连云港市6例新冠感染病例样本病毒全基因组测序分析

doi:10.3969/j.issn.1006-3110.2024.01.002

摘要
图/表
参考文献
相关文章 (15)

全文: PDF (829 KB) HTML (1 KB)
输出: BibTeX | EndNote (RIS)

摘要目的应用高通量测序技术,从新冠感染病例样本中直接测定新冠病毒基因组,获得全基因组序列,分析基因组特征和变异情况,进行分子溯源。方法采用Illumina iSeq100二代测序平台对连云港市6例不同时期新冠感染确诊病例的呼吸道样本进行全基因组测序,运用多种在线病毒变异分析平台分析病毒基因变异情况,用CLC、MEGA等多种生物信息学软件分析病毒全基因组序列,并结合病例的流行病学资料,推断病毒的来源。结果成功从6份样本中获得29 873~29 903 bp长度的基因组序列,基因组覆盖度91.0%~100.0%,与Wuhan/WH01/2019株相比,分别检出28、56、82、75、78、79个核苷酸位点突变,涉及19、40、62、52、56、57处氨基酸变异,非同义突变占比分别为67.9%(19/28)、71.4%(40/56)、75.6%(62/82)、69.3%(52/75)、71.8%(56/78)、72.1%(57/79)。进化分析显示,6份样本分属于B.1.351(LYG20210406)、AY.42(LYG20210723)、BA.2.3(LYG20220312)、BA.2.2.1(LYG20220709)、BA.2.76(LYG20220825)、BA.5.2(LYG20221006)进化分支,LYG20210406与菲律宾流行株密切相关,LYG20210723、LYG20220312、LYG20220709、LYG20220825和LYG20221006与同时期国际流行新冠株基因组序列相似性高,与各自流行病学调查结果一致。结论本研究中的二代测序方法和数据分析流程可用于新冠病毒的变异分析和分子溯源,在地市疾控应用前景好,对新冠疫情防控具有重要意义。

	服务

	把本文推荐给朋友
	加入我的书架
	加入引用管理器
	E-mail Alert
	RSS
	作者相关文章
	于翔翔
	杨焕森
	史进军
	汤冬阳
	李续炎
	尹笑笑
	王一力

关键词 ：新型冠状病毒, 全基因组特征, 高通量测序, 进化分析

Abstract：Objective To directly determine and sequence the whole genome of SARS-CoV-2 from specimens of SARS-CoV-2 infection cases by high-throughput sequencing technology, and to analyze the genome characteristics and variation of SARS-CoV-2 and conduct molecular traceability. Methods The throat swab specimens from six confirmed cases of SARS-CoV-2 infection in different periods in Lianyungang City were selected to perform the whole genome sequencing for SARS-CoV-2 using the Illumina iSeq100 next-generation sequencing (NGS) technology. Many varieties of online virus variation analysis platforms were used to analyze the genome variation of SARS-CoV-2. The whole genome sequencing was performed by using phylogenetic analysis softwares like CLC and MEGA, and then we speculated about the source of SARS-CoV-2 combined with the epidemiological data of the cases. Results We successfully obtained the complete genome sequences of SARS-CoV-2 from six samples, and the complete genomes of SARS-CoV-2 were 29,873-29,903 bp in length, with the genome coverage of 91.0%-100.0%. Compared with the Wuhan/WH01/2019 reference strain, a total of 28, 56, 82, 75, 78 and 79 nucleotide mutation sites were detected, involving 19, 40, 62, 52, 56 and 57 amino acid mutations, with the nonsynonymous mutations covering 67.9%(19/28), 71.4%(40/56), 75.6%(62/82), 69.3%(52/75), 71.8%(56/78)and 72.1%(57/79)respectively. Phylogenetic analysis displayed that sample LYG20210406 belonged to clade B.1.351, sample LYG20210723 to clade AY.42, sample LYG20220312 to clade BA.2.3, sample LYG20220709 to clade BA.2.2.1, sample LYG20220825 to clade BA.2.76, and sample LYG20221006 to clade BA.5.2. Sample LYG20210406 showed a close connection with the epidemic strain in Philippines. The genome sequences of LYG20210723, LYG20220312, LYG20220709, LYG20220825 and LYG20221006 were closest to those of the SARS-CoV-2 strains prevalent internationally during the same period, which were consistent with the results of epidemiological surveys. Conclusion The next-generation sequencing method and data analysis process in this study can be applied to SARS-CoV-2 variation analysis and molecular traceability, and also have a good application prospect in municipal-level CDCs. Therefore, they are of great significance for prevention and control of the SARS-CoV-2 epidemic.

Key words： severe acute respiratory syndrome coronavirus 2 whole genome characteristic high-throughput sequencing phylogenetic analysis

收稿日期: 2023-02-15

R563.1+4

基金资助:连云港市卫生健康科技项目(QN202013);连云港市卫生健康科技项目(ZD202207);连云港市科协软课题研究项目(Lkxqt2138)

通讯作者: 杨焕森,E-mail:yanghuansenjuye@qq.com。

作者简介: 于翔翔(1983-),女,烟台人,硕士,副主任技师,研究方向:微生物检验。

引用本文:

于翔翔, 杨焕森, 史进军, 汤冬阳, 李续炎, 尹笑笑, 王一力. 连云港市6例新冠感染病例样本病毒全基因组测序分析[J]. 实用预防医学, 2024, 31(1): 4-8. YU Xiangxiang, YANG Huansen, SHI Jinjun, TANG Dongyang, LI Xuyan, YIN Xiaoxiao, WANG Yili. Whole genome sequencing of SARS-CoV-2 from specimens of six cases of SARS-CoV-2 infection in Lianyungang City. , 2024, 31(1): 4-8.

链接本文:

https://www.syyfyx.com/CN/10.3969/j.issn.1006-3110.2024.01.002 或 https://www.syyfyx.com/CN/Y2024/V31/I1/4

[1] Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China[J]. Nature. 2020,579(7798):265-269.
[2] 国家卫生健康委员会. 关于印发《新型冠状病毒感染“乙类乙管”疫情监测方案》等5个文件的通知[EB/OL].(2022-12-27)[2023-02-15]. http://www.nhc.gov.cn/xcs/zhengcwj/202212/ce0210b36e314e4e846a940bd859b828.shtml
[3] 国家卫生健康委员会. 关于印发新型冠状病毒肺炎诊疗方案(试行第8版修订版)的通知(国卫办医函[2021]191号)[EB/OL].(2021-04-14)[2023-02-15] http://www.gov.cn/zhengce/zhengceku/2021-04/15/content_5599795.htm.
[4] World Health Organization. Genomic sequencing of SARS-CoV-2[EB/OL]. (2021-01-08) [2023-02-15]. https://www.who.int/publications/i/item/9789240018440.
[5] 何丽红,刘文军,李晶. 新型冠状病毒感染与复制的进展[J]. 生物工程学报,2020,36(10):1961-1969.
[6] Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness[J]. Nature, 2021,592(7852):116-121.
[7] Pango Network. SARS-CoV-2 lineages [EB/OL].(2022-11-11)[2023-02-15]. https://cov-lineages.org/lineage_list.html
[8] Wang CT,Liu ZP,Chen ZX,et al. The establishment of reference sequence for SARS-CoV-2 and variation analysis[J]. J Med Virol, 2020,92(6):667-674.
[9] 李亚飞,范威,王文华,等. 一起由新冠奥密克戎变异株引起的学校聚集性疫情[J]. 中国公共卫生,2022,36(5):614-618.
[10] Saxena SK, Kumar S, Ansari S, et al. Characterization of the novel SARS-CoV-2 Omicron (B.1.1.529) variant of concern and its golbal perspective[J]. J Med Virol, 2022,94(4):1738-1744.
[11] Liu J, Chandrashekar A, Sellers D, et al. Vaccines elicit highly conserved cellular immunity to SARS-CoV-2 Omicron[J]. Nature, 2022,603(7901):493-496.
[12] Viana R, Moyo S, Amoako DG, et al. Rapid epidemic expansion of the SARS--CoV-2 Omicron variant in southern Africa[J]. Nature, 2022, 603(7902):679-686.
[13] Ceraolo C,Giorgi FM. Genomic variance of the 2019-nCoV coronavirus[J].J Med Virol, 2020,92(5):522-528.
[14] Tang X, Wu C, Li X, et al. On the origin and continuing evolution of SARS-CoV-2[J].Natl Sci Rev, 2020,7(6):1012-1023.
[15] 国家卫生健康委员会. 新型冠状病毒肺炎疫情防控疫情通报[EB/OL].(2022-03-29)[2023-02-15].http://www.nhc.gov.cn/xcs/yqtb/202203/e642fa60e7ca40938e029cbdbd49f62b.shtml.
[16] 刘秀玮, 林京涛,侯舒婷,等. 烟台市一起由奥密克戎变异株BA.2.3引起的新冠感染本土疫情流行特征分析[J].实用预防医学, 2023,30(11):1329-1332.
[17] Kim MK, Lee B, Choi YY, et al. Clinical characteristics of 40 patients infected with the SARS-CoV-2 Omicron variant in Korea[J]. J Korean Med Sci, 2022,37(3):e31.