A Genome Epidemiological Study of SARS-CoV-2 Introduction into 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...

Description complète

Enregistré dans:

Détails bibliographiques
Auteurs principaux:	Tsuyoshi Sekizuka, Kentaro Itokawa, Masanori Hashino, Tetsuro Kawano-Sugaya, Rina Tanaka, Koji Yatsu, Asami Ohnishi, Keiko Goto, Hiroyuki Tsukagoshi, Hayato Ehara, Kenji Sadamasu, Masakatsu Taira, Shinichiro Shibata, Ryohei Nomoto, Satoshi Hiroi, Miho Toho, Tomoe Shimada, Tamano Matsui, Tomimasa Sunagawa, Hajime Kamiya, Yuichiro Yahata, Takuya Yamagishi, Motoi Suzuki, Takaji Wakita, Makoto Kuroda
Format:	article
Langue:	EN
Publié:	American Society for Microbiology 2020
Sujets:	SARS-CoV-2 COVID-19 genome haplotypes epidemiology immigration Microbiology QR1-502
Accès en ligne:	https://doaj.org/article/7d14a3ea31d7436ca54d4f80f913084d
Tags:	Ajouter un tag Pas de tags, Soyez le premier à ajouter un tag!

id	oai:doaj.org-article:7d14a3ea31d7436ca54d4f80f913084d
record_format	dspace
spelling	oai:doaj.org-article:7d14a3ea31d7436ca54d4f80f913084d2021-11-15T15:31:13ZA Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan10.1128/mSphere.00786-202379-5042https://doaj.org/article/7d14a3ea31d7436ca54d4f80f913084d2020-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00786-20https://doaj.org/toc/2379-5042ABSTRACT 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.Tsuyoshi SekizukaKentaro ItokawaMasanori HashinoTetsuro Kawano-SugayaRina TanakaKoji YatsuAsami OhnishiKeiko GotoHiroyuki TsukagoshiHayato EharaKenji SadamasuMasakatsu TairaShinichiro ShibataRyohei NomotoSatoshi HiroiMiho TohoTomoe ShimadaTamano MatsuiTomimasa SunagawaHajime KamiyaYuichiro YahataTakuya YamagishiMotoi SuzukiTakaji WakitaMakoto KurodaAmerican Society for MicrobiologyarticleSARS-CoV-2COVID-19genomehaplotypesepidemiologyimmigrationMicrobiologyQR1-502ENmSphere, Vol 5, Iss 6 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 COVID-19 genome haplotypes epidemiology immigration Microbiology QR1-502
spellingShingle	SARS-CoV-2 COVID-19 genome haplotypes epidemiology immigration Microbiology QR1-502 Tsuyoshi Sekizuka Kentaro Itokawa Masanori Hashino Tetsuro Kawano-Sugaya Rina Tanaka Koji Yatsu Asami Ohnishi Keiko Goto Hiroyuki Tsukagoshi Hayato Ehara Kenji Sadamasu Masakatsu Taira Shinichiro Shibata Ryohei Nomoto Satoshi Hiroi Miho Toho Tomoe Shimada Tamano Matsui Tomimasa Sunagawa Hajime Kamiya Yuichiro Yahata Takuya Yamagishi Motoi Suzuki Takaji Wakita Makoto Kuroda A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
description	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.
format	article
author	Tsuyoshi Sekizuka Kentaro Itokawa Masanori Hashino Tetsuro Kawano-Sugaya Rina Tanaka Koji Yatsu Asami Ohnishi Keiko Goto Hiroyuki Tsukagoshi Hayato Ehara Kenji Sadamasu Masakatsu Taira Shinichiro Shibata Ryohei Nomoto Satoshi Hiroi Miho Toho Tomoe Shimada Tamano Matsui Tomimasa Sunagawa Hajime Kamiya Yuichiro Yahata Takuya Yamagishi Motoi Suzuki Takaji Wakita Makoto Kuroda
author_facet	Tsuyoshi Sekizuka Kentaro Itokawa Masanori Hashino Tetsuro Kawano-Sugaya Rina Tanaka Koji Yatsu Asami Ohnishi Keiko Goto Hiroyuki Tsukagoshi Hayato Ehara Kenji Sadamasu Masakatsu Taira Shinichiro Shibata Ryohei Nomoto Satoshi Hiroi Miho Toho Tomoe Shimada Tamano Matsui Tomimasa Sunagawa Hajime Kamiya Yuichiro Yahata Takuya Yamagishi Motoi Suzuki Takaji Wakita Makoto Kuroda
author_sort	Tsuyoshi Sekizuka
title	A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
title_short	A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
title_full	A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
title_fullStr	A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
title_full_unstemmed	A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
title_sort	genome epidemiological study of sars-cov-2 introduction into japan
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/7d14a3ea31d7436ca54d4f80f913084d
work_keys_str_mv	AT tsuyoshisekizuka agenomeepidemiologicalstudyofsarscov2introductionintojapan AT kentaroitokawa agenomeepidemiologicalstudyofsarscov2introductionintojapan AT masanorihashino agenomeepidemiologicalstudyofsarscov2introductionintojapan AT tetsurokawanosugaya agenomeepidemiologicalstudyofsarscov2introductionintojapan AT rinatanaka agenomeepidemiologicalstudyofsarscov2introductionintojapan AT kojiyatsu agenomeepidemiologicalstudyofsarscov2introductionintojapan AT asamiohnishi agenomeepidemiologicalstudyofsarscov2introductionintojapan AT keikogoto agenomeepidemiologicalstudyofsarscov2introductionintojapan AT hiroyukitsukagoshi agenomeepidemiologicalstudyofsarscov2introductionintojapan AT hayatoehara agenomeepidemiologicalstudyofsarscov2introductionintojapan AT kenjisadamasu agenomeepidemiologicalstudyofsarscov2introductionintojapan AT masakatsutaira agenomeepidemiologicalstudyofsarscov2introductionintojapan AT shinichiroshibata agenomeepidemiologicalstudyofsarscov2introductionintojapan AT ryoheinomoto agenomeepidemiologicalstudyofsarscov2introductionintojapan AT satoshihiroi agenomeepidemiologicalstudyofsarscov2introductionintojapan AT mihotoho agenomeepidemiologicalstudyofsarscov2introductionintojapan AT tomoeshimada agenomeepidemiologicalstudyofsarscov2introductionintojapan AT tamanomatsui agenomeepidemiologicalstudyofsarscov2introductionintojapan AT tomimasasunagawa agenomeepidemiologicalstudyofsarscov2introductionintojapan AT hajimekamiya agenomeepidemiologicalstudyofsarscov2introductionintojapan AT yuichiroyahata agenomeepidemiologicalstudyofsarscov2introductionintojapan AT takuyayamagishi agenomeepidemiologicalstudyofsarscov2introductionintojapan AT motoisuzuki agenomeepidemiologicalstudyofsarscov2introductionintojapan AT takajiwakita agenomeepidemiologicalstudyofsarscov2introductionintojapan AT makotokuroda agenomeepidemiologicalstudyofsarscov2introductionintojapan AT tsuyoshisekizuka genomeepidemiologicalstudyofsarscov2introductionintojapan AT kentaroitokawa genomeepidemiologicalstudyofsarscov2introductionintojapan AT masanorihashino genomeepidemiologicalstudyofsarscov2introductionintojapan AT tetsurokawanosugaya genomeepidemiologicalstudyofsarscov2introductionintojapan AT rinatanaka genomeepidemiologicalstudyofsarscov2introductionintojapan AT kojiyatsu genomeepidemiologicalstudyofsarscov2introductionintojapan AT asamiohnishi genomeepidemiologicalstudyofsarscov2introductionintojapan AT keikogoto genomeepidemiologicalstudyofsarscov2introductionintojapan AT hiroyukitsukagoshi genomeepidemiologicalstudyofsarscov2introductionintojapan AT hayatoehara genomeepidemiologicalstudyofsarscov2introductionintojapan AT kenjisadamasu genomeepidemiologicalstudyofsarscov2introductionintojapan AT masakatsutaira genomeepidemiologicalstudyofsarscov2introductionintojapan AT shinichiroshibata genomeepidemiologicalstudyofsarscov2introductionintojapan AT ryoheinomoto genomeepidemiologicalstudyofsarscov2introductionintojapan AT satoshihiroi genomeepidemiologicalstudyofsarscov2introductionintojapan AT mihotoho genomeepidemiologicalstudyofsarscov2introductionintojapan AT tomoeshimada genomeepidemiologicalstudyofsarscov2introductionintojapan AT tamanomatsui genomeepidemiologicalstudyofsarscov2introductionintojapan AT tomimasasunagawa genomeepidemiologicalstudyofsarscov2introductionintojapan AT hajimekamiya genomeepidemiologicalstudyofsarscov2introductionintojapan AT yuichiroyahata genomeepidemiologicalstudyofsarscov2introductionintojapan AT takuyayamagishi genomeepidemiologicalstudyofsarscov2introductionintojapan AT motoisuzuki genomeepidemiologicalstudyofsarscov2introductionintojapan AT takajiwakita genomeepidemiologicalstudyofsarscov2introductionintojapan AT makotokuroda genomeepidemiologicalstudyofsarscov2introductionintojapan
_version_	1718427833433325568

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Documents similaires