VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern
VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern
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DOI：
10.1093/bioinformatics/btac370
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发表时间：
2022-06-09
期刊：
影响因子：
5.8
通讯作者：
Jin, Guangxu
中科院分区：
文献类型：
--
作者：
Zhao, Hongyu;Han, Kun;Jin, Guangxu
突变是一个变异的关注（VOC）克服选择压力的关键，但这一过程仍然不清楚。理解突变过程与VOC的关联是一个未满足的需求。动机：在这里，我们开发了VOC警报，一种预测VOC及其引起的COVID激增的方法，使用约570万SARS-CoV-2完整序列的突变。我们发现VOC依赖于突变数的谱系水平熵值来与其他变体竞争，暗示了群体水平突变在病毒进化中的重要性。因此，我们假设VOC是地球仪突变过程的结果。结果如下：通过分析2020年1月至2021年12月的突变，我们通过估计进化速度来模拟突变过程，从而将2020年1月至2022年3月的时间段划分为八个阶段。我们预测阿尔法，三角洲，三角洲加（AY.4.2）和Omicron（B.1.1.529）的突变熵值在阶段I，III，V和VII与加速的步伐，分别。2021年11月下旬，VOC警报提醒Omicron与Delta和Delta plus激烈竞争，成为一种高度传播的变种。使用模拟数据，VOC警报还预测Omicron可能导致2022年1月至2022年3月的另一次COVID激增。
Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Motivation: Here, we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Results: Analyzing the mutations from January 2020 to December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020-March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the Stages I, III, V and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022 to March 2022.