一宿主体内的全部病毒测序数据进行宿主内单核苷酸变异（iSNVs）分析表明，F06和F11体内病毒基因区的单核苷酸变异与来自同一家意大利餐厅的其他5个病例样本的SNVs突变结果意外一致，表明同一患者中可能存在重复感染。
关键词：SARS-CoV-2；基因组；变异；捕获测序
中图分类号：R563.1；R181.3　　　　　文献标志码：ADOI：10.3969/j.issn.1007-7146.2021.04.003

Abstract: In order to further screen and identify SARS-CoV-2 accurately and to look for mutation sites which may be related to the ability of transmission and the intensity of symptoms, we have conducted metatranscriptome sequencing and hybrid capture-based sequencing for 12 imported cases confirmed COVID-19 back from Europe to Zhejiang province and 7 domestic SARS-CoV-2 infected cases from China. The result indicated that the capture sequencing samples have accurate mutation detection results, whereas the required data is only～1/10 or less of metatranscriptomic sequencing, which is a more suitable detection method for low viral load samples. Mutation analysis with reference genome (EPI_ISL_402119) showed that most of the domestic virus samples are ORF8:L84S mutation, foreign virus samples are mainly S:D614G mutation, and the rest of the samples were found 2 mutations in the virus gene ORF1a, namely ORF1a:C409S and ORF1a:P1207H. Variation analysis indicated that there are different mutation groups of the SARS-CoV-2 virus genomes in patients with SARS-CoV-2 between China and Italy. The detection of different single nucleotide variations (SNVs) between samples indicated the variation polymorphism of SARS-CoV-2 genomes. Analysis of intra-individual single nucleotide variations (iSNVs) of virus sequencing data in the same host indicated that the iSNVs in gene region of F06 and F11 were unexpectedly the same as the mutation of the other 5 samples from the same Italian restaurant, which indicated they might had co-infection in the same patient.
Key words: SARS-CoV-2; genomes; variation; capture sequencing
（Acta Laser Biology Sinica, 2021, 30(4): 305-315）