A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan Tsuyoshi Sekizuka, a Kentaro Itokawa, a Masanori Hashino, a Tetsuro Kawano-Sugaya, a Rina Tanaka, a Koji Yatsu, a Asami Ohnishi, b Keiko Goto, c Hiroyuki Tsukagoshi, d Hayato Ehara, e Kenji Sadamasu, f Masakatsu Taira, g Shinichiro Shibata, h Ryohei Nomoto, i Satoshi Hiroi, j Miho Toho, k Tomoe Shimada, l Tamano Matsui, l Tomimasa Sunagawa, l Hajime Kamiya, l Yuichiro Yahata, l Takuya Yamagishi, l Motoi Suzuki, l Takaji Wakita, m Makoto Kuroda, a the COVID-19 Genomic Surveillance Network in Japan a Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan b Sapporo City Institute of Public Health, Sapporo, Japan c Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan d Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan e Saitama Prefectural Institute of Public Health, Saitama, Japan f Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan g Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan h Microbiology Department, Nagoya City Public Health Research Institute, Aichi, Japan i Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan j Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan k Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan l Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan m National Institute of Infectious Diseases, Tokyo, Japan ABSTRACT After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and re- verse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype net- work analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related iso- lates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster re- lated to the outbreak in Europe, leading to additional spread within Japan. In con- clusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries. IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to charac- terize their genealogical networks to demonstrate possible routes of spread in Ja- pan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to Citation Sekizuka T, Itokawa K, Hashino M, Kawano-Sugaya T, Tanaka R, Yatsu K, Ohnishi A, Goto K, Tsukagoshi H, Ehara H, Sadamasu K, Taira M, Shibata S, Nomoto R, Hiroi S, Toho M, Shimada T, Matsui T, Sunagawa T, Kamiya H, Yahata Y, Yamagishi T, Suzuki M, Wakita T, Kuroda M, the COVID-19 Genomic Surveillance Network in Japan. 2020. A genome epidemiological study of SARS-CoV-2 introduction into Japan. mSphere 5:e00786-20. https://doi.org/10.1128/mSphere.00786-20. Editor Michael J. Imperiale, University of Michigan—Ann Arbor Copyright © 2020 Sekizuka et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Makoto Kuroda, makokuro@niid.go.jp. Received 3 August 2020 Accepted 28 October 2020 Published RESEARCH ARTICLE Clinical Science and Epidemiology crossm November/December 2020 Volume 5 Issue 6 e00786-20 msphere.asm.org 1 11 November 2020 Downloaded from https://journals.asm.org/journal/msphere on 05 September 2021 by 54.144.218.150.