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

Kawano-Sugaya, Tetsuro; Yatsu, Koji; Sekizuka, Tsuyoshi; Itokawa, Kentaro; Hashino, Masanori; Tanaka, Rina; Kuroda, Makoto

SUMMARY: Many of software for network visualization are available, but existing software have not been optimized to infection cluster visualization, especially the current worldwide invasion of COVID-19 since 2019. To reach the spatiotemporal understanding of epidemics, we have developed Haplotype Explorer. In Haplotype Explorer, users can explore the network interactively with metadata like accession number, locations, and collection dates. Time dependent transition of the network can be exported as continuous sections for making a movie. Here, we introduce features and products of Haplotype Explorer, demonstrating time-dependent snapshots and a movie of haplotype networks inferred from total of 4,282 SARS-CoV-2 genomes. ABSTRACT: The worldwide eruption of 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 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.