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

Nakagawa, So; Katayama, Toshiaki; Jin, Lihua; Wu, Jiaqi; Kryukov, Kirill; Oyachi, Rise; Takeuchi, Junko; Fujisawa, Takatomo; Asano, Satomi; Komatsu, Momoka; Onami, Jun-ichi; Abe, Takashi; Arita, Masanori

doi:10.51094/jxiv.338

##article.authors##

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

DOI:

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

キーワード:

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

抄録

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/.

利益相反に関する開示

The authors have no competing interests.

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引用文献

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