Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, Australia.
Data Science Hub, School of Mathematics and Statistics, University of New South Wales, Sydney, Australia.
Analyst. 2023 Jun 12;148(12):2834-2843. doi: 10.1039/d3an00614j.
The evolution of the SARS-CoV2 coronavirus spike S-protein is studied using a mass spectrometry based protein phylogenetic approach. A study of a large dataset comprising sets of peptide masses derived from over 3000 proteins of the SARS-CoV2 virus shows that the approach is capable of resolving and correctly displaying the evolution of the major variants of concern. Using these numerical datasets, through a pairwise comparison of sets of proteolytic peptide masses for each protein, the tree is built without the need for the sequence data itself or any sequence alignment. In the same analysis, single point mutations are calculated from peptide mass differences of different protein sets and these are displayed at the branch nodes on the tree. The tree topology is found to be consistent with that generated using conventional sequence-based phylogenetics by a manual visualisation and using a tree comparison algorithm. The mass tree resolves major variants of the virus and displays non-synonymous mutations, calculated based on the mass data alone, on the tree that enable protein evolution to be charted and tracked along interconnected branches. Tracking the evolution of the SARS-CoV2 coronavirus S-protein is of particular importance given its role in the attachment of the virus to host cells ahead of viral replication.
利用基于质谱的蛋白质系统发育方法研究了 SARS-CoV2 冠状病毒刺突 S 蛋白的进化。对包含来自 SARS-CoV2 病毒的 3000 多种蛋白质的肽质量数据集的研究表明，该方法能够解析和正确显示主要关注变体的进化。使用这些数值数据集，通过对每个蛋白质的蛋白酶解肽质量集进行成对比较，构建了无需序列数据本身或任何序列比对的树。在相同的分析中，从不同蛋白质集的肽质量差异计算单点突变，并在树的分支节点上显示这些突变。通过手动可视化和使用树比较算法发现，树拓扑结构与使用传统基于序列的系统发育学生成的拓扑结构一致。质量树解析了病毒的主要变体，并在树中显示了基于质量数据单独计算的非同义突变，从而能够绘制和跟踪连接分支上的蛋白质进化。鉴于 SARS-CoV2 冠状病毒 S 蛋白在病毒复制前与宿主细胞结合中的作用，追踪其进化尤为重要。
