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SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan
So Nakagawa1,2,3,4, Toshiaki Katayama5, Lihua Jin6
1Bioinformation and DDBJ Center, National Institute of Genetics.
A new web platform, SARS-CoV-2 HaploGraph, visualizes the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) haplotypes in Japan. This tool aids in understanding virus evolution and geographical transmission patterns during the COVID-19 pandemic.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- The COVID-19 pandemic necessitated tracking the spread of SARS-CoV-2.
- Research institutes shared genomic data to understand infection routes in Japan.
Purpose of the Study:
- To develop a tool for visualizing SARS-CoV-2 haplotype emergence and geographical transmission in Japan.
- To provide insights into the evolution and spread of SARS-CoV-2 during different epidemic waves.
Main Methods:
- Developed the SARS-CoV-2 HaploGraph web platform.
- Utilized GISAID EpiCoV database data up to June 4, 2022.
- Established a haplotype naming system based on ancestral haplotypes for each wave.
Main Results:
- Identified and visualized prefecture- or region-specific SARS-CoV-2 haplotypes across four major epidemic waves in Japan.
- Enabled interactive tracking of virus evolution and haplotype prevalence.
- Demonstrated geographical transmission patterns of different viral lineages.
Conclusions:
- The SARS-CoV-2 HaploGraph platform effectively visualizes viral evolution and geographical spread.
- The tool supports the development of public health strategies for pandemic control.
- Publicly available code and data facilitate further research and application.
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