The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China.
Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361100, China.
Viruses. 2023 Sep 28;15(10):2017. doi: 10.3390/v15102017.
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuing to evolve and accumulate mutations. While various bioinformatics tools have been developed for SARS-CoV-2, a well-curated mutation-tracking database integrated with in silico evaluation for molecular diagnostic assays is currently unavailable. To address this, we introduce CovidShiny, a web tool that integrates mutation profiling, in silico evaluation, and data download capabilities for genomic sequence-based SARS-CoV-2 assays and data download. It offers a feasible framework for surveilling the mutation of SARS-CoV-2 and evaluating the coverage of the molecular diagnostic assay for SARS-CoV-2. With CovidShiny, we examined the dynamic mutation pattern of SARS-CoV-2 and evaluated the coverage of commonly used assays on a large scale. Based on our in silico analysis, we stress the importance of using multiple target molecular diagnostic assays for SARS-CoV-2 to avoid potential false-negative results caused by viral mutations. Overall, CovidShiny is a valuable tool for SARS-CoV-2 mutation surveillance and in silico assay design and evaluation.
新型冠状病毒病 2019（COVID-19）大流行仍在继续，严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）仍在不断进化和积累突变。虽然已经开发了各种用于 SARS-CoV-2 的生物信息学工具，但目前还没有与计算机模拟评估相结合的精心整理的突变跟踪数据库。为了解决这个问题，我们引入了 CovidShiny，这是一个网络工具，它集成了突变分析、计算机模拟评估以及基于基因组序列的 SARS-CoV-2 检测和数据下载的能力。它为监测 SARS-CoV-2 的突变和评估 SARS-CoV-2 分子诊断检测的覆盖范围提供了一个可行的框架。使用 CovidShiny，我们研究了 SARS-CoV-2 的动态突变模式，并在大规模上评估了常用检测方法的覆盖范围。基于我们的计算机分析，我们强调了使用多种目标分子诊断检测方法来检测 SARS-CoV-2 的重要性，以避免由病毒突变引起的潜在假阴性结果。总的来说，CovidShiny 是 SARS-CoV-2 突变监测和计算机模拟检测设计和评估的有价值的工具。
