Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
Malawi Med J. 2023 Jun;35(2):101-105. doi: 10.4314/mmj.v35i2.5.
The Coronavirus disease 2019 (COVID-19) pandemic influences all around the world. The SARS-CoV-2 ORF8 accessory gene represents multiple functions in virus-host interaction. The current study aimed to compare the ORF8 substitutions and epitope features of these substitutions in the various SARS-CoV-2 outbreaks including delta, alpha, and wild type variants in Iran from 2020 to 2022. In addition, we evaluate B cell, HLA I and II epitopes, by in-silico approach to ORF8 binding site prediction.
The samples were collected from patients diagnosed with SARS-CoV-2 infection via a real-time PCR assay. Then, a conventional PCR was carried out for ORF8 mutations analysis and further Sanger sequencing. Possible important alterations in epitope features of the ORF8 were evaluated by epitope mapping. B cell, HLA class I and II epitopes, evaluated by online databases ABCpred, NetMHCpan-4.1, and NetMHCIIpan-3.2, respectively.
The current study results could not represent novel variations in seven full-length ORF8 sequences or major ORF8 deletions in 80 evaluated samples. In addition, we could not find any ORF8 A382 during each outbreak of variants. Epitope mapping represents differences between the Alpha and other variants, especially in B cell potential epitopes and HLA I.
The immunoinformatic evaluation of ORF8 suggested epitopes represent major differences for the Alpha variant in comparison with other variants. In addition, having mild pathogenesis of the Omicron variant does not seem to be associated with ORF8 alteration by phylogenetic evaluation. Future in-vitro studies for a clear conclusion about the epitope features of ORF8 are required.
2019 年冠状病毒病（COVID-19）大流行影响着全世界。SARS-CoV-2 ORF8 辅助基因在病毒-宿主相互作用中具有多种功能。本研究旨在比较包括德尔塔、阿尔法和野生型在内的各种 SARS-CoV-2 爆发中 ORF8 取代和取代特征在伊朗的 2020 年至 2022 年。此外，我们通过计算机方法评估 B 细胞、HLA I 和 II 表位，以预测 ORF8 结合位点。
从通过实时 PCR 检测诊断为 SARS-CoV-2 感染的患者中采集样本。然后，进行常规 PCR 以分析 ORF8 突变并进一步进行 Sanger 测序。通过表位作图评估 ORF8 表位特征中可能的重要变化。通过在线数据库 ABCpred、NetMHCpan-4.1 和 NetMHCIIpan-3.2 分别评估 B 细胞、HLA I 和 II 表位。
本研究结果无法代表 80 个评估样本中七个全长 ORF8 序列或主要 ORF8 缺失的新变异。此外，在每个变异爆发期间，我们都没有发现任何 ORF8 A382。表位作图代表了阿尔法变异与其他变异之间的差异，特别是在 B 细胞潜在表位和 HLA I 方面。
ORF8 的免疫信息学评价表明，与其他变异相比，阿尔法变异的表位代表主要差异。此外，奥密克戎变异的发病机制较轻似乎与进化评估中 ORF8 的改变无关。需要进一步进行体外研究以得出关于 ORF8 表位特征的明确结论。
