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)

[1] Chinese Society of Hepatology and Chinese Society of Infectious Disease,Chinese Medical Association. The guideline of prevention and treatment for hepatitis C:A 2015 update[J]. J Clin Hepatol,2015,31(12):1961-1979.(in Chinese)中华医学会肝病学分会，中华医学会感染病学分会．丙型肝炎防治指南(2015年更新版)[J]．临床肝胆病杂志，2015,31(12):1961-1979.

[2] THOMAS DL. Global control of hepatitis C:Where challenge meets opportunity[J]. Nat Med,2013,19(7):850-858.

[3] SMITH DB,BUKH J,KUIKEN C,et al. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes:Updated criteria and genotype assignment web resource[J].Hepatology,2014,59(1):318-327.

[4] XU R,TONG W,GU L,et al. A panel of 16 full-length HCV genomes was characterized in China belonging to genotypes 1-6 including subtype 2f and two novel genotype 6 variants[J]. Infect Genet Evol,2013,20:225-229.

[5] MIAO ZQ. Application of direct-acting antiviral agents in treatment of hepatitis C[J]. Mod Pract Med,2018,30(3):284-286.(in Chinese)缪正秋．直接抗病毒药物治疗丙型肝炎的应用[J]．现代实用医学，2018,30(3):284-286.

[6] AN ZY,DING Y,DOU XG. Selection and evaluation of treatment regimens with direct-acting antiviral agents for patients with chronic hepatitis C in the real world in China[J]. J Clin Hepatol,2018,34(2):233-237.(in Chinese)安子英，丁洋，窦晓光．我国慢性丙型肝炎患者真实世界中直接抗病毒药物治疗方案的选择与评价[J]．临床肝胆病杂志，2018,34(2):233-237.

[7] QUAN M,XING HC. Effects of hepatitis C virus resistance associated variants on the efficacy of direct-acting antiviral agents[J/CD]. Chin J of Liver Diseases(Electronic Version),2018,10(3):32-36.(in Chinese)全敏，邢卉春．丙型肝炎病毒耐药相关变异对直接抗病毒药物疗效的影响[J/CD]．中国肝脏病杂志(电子版)，2018,10(3):32-36.

[8] KJELLIN M,KILENG H,AKABERI D,et al. Effect of the baseline Y93H resistance-associated substitution in HCV genotype3 for direct-acting antiviral treatment:Real-life experience from a multicenter study in Sweden and Norway[J]. Scand J Gastroenterol,2019,54(8):1042-1050.

[9] NG TF,KONDOV NO,DENG X,et al. A metagenomics and case-control study to identify viruses associated with bovine respiratory disease[J]. J Virol,2015,89(10):5340-5349.

[10] THOMSON E,IP CL,BADHAN A,et al. Comparison of nextgeneration sequencing technologies for comprehensive assessment of full-length hepatitis C viral genomes[J]. J Clin Microbiol,2016,54(10):2470-2484.

[11] RONG X,XU R,XIONG H,et al. Increased prevalence of hepatitis C virus subtype 6a in China:A comparison between2004-2007 and 2008-2011[J]. Arch Virol,2014,159(12):3231-3237.

[12] European Association for the Study of the Liver. EASL recommendations on treatment of hepatitis C 2016[J]. J Hepatol,2017,66(1):153-194.

[13] PERALES C,CHEN Q,SORIA ME,et al. Baseline hepatitis C virus resistance-associated substitutions present at frequencies lower than 15%may be clinically significant[J]. Infect Drug Resist,2018,11:2207-2210.

[14] KAI Y,HIKITA H,MORISHITA N,et al. Baseline quasispecies selection and novel mutations contribute to emerging resistance-associated substitutions in hepatitis C virus after direct-acting antiviral treatment[J]. Sci Rep,2017,7:41660.

[15] NAKANO K,SHIROMA A,SHIMOJI M,et al. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area[J]. Hum Cell,2017,30(3):149-161.

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