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

Huang JieTing; Xu Ru; Liao Qiao; Wang Min; Dan ZhenGang; You QingZhu; Rong Xia; Fu YongShui

doi:10.3969/j.issn.1001-5256.2020.01.021

Volume 36 Issue 1

Jan. 2020

Turn off MathJax

Article Contents

Abstract

References

Article Navigation > Journal of Clinical Hepatology > 2020 > 36(1): 94-97

PDF( 3648 KB)

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

DOI: 10.3969/j.issn.1001-5256.2020.01.021

Guangzhou Blood Center

Research funding:

Received Date: 2019-09-02
Published Date: 2020-01-20

Abstract

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

FullText(HTML)

References(15)

References

[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.

Relative Articles

[1]	Wenjing NI, Nan GENG, Xue BAI, Jie LI. An excerpt of EASL-EASD-EASO clinical practice guidelines on the management of metabolic dysfunction-associated steatotic liver disease in 2024[J]. Journal of Clinical Hepatology, 2024, 40(8): 1567-1574. doi: 10.12449/JCH240810
[2]	Xiaoyong DUO, Shijie ZHANG, Hongwei ZHANG, Jing YANG, Wenqiang WANG, Linzhi YU, Baocai ZHANG, Yicheng ZHUO, Yunchao JIA, Yan PENG, Shuai HU. Association between gallstones and metabolic syndrome in southern Xinjiang, China[J]. Journal of Clinical Hepatology, 2022, 38(8): 1859-1864. doi: 10.3969/j.issn.1001-5256.2022.08.026
[3]	CHEN Huan, LI Ting, WANG ZiJie, WANG ZhongQiong, LUO Gang, DENG MingMing. Influence of metabolic syndrome and its components on the prognosis of patients with pancreatic cancer[J]. Journal of Clinical Hepatology, 2020, 36(12): 2788-2794. doi: 10.3969/j.issn.1001-5256.2020.12.029
[4]	Tian Tian, Hu WenWei, Li Xue, Li Ji, Zhang Dan, Li ZhangZheng. Metabolic characteristics of nonalcoholic fatty liver disease and related risk factors in non-obese population[J]. Journal of Clinical Hepatology, 2020, 36(6): 1310-1313. doi: 10.3969/j.issn.1001-5256.2020.06.024
[5]	Niu ChunYan, Liu Qin, Luo XiaoChun. Reexamination of the diagnosis of fatty liver disease under the background of disease spectrum progression[J]. Journal of Clinical Hepatology, 2020, 36(10): 2356-2359. doi: 10.3969/j.issn.1001-5256.2020.10.043
[6]	Chinese Society of EndocrinologyChinese Medical Association. Consensus for diagnosis and treatment of nonalcoholic fatty liver diseases and metabolic disorders (2nd Edition)[J]. Journal of Clinical Hepatology, 2018, 34(10): 2103-2108. doi: 10.3969/j.issn.1001-5256.2018.10.010
[7]	Wu QiQi, Ma Yan, Wang XiaoBo, Xu Qiang, Wang Yan, Bai Li. Influence of metabolic syndrome on significant hepatic fibrosis in patients with chronic hepatitis B[J]. Journal of Clinical Hepatology, 2018, 34(12): 2572-2577. doi: 10.3969/j.issn.1001-5256.2018.12.013
[8]	Zhou BingBing, Wang XueMei, Zhang Qian, Xu ShiYi, Dan ZhongYan, Lai YaXin, Wang HaoYu. Association between metabolic syndrome and gallstones[J]. Journal of Clinical Hepatology, 2017, 33(5): 880-882. doi: 10.3969/j.issn.1001-5256.2017.05.017
[9]	Xu BeiBei, Wang BingYuan. Nonalcoholic fatty liver disease and serum uric acid[J]. Journal of Clinical Hepatology, 2016, 32(3): 437-441. doi: 10.3969/j.issn.1001-5256.2016.03.007
[10]	Li LiangPing. Nonalcoholic fatty liver disease and hepatocellular carcinoma[J]. Journal of Clinical Hepatology, 2016, 32(3): 432-436. doi: 10.3969/j.issn.1001-5256.2016.03.006
[11]	Fan JianGao, Yan ShiYan. Metabolic syndrome and fatty liver[J]. Journal of Clinical Hepatology, 2016, 32(3): 407-410. doi: 10.3969/j.issn.1001-5256.2016.03.001
[12]	Zhao HongXin, Yan Rong, Niu ChunYan, Zhou YongLi, Wang Jia, Cao RuiQi. Prevalence and associated risk factors for obesity and nonalcoholic fatty liver disease in adolescents in Xi′an, Shaanxi province, China[J]. Journal of Clinical Hepatology, 2015, 31(8): 1248-1251. doi: 10.3969/j.issn.1001-5256.2015.08.016
[13]	Huang Ying, Chen Hong. Research progress in association between nonalcoholic fatty liver disease and gallstone disease[J]. Journal of Clinical Hepatology, 2014, 30(11): 1217-1220. doi: 10.3969/j.issn.1001-5256.2014.11.033
[14]	Fan JianGao, Zhu ChanYan. Strengthening research on relationship between metabolic syndrome and chronic liver disease[J]. Journal of Clinical Hepatology, 2013, 29(12): 881-884. doi: 10.3969/j.issn.1001-5256.2013.12.001
[15]	Yan Jie, Xie Wen. Relationship between metabolic syndrome and chronic hepatitis C[J]. Journal of Clinical Hepatology, 2013, 29(12): 887-889. doi: 10.3969/j.issn.1001-5256.2013.12.003
[16]	Li LiangPing, Zhong Huang. The study of cytokeratin 18 fragments and inflammation related factors in non-alcoholic fatty liver disease[J]. Journal of Clinical Hepatology, 2012, 28(5): 359-363.
[17]	Zhang YiNing, Du HongWei, Liu YanJun, Wang ChaoXia. The diagnosis and risk factors for evaluation of nonalcoholic fatty liver disease in children and adolescents[J]. Journal of Clinical Hepatology, 2011, 27(7): 690-693.
[18]	Wu Tao, Yin ShouYi, Wang HongZhang, Zhang Hong, Jia Wei, Ji Guang. The clinical features and risk factors of patient with metabolic syndrome combined with non-alcoholic fatty liver disease[J]. Journal of Clinical Hepatology, 2011, 27(10): 1036-1040.
[19]	Ruan JianWen, Yang Jing, Gao LiJuan. Advances in the relationship between metabolic syndrome and nonalcoholic fatty liver disease[J]. Journal of Clinical Hepatology, 2011, 27(10): 1102-1105.
[20]	Niu ChunYan, Yan Rong, Tian Yu, Ma HuiXia, Jiao ShuJiang. The prevalence of fatty liver disease and its relationship with metabolic syndrome[J]. Journal of Clinical Hepatology, 2010, 26(2): 167-169.

Supplements(0)

Cited By

Cited by

Periodical cited type(3)

1.	梁海锋，梁国志，袁观斗，郭振亚，何松青. 小肝综合征的发病机制及防治研究进展. 中华实验外科杂志. 2024(03): 639-643 .
2.	蔡景治，郑扬，仲伟明，刘波. 基于Bcl-2/CytC探究槲皮素对肝硬化大鼠微循环及肝脏病变的影响. 现代生物医学进展. 2023(05): 818-823 .
3.	赵媛，赵明，范玉梅，邵建营. 失代偿期乙型肝炎肝硬化患者不同病毒学应答状态对生存率及肝癌患病率的影响. 中国实用医刊. 2020(23): 50-52 .

Other cited types(0)

Proportional views

Proportional views

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Get Citation

PDF

XML

Article Metrics

Article views (1345) PDF downloads(225)

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

DOI: 10.3969/j.issn.1001-5256.2020.01.021