Matlou Mmatsatsi K, Gaelejwe Lucinda R, Musyoki Andrew M, Rakgole J Nare, Selabe Selokela G, Amponsah-Dacosta Edina
HIV and Hepatitis Research Unit, Department of Virology, Sefako Makgatho Health Sciences University and National Health Laboratory Services, Pretoria, South Africa.
Department of Microbiological Pathology, Sefako Makgatho Health Sciences University, Pretoria, South Africa.
Heliyon. 2019 Apr 6;5(4):e01477. doi: 10.1016/j.heliyon.2019.e01477. eCollection 2019 Apr.
Genetic diversity is a characteristic trait of the hepatitis B virus (HBV) and has been associated with different clinical outcomes. In South Africa, HBV infection is a major public health concern. Most HBV infections are caused by genotype A strains. However rare cases of infection with HBV genotype D have been reported. The purpose of this study was to investigate the molecular characteristics of a rare HBV subgenotype D4 isolate.
The full-length genome of isolate ZADGM6964 was amplified in a one-step polymerase chain reaction. The amplified product was purified and cloned into a pGEM®-T Easy Vector System to investigate the genetic diversity of the viral quasi-populations. The primary isolate and clones were then directly sequenced and analysed using an array of bioinformatics software.
Phylogenetic analysis showed that the primary isolate and cloned sequences formed a monophyletic cluster away from subgenotype D4 reference strains. Further recombination analysis revealed that isolate ZADGM6964 was in fact a D4/E recombinant strain with breakpoints identified within the X and overlapping pre-Core/Core open reading frames with a >70% bootstrap confidence level. The recombinant genotype D4/E was found to be unique from other D/E strains archived in the genetic database, GenBank.
This study represents the first ever report on the isolation and molecular characterization of an HBV D4/E recombinant strain in South Africa. The findings provide evidence of further HBV genetic diversity in South Africa than has been previously reported.
基因多样性是乙型肝炎病毒（HBV）的一个特征性特点，并且与不同的临床结果相关。在南非，HBV感染是一个主要的公共卫生问题。大多数HBV感染是由A型基因型毒株引起的。然而，已报告了罕见的HBV D型基因型感染病例。本研究的目的是调查一株罕见的HBV D4亚基因型分离株的分子特征。
在一步聚合酶链反应中扩增分离株ZADGM6964的全长基因组。将扩增产物纯化并克隆到pGEM®-T Easy载体系统中，以研究病毒准种的基因多样性。然后对原始分离株和克隆进行直接测序，并使用一系列生物信息学软件进行分析。
系统发育分析表明，原始分离株和克隆序列形成了一个与D4亚基因型参考毒株不同的单系聚类。进一步的重组分析显示，分离株ZADGM6964实际上是一株D4/E重组毒株，其断点在X基因以及重叠的前核心/核心开放阅读框内被确定，自展置信水平>70%。发现该重组基因型D4/E与遗传数据库GenBank中存档的其他D/E毒株不同。
本研究是南非关于HBV D4/E重组毒株分离和分子特征的首次报道。这些发现提供了证据，表明南非的HBV基因多样性比以前报道的更多。
