DataSheet_3_Development and application of EpitopeScan, a Python3 toolset for mutation tracking in SARS-CoV-2 immunogenic epitopes.zip

IntroductionOutbreaks of coronaviruses and especially the recent COVID-19 pandemic emphasize the importance of immunological research in this area to mitigate the effect of future incidents. Bioinformatics approaches are capable of providing multisided insights from virus sequencing data, although currently available software options are not entirely suitable for a specific task of mutation surveillance within immunogenic epitopes of SARS-CoV-2.
MethodHere, we describe the development of a mutation tracker, EpitopeScan, a Python3 package with command line and graphical user interface tools facilitating the investigation of the mutation dynamics in SARS-CoV-2 epitopes via analysis of multiple-sequence alignments of genomes over time. We provide an application case by examining three Spike protein-derived immunodominant CD4+ T-cell epitopes restricted by HLA-DRB1*04:01, an allele strongly associated with susceptibility to rheumatoid arthritis (RA). Mutations in these peptides are relevant for immune monitoring of CD4+ T-cell responses against SARS-CoV-2 spike protein in patients with RA. The analysis focused on 2.3 million SARS-CoV-2 genomes sampled in England.
ResultsWe detail cases of epitope conservation over time, partial loss of conservation, and complete divergence from the wild type following the emergence of the N969K Omicron-specific mutation in November 2021. The wild type and the mutated peptide represent potential candidates to monitor variant-specific CD4+ T-cell responses. EpitopeScan is available via GitHub repository https://github.com/Aleksandr-biochem/EpitopeScan.

引言：冠状病毒暴发事件，尤其是近期的新冠（COVID-19）大流行，凸显了该领域免疫学研究对减轻未来同类公共卫生事件影响的重要性。生物信息学方法可从病毒测序数据中获取多维度研究洞察，但现有软件大多无法完全适配严重急性呼吸综合征冠状病毒2（SARS-CoV-2）免疫原性表位内的突变监测这一特定任务。

方法：本文介绍了突变追踪工具EpitopeScan的开发流程。该工具为支持命令行与图形用户界面的Python3软件包，可通过对不同时间点采集的病毒全基因组开展多序列比对，分析SARS-CoV-2表位的突变动态。本研究以与类风湿关节炎（rheumatoid arthritis, RA）易感性显著相关的HLA-DRB1*04:01等位基因限制性的3种源自刺突蛋白（Spike protein）的免疫优势CD4+ T细胞（CD4+ T-cell）表位为例，展示了该工具的应用场景。上述表位肽的突变，可用于监测类风湿关节炎患者体内针对SARS-CoV-2刺突蛋白的CD4+ T细胞免疫应答。本次分析共纳入英国地区采集的230万条SARS-CoV-2基因组序列。

结果：本文详细阐述了2021年11月奥密克戎（Omicron）特异性突变N969K出现后，表位随时间推移出现的三类变化：持续保守、保守性部分丢失，以及与野生型完全趋异。野生型与突变型表位肽均可作为监测变异株特异性CD4+ T细胞应答的潜在候选标志物。EpitopeScan工具可通过GitHub仓库https://github.com/Aleksandr-biochem/EpitopeScan获取。