Ullah Amin, Rehman Irshad Ur, Ahmad Jamshaid, Odenthal Margaret, Ahmad Saad, Nadeem Tariq, Ali Qurban, Rizwan Muhammad, Khan Muhammad Ajmal, Hassan Said, Ahsan Hina, Ahmad Bashir
Department of Microbiology and Biotechnology, Abasyn University Peshawar, Khyber Pakhtunkhwa, Pakistan.
Institute of Pathology, Laboratory of Translational Molecular Pathology, University Hospital of Cologne, Cologne, Germany.
Sci Rep. 2021 Jul 22;11(1):15023. doi: 10.1038/s41598-021-94063-1.
Hepatitis C virus (HCV), a small, single-stranded RNA virus with a 9.6 kb genome, is one of the most common causes of liver diseases. Sequencing of the 5' untranslated region (UTR) is usually used for HCV genotyping, but it is less important in numerous subtypes due to its scarce sequence variations. This study aimed to identify genotypes using the 5' UTR of HCV from cirrhotic patients of Khyber Pakhtunkhwa (KP). Serum RNA samples (44) were screened by real time PCR to determine the HCV viral load. Nested PCR was performed to identify cDNA and the 5' UTR. The HCV 5' UTR was sequenced using the Sanger method. MEGA-7 software was used to analyze evolutionary relatedness. After 5' UTR sequencing, 26 samples (59%) were identified as genotype 3, and 2 samples (6%) were identified as genotypes 1, 2 and 4. The most predominant genotype was 3a, and genotype 4 was rarely reported in the phylogenetic tree. Analysis of the HCV 5' UTR is an efficient alternative method for confirmation of various genotypes. Phylogenetic analysis showed that genotype 3 was dominant in the area of KP, Pakistan.
丙型肝炎病毒（HCV）是一种小型单链RNA病毒，基因组为9.6 kb，是肝病最常见的病因之一。5'非翻译区（UTR）测序通常用于HCV基因分型，但由于其序列变异稀少，在众多亚型中不太重要。本研究旨在利用开伯尔-普赫图赫瓦省（KP）肝硬化患者的HCV 5'UTR鉴定基因型。通过实时PCR筛选血清RNA样本（44份）以确定HCV病毒载量。进行巢式PCR以鉴定cDNA和5'UTR。使用桑格法对HCV 5'UTR进行测序。使用MEGA-7软件分析进化相关性。5'UTR测序后，26份样本（59%）被鉴定为3型基因型，2份样本（6%）被鉴定为1、2和4型基因型。最主要的基因型是3a，4型基因型在系统发育树中很少报道。分析HCV 5'UTR是确认各种基因型的一种有效替代方法。系统发育分析表明，3型基因型在巴基斯坦开伯尔-普赫图赫瓦省地区占主导地位。
