首 页   本刊简介  编委会  审稿专家  在线期刊  写作规范  广告合作  联系我们
您现在的位置:首页 => 在线期刊 => 2020年 1期 “肝胆胰疾病的中西医结合治疗” => 病毒性肝炎 =>HCV 3b亚型全长..
HCV 3b亚型全长序列测定及基线耐药相关置换的分析
Full-length sequencing and baseline resistance-associated substitution of hepatitis C virus subtype 3b
文章发布日期:2019年12月20日  来源:  作者:黄杰庭,许茹,廖峭,等  点击次数:90次  下载次数:9次

调整字体大小:

(此处下载失败可以在在线预览处保存副本或者右键另存为)

【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的流行病学研究和DAA治疗方案的制订有重要意义。
【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 3b. 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 3b subtype. A total of 12 RASs were identified in HCV amino acid sequence, i.e., Y56H, Q80K, Q80R, and A156G located in NS3, M28G, Q/A30G, Q/A30K, L31F, L31M, and Y93H located in NS5A, and S282T and V321A located in NS5B, among which Q/A30K and L31M located in NS5A 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 3b and identify baseline RASs, which has great significance in the epidemiological study of HCV subtype 3b and the development of DAA treatment regimens.
【关键字】:肝炎病毒属; 高通量核苷酸序列分析; 基因型
【Key words】:hepacivirus; high-throughput nucleotide sequencing; genotype
【引证本文】:HUANG JT, XU R, LIAO Q, et al. Full-length sequencing and baseline resistance-associated substitution of hepatitis C virus subtype 3b[J]. J Clin Hepatol, 2020, 36(1): 94-97. (in Chinese)
黄杰庭, 许茹, 廖峭, 等. HCV 3b亚型全长序列测定及基线耐药相关置换的分析[J]. 临床肝胆病杂志, 2020, 36(1): 94-97.

地址:长春市东民主大街519号《临床肝胆病杂志》编辑部 邮编:130061 电话:0431-88782542/3542
临床肝胆病杂志 版权所有 Copyright © 2009 - 2013 Lcgdbzz.org. All Rights Reserv 吉ICP备10000617号

吉公网安备 22010402000041号