Salehi Moghadam Faraz, Mohebbi Seyed Reza, Hosseini Seyed Masoud, Damavand Behzad, Zali Mohammad Reza
Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran ; Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, IR Iran.
Hepat Mon. 2013 Aug 17;13(8):e13380. doi: 10.5812/hepatmon.13380. eCollection 2013.
Hepatitis C virus (HCV) is one of the leading causes of chronic liver disease. Seven genotypes and more than 80 subtypes have been identified for HCV so far. To date, 10 subtypes (3a to 3i; and 3k) of HCV genotype 3 have been identified. In 2006, two HCV isolates were reported from Iran that belonged to a new subtype of genotype 3. However, considering the consensus proposal for HCV genotype nomenclature, the available sequences of the new subtype did not correspond to the regions that are required to be analyzed prior to subtype assignment. During a study on the molecular epidemiology of HCV in Iran, an HCV isolate (FSM165) which seemed to belong to a new subtype of genotype 3 was obtained from a patient residing in Tehran, Iran.
The aim of this study was to assess the relatedness of isolate FM165 together with several sequences retrieved from the database to the new HCV-3 subtype reported from Iran in 2006.
Various parts of the genome including the core/E1 region and two segments of the NS5B region were amplified and sequenced for isolate FSM165. Furthermore, using the Basic Local Alignment Search Tool (BLAST), the HCV database was searched for sequences that had a high level of similarity with sequences of FSM165 isolate and such sequences were retrieved from the database. To investigate the relatedness of isolate FSM165 and also the retrieved sequences to a new HCV-3 subtype reported previously, phylogenetic analyses were performed using the Kimura two-parameter model and the neighbor joining method.
Phylogenetic analysis of the partial NS5B region demonstrated the relatedness of isolate FSM165 to the new subtype reported from Iran in 2006. Moreover, some core/E1 and NS5B sequences that had a high level of similarity with FSM165 isolate were found through searching the HCV database. These sequences were previously either misclassified or could not be accurately classified. Phylogenetic analyses showed that all of the described sequences belonged to the new subtype of HCV genotype 3.
Data suggests that the new subtype has a vast geographical distribution in Iran. The core/E1 and the NS5B sequences described in this paper can be used as references for the new HCV-3 subtype in future studies.
丙型肝炎病毒（HCV）是慢性肝病的主要病因之一。迄今为止，已鉴定出HCV的7种基因型和80多种亚型。目前，已鉴定出HCV基因型3的10个亚型（3a至3i；以及3k）。2006年，伊朗报告了两株属于基因型3新亚型的HCV分离株。然而，根据HCV基因型命名的共识提议，新亚型的可用序列与亚型指定前所需分析的区域不对应。在一项关于伊朗HCV分子流行病学的研究中，从伊朗德黑兰的一名患者中获得了一株似乎属于基因型3新亚型的HCV分离株（FSM165）。
本研究的目的是评估分离株FM165以及从数据库中检索到的几个序列与2006年伊朗报告的新HCV-3亚型的相关性。
对分离株FSM165的基因组各个部分，包括核心/E1区域和NS5B区域的两个片段进行扩增和测序。此外，使用基本局部比对搜索工具（BLAST）在HCV数据库中搜索与FSM165分离株序列具有高度相似性的序列，并从数据库中检索这些序列。为了研究分离株FSM165以及检索到的序列与先前报道的新HCV-3亚型的相关性，使用Kimura双参数模型和邻接法进行系统发育分析。
部分NS5B区域的系统发育分析表明分离株FSM165与2006年伊朗报告的新亚型相关。此外，通过搜索HCV数据库发现了一些与FSM165分离株具有高度相似性的核心/E1和NS5B序列。这些序列以前要么分类错误，要么无法准确分类。系统发育分析表明，所有描述的序列都属于HCV基因型3的新亚型。
数据表明新亚型在伊朗有广泛的地理分布。本文描述的核心/E1和NS5B序列可作为未来研究中新HCV-3亚型的参考。
