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. 2023 Nov 21;98(5):221-237.
doi: 10.1266/ggs.23-00085. Epub 2023 Oct 14.

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

So Nakagawa  1   2   3   4 , Toshiaki Katayama  5 , Lihua Jin  6 , Jiaqi Wu  2 , Kirill Kryukov  1   7 , Rise Oyachi  2 , Junko S Takeuchi  8 , Takatomo Fujisawa  1 , Satomi Asano  7 , Momoka Komatsu  9 , Jun-Ichi Onami  10 , Takashi Abe  1   9 , Masanori Arita  1   7   11
Affiliations
Free article

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

So Nakagawa et al. Genes Genet Syst. .
Free article

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 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 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. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

Keywords: COVID-19; SARS-CoV-2; genomic surveillance; haplotype; web visualization.

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