Whole genome sequencing on SARS-CoV-2 strains isolated among local COVID-19 patients during an Omicron epidemic in Tianshui city
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摘要:
目的 分析新冠病毒（SARS-CoV-2）奥密克戎（Omicron）变异株流行期间甘肃省天水市本土SARS-CoV-2基因组特征和变异情况，为疫情防控提供参考依据。 方法 收集2022年12月甘肃省天水市新冠病毒感染（COVID-19）重症病例咽拭子样本共136份，采用突变核酸检测试剂盒进行变异株核酸检测，采用二代测序技术进行全基因组测序，Pangolin和Nextclade平台判定病毒谱系及型别，MAFFT软件进行多重序列比对，使用MEGA软件基于邻接法构建系统进化树。 结果 共获得32条SARS-CoV-2全基因组序列，Pangolin分型31条为 Omicron变异株BA.5.2进化分支，1条为Omicron变异株BF.7进化分支；共有68个核苷酸位点和32个氨基酸位点发生突变。S蛋白的受体结合域（RBD）关键位点存在S494P和A522S变异。 结论 Omicron变异株的编码区突变位点多，编码区的多变异性影响病毒的致病性、传染力和免疫逃逸水平。 -
关键词:
- 新型冠状病毒 /
- Omicron变异株 /
- 氨基酸突变 /
- 核苷酸突变 /
- 天水市
Abstract:Objective To analyze the genomic characteristics and variation of severe acute respiratory disease coronavirus 2 (SARS-CoV-2) strains prevalent in a local epidemic of coronavirus disease 2019 (COVID-19) in Tianshui city of Gansu province. Methods Pharyngeal swab samples were collected from 136 severe COVID-19 cases in Tianshui city during December 2022. Nucleic acid detection was performed on the isolated SARS-CoV-2 strains with mutant nucleic acid detection kits; whole genome sequencing of the isolated strains was performed using second generation sequencing technology; virus lineage and type were determined with Pangolin and Nextclade platforms and MAFFT software was used for multiple sequences comparison; a phylogenetic tree was constructed using MEGA software with neighbor-joining method. Results Whole genome sequences of 32 isolated SARS-CoV-2 strains were obtained. Pangolin typing analysis showed that of the 32 isolated strains, 31 belonged to Omicron variant BA.5.2 evolutionary branch and only one belonged to Omicron variant BF.7 evolutionary branch. Totally 68 nucleotide mutation sites and 32 amino acid mutation sites were identified. The S494P and A522S variants exist in the key sites of the receptor binding domain (RBD) of the S protein. Conclusion There were multiple coding region mutations for the SARS-CoV-2 Omicron virus variants isolated from local COVID-19 patients in Tianshui city and the mutations could affect the pathogenicity, infectivity and immune escape of the prevalent viral stains. -
Key words:
- SARS-CoV-2 /
- Omicron variant /
- amino acid mutation /
- nucleotide mutation /
- Tianshui city
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图 1 天水市32份重型新冠病例咽拭子样本SARS-CoV-2序列与武汉参考株(NC_045512.2)核苷酸与氨基酸序列比对
注：Nt：核苷酸；AA：氨基酸；ORF：开放阅读框；S：刺突；E：包膜；M：膜；N：核衣壳；非同义突变（红色字体标注的氨基酸简称）；L型欧洲家系（
Figure 1. Nucleotide and amino acid sequence alignment of SARS-CoV-2 strains isolated from pharyngeal swab samples of 32 severe COVID-19 patients in Tianshui city of Gansu province, December 2022- compared with Wuhan reference strain (NC_045512.2)
图 2 天水市32份重型新冠病例咽拭子样本SARS-CoV-2全基因组系统进化树
注：红色字体部分为本研究中本土病例基因序列
Figure 2. Genome-wide phylogenetic tree of SARS-CoV-2 strains isolated from pharyngeal swab samples of 32 severe COVID-19 patients in Tianshui city of Gansu province, December 2022
表 1 2022年12月天水市32份重型新冠病例咽拭子样本SARS-CoV-2全基因组序列测序分析
Table 1. Whole genome sequencing on SARS-CoV-2 strains isolated from pharyngeal swab samples of 32 severe COVID-19 patients in Tianshui city of Gansu province, December 2022
序列名称 平均测序深度 覆盖度（%） Nextstrain 分型 Pangolin分型 新增核苷酸突变位点数 核苷酸同源性（%） TS20230112-01 12977.89 99.50 22B Omicron BA.5.2 3 99.52 TS20230112-02 13222.23 99.53 22B Omicron BA.5.2 0 99.53 TS20230112-03 4227.11 99.53 22B Omicron BA.5.2 2 99.52 TS20230112-04 9364.77 99.53 22B Omicron BA.5.2 1 99.53 TS20230112-05 12793.19 99.53 22B Omicron BA.5.2 3 99.53 TS20230112-06 11526.72 99.53 22B Omicron BA.5.2 3 99.52 TS20230112-07 11558.92 99.53 22B Omicron BF.7 12 99.54 TS20230112-08 9260.64 99.53 22B Omicron BA.5.2 1 99.53 TS20230112-09 8148.91 99.50 22B Omicron BA.5.2 2 99.52 TS20230112-10 12636.94 99.53 22B Omicron BA.5.2 8 99.53 TS20230112-11 4066.38 99.51 22B Omicron BA.5.2 1 99.53 TS20230112-12 5345.37 88.35 22B Omicron BA.5.2 1 99.61 TS20230112-13 8337.32 97.63 22B Omicron BA.5.2 8 99.52 TS20230112-14 5030.48 99.18 22B Omicron BA.5.2 1 99.53 TS20230112-15 9274.21 99.03 22B Omicron BA.5.2 0 99.62 TS20230112-16 8228.34 98.39 22B Omicron BA.5.2 8 99.62 TS20230116-01 27567.22 98.83 22B Omicron BA.5.2 1 99.53 TS20230116-02 7156.60 99.53 22B Omicron BA.5.2 1 99.53 TS20230116-03 9083.86 99.53 22B Omicron BA.5.2 1 99.53 TS20230116-04 16722.47 99.58 22B Omicron BA.5.2 1 99.61 TS20230116-05 17067.81 99.53 22B Omicron BA.5.2 1 99.53 TS20230116-06 17256.98 99.59 22B Omicron BA.5.2 4 99.52 TS20230116-07 8577.01 99.53 22B Omicron BA.5.2 0 99.53 TS20230116-08 10457.47 99.53 22B Omicron BA.5.2 4 99.54 TS20230116-09 25176.47 99.53 22B Omicron BA.5.2 1 99.53 TS20230116-10 11234.04 99.53 22B Omicron BA.5.2 3 99.52 TS20230116-11 16369.25 99.53 22B Omicron BA.5.2 1 99.53 TS20230116-12 8973.04 99.59 22B Omicron BA.5.2 1 99.56 TS20230116-13 13082.67 99.36 22B Omicron BA.5.2 2 99.52 TS20230116-14 8069.67 99.53 22B Omicron BA.5.2 3 99.52 TS20230116-15 13029.43 99.53 22B Omicron BA.5.2 5 99.51 TS20230116-16 16296.36 99.75 22B Omicron BA.5.2 4 99.52 
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