Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan.
PLoS One. 2012;7(2):e32553. doi: 10.1371/journal.pone.0032553. Epub 2012 Feb 27.
Hepatitis B virus (HBV) is one of the most common DNA viruses that can cause aggressive hepatitis, cirrhosis and hepatocellular carcinoma. Although many people are persistently infected with HBV, the kinetics in serum levels of viral loads and the host immune responses vary from person to person. HBV precore/core open reading frame (ORF) encoding proteins, hepatitis B e antigen (HBeAg) and core antigen (HBcAg), are two indicators of active viral replication. The aim of this study was to discover a variety of amino acid covariances in responses to viral kinetics, seroconversion and genotypes during the course of HBV infection. A one year follow-up study was conducted with a total number of 1,694 clones from 23 HBeAg-positive chronic hepatitis B patients. Serum alanine aminotransferase, HBV DNA and HBeAg levels were measured monthly as criteria for clustering patients into several different subgroups. Monthly derived multiple precore/core ORFs were directly sequenced and translated into amino acid sequences. For each subgroup, time-dependent covariances were identified from their time-varying sequences over the entire follow-up period. The fluctuating, wavering, HBeAg-nonseroconversion and genotype C subgroups showed greater degrees of covariances than the stationary, declining, HBeAg-seroconversion and genotype B. Referring to literature, mutation hotspots within our identified covariances were associated with the infection process. Remarkably, hotspots were predominant in genotype C. Moreover, covariances were also identified at early stage (spanning from baseline to a peak of serum HBV DNA) in order to determine the intersections with aforementioned time-dependent covariances. Preserved covariances, namely representative covariances, of each subgroup are visually presented using a tree-based structure. Our results suggested that identified covariances were strongly associated with viral kinetics, seroconversion and genotypes. Moreover, representative covariances may benefit clinicians to prescribe a suitable treatment for patients even if they have no obvious symptoms at the early stage of HBV infection.
乙型肝炎病毒（HBV）是最常见的 DNA 病毒之一，可导致急性肝炎、肝硬化和肝细胞癌。尽管许多人持续感染 HBV，但血清病毒载量和宿主免疫反应的动力学因人而异。HBV 前核心/核心开放阅读框（ORF）编码蛋白乙型肝炎 e 抗原（HBeAg）和核心抗原（HBcAg）是病毒复制活跃的两个指标。本研究旨在发现 HBV 感染过程中病毒动力学、血清学转换和基因型反应的各种氨基酸协变。对 23 例 HBeAg 阳性慢性乙型肝炎患者的 1694 个克隆进行了为期 1 年的随访研究。每月测量血清丙氨酸氨基转移酶、HBV DNA 和 HBeAg 水平，根据这些指标将患者聚类为几个不同的亚组。直接对每月获得的多个前核心/核心 ORF 进行测序，并将其翻译为氨基酸序列。对于每个亚组，根据整个随访期间时变序列确定时间依赖性协变。波动、摇摆、HBeAg 未转换和基因型 C 亚组的协变程度大于稳定、下降、HBeAg 转换和基因型 B 亚组。参照文献，我们鉴定的协变中的突变热点与感染过程有关。值得注意的是，热点主要存在于基因型 C 中。此外，还在早期（从基线到血清 HBV DNA 峰值）鉴定出协变，以确定与上述时间依赖性协变的交点。使用基于树的结构直观地呈现每个亚组的保留协变，即代表性协变。我们的研究结果表明，鉴定的协变与病毒动力学、血清学转换和基因型密切相关。此外，代表性协变可能有助于临床医生为患者制定合适的治疗方案，即使他们在 HBV 感染的早期阶段没有明显症状。
