HCV 3b亚型全长序列测定及基线耐药相关置换的分析

黄杰庭; 许茹; 廖峭; 王敏; 单振刚; 尤庆柱; 戎霞; 付涌水

doi:10.3969/j.issn.1001-5256.2020.01.021

HCV 3b亚型全长序列测定及基线耐药相关置换的分析

DOI: 10.3969/j.issn.1001-5256.2020.01.021

1. 广州血液中心
2. 广州市医学重点实验室(血液安全重点实验室)
3. 韶关市第一人民医院耳鼻喉科
4. 南方医科大学检验与生物技术学院输血医学系

基金项目:

广州市医药卫生科技项目(20161A011058)；广东省医学科学技术研究基金项目(A2018499)；广州市医学重点学科建设项目；

详细信息

中图分类号: R512.63
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出版历程
- 收稿日期: 2019-09-02
- 出版日期: 2020-01-20

Full-length sequencing and baseline resistance-associated substitution of hepatitis C virus subtype 3b

Guangzhou Blood Center

Research funding:

摘要

摘要: 目的探讨二代测序法(NGS)在HCV 3b全长序列及基线耐药相关置换(RAS)检测中的应用。方法从1例2016年7月在广州血液中心献血的献血者(HCV RNA阳性)血浆中提取核酸,经序列非依赖性扩增后,构建测序文库并采用illumina Hiseq进行深度测序,然后通过生物信息学方法分析HCV全长序列、病毒基因分型以及针对直接抗病毒药物(DAA)的基线RAS。结果NGS获得8. 4 Gb原始测序数据,序列数(reads)超过56 M。经生物信息学分析获得HCV全长序列,平均测序深度为488 007,基因分型结果为3b亚型。病毒氨基酸序列里含有12个RAS,分别是NS3区域的Y56H、Q80K、Q80R、A156G,NS5A区域的M28G、Q/A30G、Q/A30K、L31F、L31M、Y93H,以及NS5B区域的S282T和V321A,其中位于NS5A区域的Q/A30K和L31M属于高丰度RAS(99. 16%和98. 37%),其余10个RAS丰度较低(<0. 5%)。结论 NGS用于HCV 3b亚型的全长序列检测和基因分型,最终鉴定出基线RAS,对于HCV 3b的流行病学研究...
- 肝炎病毒属 /
- 高通量核苷酸序列分析 /
- 基因型
Abstract: Objective To investigate the application of next-generation sequencing(NGS) in determining the full-length sequence and baseline resistance-associated substitution(RAS) of hepatitis C virus(HCV) subtype 3 b. Methods Nucleic acid was extracted from plasma of a HCV RNA-positive blood donor,and after sequence-independent amplification,a sequencing library was constructed and NGS was performed using Illumina Hiseq. Bioinformatics methods were used to analyze full-length HCV sequence,viral genotype,and baseline RAS to direct-acting antivirals(DAAs). Results A total of 8. 4 Gb data with more than 56 million reads were obtained. The full-length HCV sequence was obtained by bioinformatics analysis,with an average sequencing depth of 488 007 and a genotype of 3 b subtype. A total of 12 RASs were identified in HCV amino acid sequence,i. e.,Y56 H,Q80 K,Q80 R,and A156 G located in NS3,M28 G,Q/A30 G,Q/A30 K,L31 F,L31 M,and Y93 H located in NS5 A,and S282 T and V321 A located in NS5 B,among which Q/A30 K and L31 M located in NS5 A had high frequencies of 99. 16% and 98. 37%,respectively,while the other 10 RASs had low frequencies of < 0. 5%.Conclusion NGS can be used to determine the full-length sequence and genotype of HCV subtype 3 b and identify baseline RASs,which has great significance in the epidemiological study of HCV subtype 3 b and the development of DAA treatment regimens.
- hepacivirus /
- high-throughput nucleotide sequencing /
- genotype

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参考文献(15)

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