Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran.
Translational Neuro-Oncology Laboratory, San Diego (UCSD) Moores Cancer Center, University of California, CA, United States.
Gene. 2022 Mar 1;813:146113. doi: 10.1016/j.gene.2021.146113. Epub 2021 Dec 9.
Since late 2019, when SARS-CoV-2 was reported at Wuhan, several sequence analyses have been performed and SARS-CoV-2 genome sequences have been submitted in various databases. Moreover, the impact of these variants on infectivity and response to neutralizing antibodies has been assessed. In the present study, we retrieved a total number of 176 complete and high-quality S glycoprotein sequences of Iranian SARS-COV-2 in public database of the GISAID and GenBank from April 2020 up to May 2021. Then, we identified the number of variables, singleton and parsimony informative sites at both gene and protein levels and discussed the possible functional consequences of important mutations on the infectivity and response to neutralizing antibodies. Phylogenetic tree was constructed to represent the relationship between Iranian SARS-COV2 and variants of concern (VOC), variants of interest (VOI) and reference sequence. We found that the four current VOCs - Alpha, Beta, Gamma and Delta - are circulated in different regions in Iran. The Delta variant is notably more transmissible than other variants, and is expected to become a dominant variant. However, some of the Delta variants in Iran carry an additional mutation, namely E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. We also observed some more common mutations such as an N-terminal domain (NTD) deletion at position I210 and P863H in fusion peptide-heptad repeat 1 span region in Iranian SARS-COV-2. The reported mutations in the current project have practical significance in prediction of disease spread as well as design of vaccines and drugs.
自 2019 年底武汉报告 SARS-CoV-2 以来，已经进行了多次序列分析，并在各种数据库中提交了 SARS-CoV-2 基因组序列。此外，还评估了这些变体对感染性和中和抗体反应的影响。在本研究中，我们从 2020 年 4 月至 2021 年 5 月，从 GISAID 和 GenBank 的公共数据库中检索了总共 176 条完整的、高质量的伊朗 SARS-CoV-2 S 糖蛋白序列。然后，我们确定了在基因和蛋白质水平上的变量、单态和简约信息位点的数量，并讨论了重要突变对感染性和中和抗体反应的可能功能后果。构建了系统发育树来表示伊朗 SARS-CoV2 与关注变异株（VOC）、感兴趣变异株（VOI）和参考序列之间的关系。我们发现，目前的四个 VOCs——Alpha、Beta、Gamma 和 Delta——在伊朗的不同地区传播。Delta 变体的传染性明显高于其他变体，预计将成为主要变体。然而，伊朗的一些 Delta 变体携带额外的突变，即在 HR2 亚结构域中的 E1202Q，这可能有助于病毒/细胞膜融合过程。我们还观察到一些更常见的突变，如 N 端结构域（NTD）在位置 I210 的缺失和融合肽-七肽重复 1 区的 P863H。本项目中报告的突变在预测疾病传播以及疫苗和药物设计方面具有实际意义。
