Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria.
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria.
Bioinformatics. 2023 Apr 3;39(4). doi: 10.1093/bioinformatics/btad160.
Environmental monitoring of pathogens provides an accurate and timely source of information for public health authorities and policymakers. In the last 2 years, wastewater sequencing proved to be an effective way of detection and quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants circulating in population. Wastewater sequencing produces substantial amounts of geographical and genomic data. Proper visualization of spatial and temporal patterns in these data is crucial for the assessment of the epidemiological situation and forecasting. Here, we present a web-based dashboard application for the visualization and analysis of data obtained from sequencing of environmental samples. The dashboard provides multi-layered visualization of geographical and genomic data. It allows to display frequencies of detected pathogen variants as well as individual mutation frequencies. The features of WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) for early tracking and detection of novel variants in the wastewater are demonstrated in an example of BA.1 variant and the signature Spike mutation S: E484A. WAVES dashboard is easily customized through the editable configuration file and can be used for different types of pathogens and environmental samples.
WAVES source code is freely available at https://github.com/ptriska/WavesDash under MIT license. A demo version of this application can be accessed at: https://wavesdashboard.azurewebsites.net/.
病原体的环境监测为公共卫生当局和政策制定者提供了准确和及时的信息来源。在过去的 2 年中，废水测序已被证明是检测和定量人群中流行的严重急性呼吸系统综合征冠状病毒 2 （SARS-CoV-2）变异株的有效方法。废水测序会产生大量的地理和基因组数据。正确显示这些数据的时空模式对于评估流行病学情况和预测至关重要。在这里，我们展示了一个基于网络的仪表板应用程序，用于可视化和分析从环境样本测序中获得的数据。该仪表板提供了地理和基因组数据的多层可视化。它允许显示检测到的病原体变异的频率以及单个突变频率。在废水 BA.1 变异体和 Spike 突变 S: E484A 特征的示例中展示了 WAVES（用于环境样本分析和可视化的基于网络的工具）在早期跟踪和检测新型变体方面的功能。WAVES 仪表板可通过可编辑的配置文件轻松自定义，并可用于不同类型的病原体和环境样本。
WAVES 的源代码可在 MIT 许可证下在 https://github.com/ptriska/WavesDash 上免费获得。此应用程序的演示版本可在：https://wavesdashboard.azurewebsites.net/ 访问。
