HBeAg血清转化者中病毒准种多样性和进化的全基因组深度测序

StephenW

Whole genome deep sequencing analysis of viral quasispecies diversity and evolution in HBeAg seroconverters
Su-Ru Lin  1 , Ta-Yu Yang  1 , Cheng-Yuan Peng  2   3 , You-Yu Lin  4 , Chia-Yen Dai  5   6 , Hurng-Yi Wang  4 , Tung-Hung Su  7   8 , Tai-Chung Tseng  7   8 , I-Jung Liu  9 , Huei-Ru Cheng  4 , Yueh-Chi Shen  1 , Fang-Yi Wu  1 , Chun-Jen Liu  4   7   8   10   11 , Ding-Shinn Chen  4   7   8   10   12 , Pei-Jer Chen  4   7   8   10   11 , Hung-Chih Yang  1   4   7   8 , Jia-Horng Kao  4   7   8   10   11
Affiliations
Affiliations

    1
    Department of Microbiology, National Taiwan University, Taipei, Taiwan.
    2
    School of Medicine, China Medical University, Taichung, Taiwan.
    3
    Department of Internal Medicine, Center for Digestive Medicine, China Medical University Hospital, Taichung, Taiwan.
    4
    Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
    5
    Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
    6
    Hepato-Biliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
    7
    Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
    8
    Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
    9
    Cardinal Tien Junior College of Healthcare and Management, New Taipei City, Taiwan.
    10
    Department of Internal Medicine, National Taiwan University, Taipei, Taiwan.
    11
    Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.
    12
    Genomics Research Center, Academia Sinica, Taipei, Taiwan.

    PMID: 33870157 PMCID: PMC8042178 DOI: 10.1016/j.jhepr.2021.100254

Free PMC article
Abstract

Background & aims: We aimed to investigate how viral quasispecies of the HBV whole genome evolves and diversifies in response to HBeAg seroconversion and viral control utilising next-generation sequencing (NGS).

Methods: Fifty HBeAg-positive chronic hepatitis B patients, including 18 treatment-naïve and 32 interferon (IFN)-treated individuals, were recruited. Serial HBV whole genomes in serum were analysed by NGS to determine sequence characteristics and viral quasispecies.

Results: HBV quasispecies diversity, measured by nucleotide diversity, was negatively correlated with viral load and hepatitis activity. Spontaneous HBeAg seroconverters exhibited significantly greater viral quasispecies diversity than treatment-naïve non-seroconverters from >1 year before seroconversion (0.0112 vs. 0.0060, p <0.01) to >1 year after seroconversion (0.0103 vs. 0.0068, p <0.01). IFN-induced HBeAg seroconverters tended to have higher viral genetic diversity than non-seroconverters along with treatment. Particularly, the IFN responders, defined as IFN-induced HBeAg seroconversion with low viraemia, exhibited significantly greater genetic diversity of whole HBV genome at 6 months post-IFN treatment than IFN non-responders (0.0148 vs. 0.0106, p = 0.048). Moreover, spontaneous HBeAg seroconverters and IFN responders exhibited significantly higher evolutionary rates and more intra-host single-nucleotide variants. Interestingly, in spontaneous HBeAg seroconverters and IFN responders, there were distinct evolutionary patterns in the HBV genome.

Conclusions: Higher HBV quasispecies diversity is associated with spontaneous HBeAg seroconversion and IFN-induced HBeAg seroconversion with low viraemia, conferring a favourable clinical outcome.

Lay summary: HBeAg seroconversion is a landmark in the natural history of chronic HBV infection. Using next-generation sequencing, we found that the nucleotide diversity of HBV was negatively correlated with viral load and hepatitis activity. Patients undergoing HBeAg seroconversion had more diverse HBV genomes and a faster viral evolution rate. Our findings suggest HBeAg seroconversion is driven by host selection pressure, likely immune selection pressure.

Keywords: ALT, alanine aminotransferase; AUC, area under curve; BCP, basal core promoter; C, core; CHB, chronic hepatitis B; Chronic hepatitis B; EOT, end of treatment; HBeAg seroconversion; IFN, interferon; IFN-NR, IFN-non-responders; IFN-No-eSC, IFN-treated HBeAg non-seroconverters; IFN-RS, IFN-responders; IFN-eSC, IFN-treated HBeAg seroconverters; Intra-host single nucleotide variants; NGS, next-generation sequencing; ORFs, open reading frames; P, polymerase; S, surface; TN-No-eSC, treatment-naïve non-seroconverters; TN-eSC, treatment-naïve HBeAg seroconverters; dN, nonsynonymous substitution rate; dS, synonymous substitution rate; iSNVs, intra-host single-nucleotide variants.

© 2021 The Author(s).

StephenW

HBeAg血清转化者中病毒准种多样性和进化的全基因组深度测序分析
林素如1，杨达玉1，彭成元2 3，林有玉4，戴家仁5 6，王洪义4，苏东雄7 8，大中井7 8，刘宜荣9，成辉如4，沉岳池1，吴芳怡1，刘纯仁4 7 8 10 11，陈定信4 7 8 10 12，陈佩杰4 7 8 10 11，杨洪志1 4 7 8，高嘉-4 7 8 10 11
隶属关系
隶属关系

    1个
    国立台湾大学微生物系，台湾台北。
    2个
    中国医科大学医学院，台湾台中。
    3
    中国医科大学附属医院消化医学中心内科，台湾台中。
    4
    国立台湾大学医学院临床医学研究所，台湾台北。
    5
    高雄医科大学医学院内科系，台湾高雄。
    6
    台湾高雄医学院，高雄医科大学附属医院内科肝胆科。
    7
    国立台湾大学附属医院消化内科，消化内科，台湾台北。
    8
    国立台湾大学附属医院内科肝炎研究中心，台湾台北。
    9
    台湾新北市天才健康与管理初级学院。
    10
    国立台湾大学内科，台湾台北。
    11
    国立台湾大学医院医学研究室，台湾台北。
    12
    中国台湾省中央研究院基因组学研究中心。

    PMID：33870157 PMCID：PMC8042178 DOI：10.1016 / j.jhepr.2021.100254

免费PMC文章
抽象的

背景与目的：我们旨在调查HBV整个基因组的病毒准种如何利用下一代测序（NGS）响应HBeAg血清转化和病毒控制而进化和多样化。

方法：招募了50例HBeAg阳性的慢性乙型肝炎患者，包括18例未经治疗和32例接受干扰素（IFN）治疗的患者。用NGS分析血清中的一系列HBV全基因组，以确定序列特征和病毒准种。

结果：通过核苷酸多样性测得的HBV准种多样性与病毒载量和肝炎活性呈负相关。自血清转化前> 1年（0.0112 vs. 0.0060，p <0.01）到血清转化后> 1年（sn = 0.0103 vs.0.0068，p <0.01），自发性HBeAg血清转化者表现出比未接受过治疗的非血清转化者明显更高的病毒准种多样性。 IFN诱导的HBeAg血清转化者与非血清转化者相比，在治疗方面往往具有更高的病毒遗传多样性。特别是，被定义为低病毒血症的IFN诱导的HBeAg血清转化的IFN应答者，在IFN治疗后6个月时，其整个HBV基因组的遗传多样性明显高于无IFN应答者（0.0148 vs. 0.0106，p = 0.048）。此外，自发的HBeAg血清转化者和IFN应答者表现出显着更高的进化速率和更多的宿主内部单核苷酸变体。有趣的是，在自发的HBeAg血清转化者和IFN应答者中，HBV基因组中存在明显的进化模式。

结论：较高的HBV准物种多样性与自发性HBeAg血清转化和IFN诱导的HBeAg血清转化低病毒血症有关，具有良好的临床效果。

内容摘要：HBeAg血清转化是慢性HBV感染自然史中的一个里程碑。使用下一代测序，我们发现HBV的核苷酸多样性与病毒载量和肝炎活性呈负相关。进行HBeAg血清转化的患者具有更多的HBV基因组和更快的病毒进化速度。我们的发现表明，HBeAg血清转化是由宿主选择压力（可能是免疫选择压力）驱动的。

关键词：ALT，丙氨酸转氨酶； AUC，曲线下面积； BCP，基础核心启动子； C，核心； CHB，慢性乙型肝炎；慢性乙型肝炎； EOT，治疗结束； HBeAg血清转化；干扰素，干扰素； IFN-NR，IFN-无应答剂； IFN-No-eSC，经IFN处理的HBeAg非血清转化剂； IFN-RS，IFN-应答剂； IFN-eSC，经IFN处理的HBeAg血清转换器；宿主内单核苷酸变体； NGS，下一代测序； ORF，开放阅读框； P，聚合酶； S，表面； TN-No-eSC，未接受过治疗的非血清转化者； TN-eSC，未经治疗的HBeAg血清转化者； dN，非同义取代率； dS，同义词替换率； iSNV，宿主内单核苷酸变体。

©2021作者。

StephenW

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042178/