Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic

作者：Tetsuro Kawano-Sugaya, Koji Yatsu, Tsuyoshi Sekizuka, Kentaro Itokawa, Masanori Hashino, Rina Tanaka, Makoto Kuroda · 发表于：G3 Genes Genomes Genetics · 年份：2021 · DOI：10.1093/g3journal/jkab126 · 被引用次数：4 · 研究领域：Bioinformatics and Genomic Networks、Genomics and Phylogenetic Studies、Machine Learning in Bioinformatics

The worldwide eruption of coronavirus disease 2019 (COVID-19) that began in Wuhan, China in late 2019 reached 10 million cases by late June 2020. In order to understand the epidemiological landscape of the COVID-19 pandemic, many studies have attempted to elucidate phylogenetic relationships between collected viral genome sequences using haplotype networks. However, currently available applications for network visualization are not suited to understand the COVID-19 epidemic spatiotemporally due to functional limitations that motivated us to develop Haplotype Explorer, an intuitive tool for visualizing and exploring haplotype networks. Haplotype Explorer enables to dissect epidemiological consequences via interactive node filters and provides the perspective on infectious disease dynamics depend on regions and time, such as introduction, outbreak, expansion, and containment. Here, we demonstrate the effectiveness of Haplotype Explorer by showing features and an example of visualization. The demo using severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes are available at https://github.com/TKSjp/HaplotypeExplorer/blob/master/Example/. There are several examples using SARS-CoV-2 genomes and Dengue virus serotype 1 E-genes sequence.