Quasispecies characteristics of hepatitis B virus full genome in Tibetans studied by the third-generation sequencing

Lin CAI; Junfeng ZHENG; Wenting TAN; Fengming SUN; Yunjie DAN; Xiaomei XIANG; Guohong DENG

doi:10.16016/j.1000-5404.201812232

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Quasispecies characteristics of hepatitis B virus full genome in Tibetans studied by the third-generation sequencing

Basic Medicine | 更新时间：2026-01-09

- Quasispecies characteristics of hepatitis B virus full genome in Tibetans studied by the third-generation sequencing
- Journal of Third Military Medical University Vol. 41, Issue 7, Pages: 637-645(2019)
- 作者机构：
  
  1.400038 重庆, 陆军军医大学(第三军医大学)：基础医学院医学遗传学教研室
  2.400038 重庆, 陆军军医大学(第三军医大学)：第一附属医院感染科
- 作者简介：
- 基金信息：
  
  the Project of Logistic Science and Technology of PLA(BWS14J025);the Key Program of National Natural Science Foundation of China(81330038);the Project of Military Medical Science and Technology Innovation Plan of Southwest Hospital(SWH2017YBXM-05)
- DOI：10.16016/j.1000-5404.201812232
  CLC： R373.21;R394-33;R394.3
- Received：29 December 2018，
  
  Revised：2019-01-17，
  
  Published：15 April 2019
- 稿件说明：
移动端阅览
Lin CAI, Junfeng ZHENG, Wenting TAN, et al. Quasispecies characteristics of hepatitis B virus full genome in Tibetans studied by the third-generation sequencing[J]. Journal of Third Military Medical University, 2019, 41(7): 637-645.
DOI：

Lin CAI, Junfeng ZHENG, Wenting TAN, et al. Quasispecies characteristics of hepatitis B virus full genome in Tibetans studied by the third-generation sequencing[J]. Journal of Third Military Medical University, 2019, 41(7): 637-645. DOI： 10.16016/j.1000-5404.201812232.

摘要

目的

利用第三代测序技术，探讨世居藏族人群乙型肝炎病毒(hepatitis B virus，HBV)准种变异特点。

方法

2016年5月至2017年7月陆军军医大学第一附属医院感染科在藏南地区进行HBV流行病学调查，采集到藏族HBsAg阳性样本24例，作为高原世居藏族组，同时在感染科门诊收集24例样本作为平原汉族对照组，提取HBV DNA并扩增病毒全长序列，构建全基因组测序文库，采用第三代测序平台PacBio RSⅡ进行测序；借助ClustalW、MEGA、SimPlot等生物信息工具进行序列准种特征分析。

结果

29例样本最终成功扩增并测序，其中高原世居藏族组9例，每个样本平均获得65条准种序列；对照组20例，每个样本平均获得124条准种序列。经比对分析，高原世居藏族组发现7例(7/9

77.8%)C/D1型重组HBV，由D4亚型与C2亚型HBV在750 nt重组而成；1例C/D2型HBV，由D3亚型与C2亚型HBV在1 500 nt重组而成；1例为C2型。C/D型HBV preC/C区复杂度、非同义突变率高于平原汉族对照组。C/D型HBV核酸变异谱与对照组不同，C/D重组型HBV核酸突变以EnhⅡ、BCP、preS区变异为主；而对照组HBV序列除了有BCP、preS变异，还有preC、S、X基因区变异。

结论

世居藏族人HBV以C/D重组型为优势毒株，且以C/D1型占多数；世居藏族人C/D型HBV preC/C区准种复杂度、非同义突变率更高，而核酸变异集中在EnhⅡ、BCP、preS区。

Abstract

Objective

To investigate the quasispecies variation characteristics of HBV in Tibetan population based on the third-generation sequencing.

Methods

An epidemiological investigation of hepatitis B virus was conducted by our department of infectious disease in southern Tibet from May 2016 to July 2017. A total of 24 HBsAg positive subjects were obtained in this investigation and were assignd into the plateau Tibetan group

and then another 24 cases subjected from our outpatient department were recruited and served as the plain Han control group. Their HBV DNA was extracted

and the full virus sequence was amplified to build a whole genome sequencing library

and then sequenced on the third-generation sequencing platform PacBio RSⅡ. Biological information tools such as ClustalW

MEGA and SimPlot were used to analyze the quasispecies characteristics.

Results

Totally 29 samples were successfully amplified and sequenced finally

including 9 cases from the Tibetan group with an average of 65 quasispecies sequences per sample

and 20 cases from the control group with an average of 124 quasispecies sequences per sample. After comparative analysis

7 cases (7/9

77.8%) of typeC/D1 HBV were found in the Tibetan group with recombining at 750 nt by type D4 and type C2 HBV

1 case of type C/D2 HBV was recombined by type D3 and type C2 HBV at 1 500 nt

and the rest 1 was type C2. The quasispecies complexity and nonsynonymous mutation ratio of HBV preC/C gen was highere in the Tibetan group than the control group. Variation spectrums of nucleic acid were different between the recombinant HBV and the control. The nucleic acid mutation of the C/D recombinant HBV was mainly in EnhⅡ

BCP

and preS regions

while the HBV sequences in the control group were dominated by mutations in preC

and X regions besides BCP and preS regions.

Conclusion

The C/D recombinant strain is the dominant strain of HBV in Tibetans

and C/D1 HBV is more common. The quasispecies complexity and nonsynonymous mutation ratio of HBV preC/C in Tibetans are higher than those of the Han

While the variants of nucleotide mainly occur in the Enh Ⅱ

BCP

and preS regions.

关键词

Keywords

references

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