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

被引：0

作者：

Nakagawa, So ^{[1
,2
,3
,4
]}

Katayama, Toshiaki ^{[5
]}

Jin, Lihua ^{[6
]}

Wu, Jiaqi ^{[2
]}

Kryukov, Kirill ^{[1
,7
]}

Oyachi, Rise ^{[2
]}

Takeuchi, Junko S. ^{[8
]}

Fujisawa, Takatomo ^{[1
]}

Asano, Satomi ^{[7
]}

Komatsu, Momoka ^{[9
]}

Onami, Jun-ichi ^{[10
]}

Abe, Takashi ^{[1
]}

Arita, Masanori ^{[1
,7
,11
]}

机构：

[1] Natl Inst Genet, Bioinformat & DDBJ Ctr, Mishima, Shizuoka 4118540, Japan

[2] Tokai Univ, Sch Med, Dept Mol Life Sci, Isehara, Kanagawa 2591193, Japan

[3] Tokai Univ, Micro Nano Technol Ctr, Hiratsuka, Kanagawa 2591292, Japan

[4] Tokai Univ, Inst Med Sci, Isehara, Kanagawa 2591193, Japan

[5] Database Ctr Life Sci, Kashiwa, Chiba 2770871, Japan

[6] Genomus Co Ltd, Sagamihara, Kanagawa 2520226, Japan

[7] Natl Inst Genet, Dept Informat, Mishima, Shizuoka 4118540, Japan

[8] Natl Ctr Global Hlth & Med, Ctr Clin Sci, Shinjuku Ku, Tokyo 1628655, Japan

[9] Niigata Univ, Fac Engn, Smart Informat Syst, Niigata, Niigata 9502181, Japan

[10] Natl Inst Informat, Res Ctr Open Sci & Data Platform, Chiyoda Ku, Tokyo 1018430, Japan

[11] RIKEN Ctr Sustainable Resource Sci, Yokohama, Kanagawa 2300045, Japan

来源：

GENES & GENETIC SYSTEMS | 2023年 / 98卷 / 05期

关键词：

COVID-19; haplotype; genomic surveillance; SARS-CoV-2; web visualization; TRANSMISSION;

D O I：

10.1266/ggs.23-00085

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplo-type naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture-or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic.

引用

页码：221 / 237

页数：17

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