Mohamadzadeh M, Keyvani H, Latifi A M, Keyvani F, Azizi M R, Ranjbar M M, Karimi G H
Applied Biotechnology Research Center, Baqiyatallah University of Medical Science, Tehran, Iran.
Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
Arch Razi Inst. 2025 Feb 1;80(1):185-192. doi: 10.32592/ARI.2025.80.1.185. eCollection 2025 Feb.
In December 2019, an outbreak of pneumonia of unknown etiology was reported in Wuhan, China. The virus, known as SARS-CoV-2, is contagious and infects the lower respiratory tract. Since various coherent research needs to be conducted in Iran to detect mutations in the SARS-CoV-2 S gene, the present study was conducted to determine the sequence, mutation pattern, and phylogenetic evaluation of this gene. To this end, 120 positive samples were included in the study to evaluate the complete S gene sequence by Reverse transcriptase-PCR.Subsequent to the sequencing process, the gene assembly, blasting, mutation analysis, and phylogenetic analysis were performed using MEGA-X.A total of 161 mutations were observed in the S gene sequences of Iran. The results of the phylogenetic tree showed that all the S gene sequences of Iranian samples were divergent from the Wuhan strain and had the most similarity to it and also alpha variants. 161 nonsynonymous variations were found along the complete coding S gene with a high frequency of A262T, D614G, and P863H, which were embedded in HVR1, HVR2, and HVR3, respectively. The majority of highly variable fragments have been identified in the loop secondary structure of protein. In the present study, the predominant variants (predominantly alpha variants) and mutations were observed to be in parallel with the evolution of the virus and its fitness. A comprehensive overview of the genetic mutation of the first three waves of SARS-CoV-2 in Iran was provided, which could be used to make significant decisions and take effective measures in future pandemics to develop vaccines, kits and effective therapeutics.
2019年12月，中国武汉报告了一起不明病因的肺炎疫情。这种病毒被称为SARS-CoV-2，具有传染性，会感染下呼吸道。由于伊朗需要开展各种相关研究以检测SARS-CoV-2 S基因的突变，因此开展了本研究以确定该基因的序列、突变模式和系统发育评估。为此，本研究纳入了120份阳性样本，通过逆转录聚合酶链反应评估完整的S基因序列。测序过程完成后，使用MEGA-X进行基因组装、比对、突变分析和系统发育分析。在伊朗的S基因序列中总共观察到161个突变。系统发育树的结果表明，伊朗样本的所有S基因序列均与武汉毒株不同，但与其及α变体的相似性最高。在完整的编码S基因中发现了161个非同义变异，其中A262T、D614G和P863H的频率较高，它们分别位于高变区1、高变区2和高变区3。大多数高变片段已在蛋白质的环二级结构中得到鉴定。在本研究中，观察到主要变体（主要是α变体）和突变与病毒的进化及其适应性并行。本研究提供了伊朗SARS-CoV-2前三波疫情基因突变的全面概述，可用于在未来大流行中做出重大决策并采取有效措施，以开发疫苗、检测试剂盒和有效的治疗方法。
