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SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotypes spread in Japan


  • Nakagawa, So Department of Molecular Life Science, Tokai University School of Medicine https://orcid.org/0000-0003-1760-3839 https://researchmap.jp/sounaka
  • Katayama, Toshiaki Database Center for Life Science https://researchmap.jp/toshiakikatayama
  • Jin, Lihua Genomus Co., Ltd.
  • Wu, Jiaqi Department of Molecular Life Science, Tokai University School of Medicine
  • Kryukov, Kirill Bioinformation and DDBJ Center, National Institute of Genetics
  • Oyachi, Rise Department of Applied Biochemistry, School of Engineering, Tokai University
  • Junko S Takeuchi Center for Clinical Sciences, National Center for Global Health and Medicine https://orcid.org/0000-0002-4844-9013
  • Fujisawa, Takatomo Bioinformation and DDBJ Center, National Institute of Genetics
  • Asano, Satomi Bioinformation and DDBJ Center, National Institute of Genetics https://orcid.org/0000-0001-5498-7240
  • Komatsu, Momoka Smart Information Systems, Faculty of Engineering, Niigata University
  • Onami, Jun-ichi Research Center for Open Science and Data Platform, National Institute of Informatics
  • Abe, Takashi Smart Information Systems, Faculty of Engineering, Niigata University
  • Arita, Masanori Bioinformation and DDBJ Center, National Institute of Genetics




COVID-19、 haplotype、 genomic surveillance、 SARS-CoV-2、 web visualization


Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of the SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each wave and showed prefectural or region-specific haplotypes in each of the four epidemic waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and geographical prevalence of haplotypes and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.


The authors have no competing interests.

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投稿日時: 2023-03-22 08:46:03 UTC

公開日時: 2023-03-23 23:06:02 UTC