Ghori Noor-Ul-Huda, Shafique Atif, Hayat Muhammad Qasim, Anjum Sadia
School of Earth and Environment, The University of Western Australia, Perth, Australia.
Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
PLoS One. 2016 Oct 20;11(10):e0164265. doi: 10.1371/journal.pone.0164265. eCollection 2016.
Hepatitis C Virus (HCV) is the most prevalent human pathogen in Pakistan and is the major cause of liver cirrhosis and hepatocellular carcinoma in infected patients. It has shifted from being hypo-endemic to being hyper-endemic. There was no information about the origin and evolution of the local variants. Here we use newly developed phyloinformatic methods of sequence analysis to conduct the first comprehensive investigation of the evolutionary and biogeographic history in unprecedented detail and breadth. Considering evolutionary rate and molecular-clock hypothesis in context, we reconstructed the spatiotemporal spread of HCV in the whole territory of its circulation using a combination of Bayesian MCMC methods utilizing all sequences available in GenBank. Comparative analysis were performed and were addressed. Whole genome and individual gene analysis have shown that sub-types 1a, 1b and 3a are recognized as epidemic strains and are distributed globally. Here we confirm that the origin of HCV 3a genotypes is in South Asia and HCV has evolved in the region to become stably adapted to the host environment.
丙型肝炎病毒（HCV）是巴基斯坦最普遍的人类病原体，也是感染患者肝硬化和肝细胞癌的主要病因。它已从低流行转变为高流行。此前没有关于当地病毒变种起源和进化的信息。在此，我们使用新开发的系统信息学序列分析方法，以前所未有的细节和广度，首次对其进化和生物地理历史进行全面研究。结合进化速率和分子钟假说，我们利用贝叶斯MCMC方法，结合GenBank中所有可用序列，重建了HCV在其整个传播区域的时空传播情况。进行了比较分析并加以探讨。全基因组和单个基因分析表明，1a、1b和3a亚型被认为是流行毒株，且分布于全球。在此我们证实，HCV 3a基因型起源于南亚，并且该病毒已在该地区进化，以稳定适应宿主环境。
