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

##article.authors##

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

DOI:

https://doi.org/10.51094/jxiv.338

Keywords:

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

Abstract

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/.

Conflicts of Interest Disclosure

The authors have no competing interests.

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Submitted: 2023-03-22 08:46:03 UTC

Published: 2023-03-23 23:06:02 UTC
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Copyright (c) 2023 So Nakagawa
Toshiaki Katayama
Lihua Jin
Jiaqi Wu
Kirill Kryukov
Rise Oyachi
Junko S Takeuchi
Takatomo Fujisawa
Satomi Asano
Momoka Komatsu
Jun-ichi Onami
Takashi Abe
Masanori Arita

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