Tags

Type your tag names separated by a space and hit enter

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan.
mSphere. 2020 11 11; 5(6)M

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 reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates 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 related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, 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 characterize their genealogical networks to demonstrate possible routes of spread in Japan. 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 increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

Authors+Show Affiliations

Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.Sapporo City Institute of Public Health, Sapporo, Japan.Ibaraki Prefectural Institute of Public Health, Ibaraki, Japan.Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan.Saitama Prefectural Institute of Public Health, Saitama, Japan.Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan.Microbiology Department, Nagoya City Public Health Research Institute, Aichi, Japan.Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan.Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan.Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.National Institute of Infectious Diseases, Tokyo, Japan.Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan makokuro@niid.go.jp.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

33177213

Citation

Sekizuka, Tsuyoshi, et al. "A Genome Epidemiological Study of SARS-CoV-2 Introduction Into Japan." MSphere, vol. 5, no. 6, 2020.
Sekizuka T, Itokawa K, Hashino M, et al. A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan. mSphere. 2020;5(6).
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., ... Kuroda, M. (2020). A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan. MSphere, 5(6). https://doi.org/10.1128/mSphere.00786-20
Sekizuka T, et al. A Genome Epidemiological Study of SARS-CoV-2 Introduction Into Japan. mSphere. 2020 11 11;5(6) PubMed PMID: 33177213.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan. AU - Sekizuka,Tsuyoshi, AU - Itokawa,Kentaro, AU - Hashino,Masanori, AU - Kawano-Sugaya,Tetsuro, AU - Tanaka,Rina, AU - Yatsu,Koji, AU - Ohnishi,Asami, AU - Goto,Keiko, AU - Tsukagoshi,Hiroyuki, AU - Ehara,Hayato, AU - Sadamasu,Kenji, AU - Taira,Masakatsu, AU - Shibata,Shinichiro, AU - Nomoto,Ryohei, AU - Hiroi,Satoshi, AU - Toho,Miho, AU - Shimada,Tomoe, AU - Matsui,Tamano, AU - Sunagawa,Tomimasa, AU - Kamiya,Hajime, AU - Yahata,Yuichiro, AU - Yamagishi,Takuya, AU - Suzuki,Motoi, AU - Wakita,Takaji, AU - Kuroda,Makoto, Y1 - 2020/11/11/ PY - 2020/11/12/entrez PY - 2020/11/13/pubmed PY - 2020/11/24/medline KW - COVID-19 KW - SARS-CoV-2 KW - epidemiology KW - genome KW - haplotypes KW - immigration JF - mSphere JO - mSphere VL - 5 IS - 6 N2 - 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 reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates 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 related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, 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 characterize their genealogical networks to demonstrate possible routes of spread in Japan. 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 increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan. SN - 2379-5042 UR - https://www.unboundmedicine.com/medline/citation/33177213/A_Genome_Epidemiological_Study_of_SARS_CoV_2_Introduction_into_Japan_ L2 - https://doi.org/10.1128/mSphere.00786-20 DB - PRIME DP - Unbound Medicine ER -