Ghorbani Abozar, Samarfard Samira, Jajarmi Maziar, Bagheri Mahboube, Karbanowicz Thomas P, Afsharifar Alireza, Eskandari Mohammad Hadi, Niazi Ali, Izadpanah Keramatollah
Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran.
Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT 0828 Australia.
Gene Rep. 2022 Mar;26:101537. doi: 10.1016/j.genrep.2022.101537. Epub 2022 Feb 2.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease (COVID-19) pandemic, has infected millions of people globally. Genetic variation and selective pressures lead to the accumulation of single nucleotide polymorphism (SNP) within the viral genome that may affect virulence, transmission rate, viral recognition and the efficacy of prophylactic and interventional measures. To address these concerns at the genomic level, we assessed the phylogeny and SNPs of the SARS-CoV-2 mutant population collected to date in Iran in relation to globally reported variants. Phylogenetic analysis of mutant strains revealed the occurrence of the variants known as B.1.1.7 (Alpha), B.1.525 (Eta), and B.1.617 (Delta) that appear to have delineated independently in Iran. SNP analysis of the Iranian sequences revealed that the mutations were predominantly positioned within the S protein-coding region, with most SNPs localizing to the S1 subunit. Seventeen S1-localizing SNPs occurred in the RNA binding domain that interacts with ACE2 of the host cell. Importantly, many of these SNPs are predicted to influence the binding of antibodies and anti-viral therapeutics, indicating that the adaptive host response appears to be imposing a selective pressure that is driving the evolution of the virus in this closed population through enhancing virulence. The SNPs detected within these mutant cohorts are addressed with respect to current prophylactic measures and therapeutic interventions.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）是冠状病毒病（COVID-19）大流行的病原体，已在全球感染了数百万人。基因变异和选择压力导致病毒基因组内单核苷酸多态性（SNP）的积累，这可能会影响病毒的毒力、传播率、病毒识别以及预防和干预措施的效果。为了在基因组水平上解决这些问题，我们评估了迄今为止在伊朗收集的SARS-CoV-2突变群体的系统发育和SNP，并与全球报告的变体进行了比较。对突变株的系统发育分析揭示了被称为B.1.1.7（阿尔法）、B.1.525（伊塔）和B.1.617（德尔塔）的变体在伊朗似乎是独立出现的。对伊朗序列的SNP分析表明，这些突变主要位于S蛋白编码区域，大多数SNP位于S1亚基。17个位于S1的SNP出现在与宿主细胞ACE2相互作用的RNA结合域中。重要的是，预计这些SNP中的许多会影响抗体和抗病毒治疗药物的结合，这表明适应性宿主反应似乎正在施加一种选择压力，通过增强毒力来推动这种封闭群体中病毒的进化。针对当前的预防措施和治疗干预，对在这些突变群体中检测到的SNP进行了讨论。
