Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Tamura, Tomokazu; Ito, Jumpei; Uriu, Keiya; Zahradnik, Jiri; Kida, Izumi; Anraku, Yuki; Nasser, Hesham; Shofa, Maya; Oda, Yoshitaka; Lytras, Spyros; Nao, Naganori; Itakura, Yukari; Deguchi, Sayaka; Suzuki, Rigel; Wang, Lei; Begum, MST Monira; Kita, Shunsuke; Yajima, Hisano; Sasaki, Jiei; Sasaki-Tabata, Kaori; Shimizu, Ryo; Tsuda, Masumi; Kosugi, Yusuke; Fujita, Shigeru; Pan, Lin; Sauter, Daniel; Yoshimatsu, Kumiko; Suzuki, Saori; Asakura, Hiroyuki; Nagashima, Mami; Sadamasu, Kenji; Yoshimura, Kazuhisa; Yamamoto, Yuki; Nagamoto, Tetsuharu; Schreiber, Gideon; Maenaka, Katsumi; The Genotype to Phenotype Japan (G2P-Japan); Hashiguchi, Takao; Ikeda, Terumasa; Fukuhara, Takasuke; Saito, Akatsuki; Tanaka, Shinya; Matsuno, Keita; Takayama, Kazuo; Sato, Kei

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http://hdl.handle.net/2433/282776

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dc.contributor.author	Tamura, Tomokazu	en
dc.contributor.author	Ito, Jumpei	en
dc.contributor.author	Uriu, Keiya	en
dc.contributor.author	Zahradnik, Jiri	en
dc.contributor.author	Kida, Izumi	en
dc.contributor.author	Anraku, Yuki	en
dc.contributor.author	Nasser, Hesham	en
dc.contributor.author	Shofa, Maya	en
dc.contributor.author	Oda, Yoshitaka	en
dc.contributor.author	Lytras, Spyros	en
dc.contributor.author	Nao, Naganori	en
dc.contributor.author	Itakura, Yukari	en
dc.contributor.author	Deguchi, Sayaka	en
dc.contributor.author	Suzuki, Rigel	en
dc.contributor.author	Wang, Lei	en
dc.contributor.author	Begum, MST Monira	en
dc.contributor.author	Kita, Shunsuke	en
dc.contributor.author	Yajima, Hisano	en
dc.contributor.author	Sasaki, Jiei	en
dc.contributor.author	Sasaki-Tabata, Kaori	en
dc.contributor.author	Shimizu, Ryo	en
dc.contributor.author	Tsuda, Masumi	en
dc.contributor.author	Kosugi, Yusuke	en
dc.contributor.author	Fujita, Shigeru	en
dc.contributor.author	Pan, Lin	en
dc.contributor.author	Sauter, Daniel	en
dc.contributor.author	Yoshimatsu, Kumiko	en
dc.contributor.author	Suzuki, Saori	en
dc.contributor.author	Asakura, Hiroyuki	en
dc.contributor.author	Nagashima, Mami	en
dc.contributor.author	Sadamasu, Kenji	en
dc.contributor.author	Yoshimura, Kazuhisa	en
dc.contributor.author	Yamamoto, Yuki	en
dc.contributor.author	Nagamoto, Tetsuharu	en
dc.contributor.author	Schreiber, Gideon	en
dc.contributor.author	Maenaka, Katsumi	en
dc.contributor.author	The Genotype to Phenotype Japan (G2P-Japan)	en
dc.contributor.author	Hashiguchi, Takao	en
dc.contributor.author	Ikeda, Terumasa	en
dc.contributor.author	Fukuhara, Takasuke	en
dc.contributor.author	Saito, Akatsuki	en
dc.contributor.author	Tanaka, Shinya	en
dc.contributor.author	Matsuno, Keita	en
dc.contributor.author	Takayama, Kazuo	en
dc.contributor.author	Sato, Kei	en
dc.contributor.alternative	田村, 友和	ja
dc.contributor.alternative	伊東, 潤平	ja
dc.contributor.alternative	瓜生, 慧也	ja
dc.contributor.alternative	紀田, 泉	ja
dc.contributor.alternative	安楽, 佑樹	ja
dc.contributor.alternative	小田, 義崇	ja
dc.contributor.alternative	直, 亨則	ja
dc.contributor.alternative	板倉, 友香里	ja
dc.contributor.alternative	出口, 清香	ja
dc.contributor.alternative	鈴木, 理滋	ja
dc.contributor.alternative	王, 磊	ja
dc.contributor.alternative	喜多, 俊介	ja
dc.contributor.alternative	矢島, 久乃	ja
dc.contributor.alternative	佐々木, 慈英	ja
dc.contributor.alternative	田畑, 香織	ja
dc.contributor.alternative	清水, 凌	ja
dc.contributor.alternative	津田, 真寿美	ja
dc.contributor.alternative	小杉, 優介	ja
dc.contributor.alternative	藤田, 滋	ja
dc.contributor.alternative	潘, 琳	ja
dc.contributor.alternative	吉松, 組子	ja
dc.contributor.alternative	鈴木, 紗織	ja
dc.contributor.alternative	浅倉, 弘幸	ja
dc.contributor.alternative	長島, 真美	ja
dc.contributor.alternative	貞升, 健志	ja
dc.contributor.alternative	吉村, 和久	ja
dc.contributor.alternative	山本, 佑樹	ja
dc.contributor.alternative	永元, 哲治	ja
dc.contributor.alternative	前仲, 勝実	ja
dc.contributor.alternative	橋口, 隆生	ja
dc.contributor.alternative	池田, 輝政	ja
dc.contributor.alternative	福原, 崇介	ja
dc.contributor.alternative	齊藤, 暁	ja
dc.contributor.alternative	田中, 伸哉	ja
dc.contributor.alternative	松野, 啓太	ja
dc.contributor.alternative	高山, 和雄	ja
dc.contributor.alternative	佐藤, 佳	ja
dc.date.accessioned	2023-05-23T09:22:47Z	-
dc.date.available	2023-05-23T09:22:47Z	-
dc.date.issued	2023	-
dc.identifier.uri	http://hdl.handle.net/2433/282776	-
dc.description	オミクロンXBB株の進化経路とウイルス学的特性の解明 --遺伝子組換えによる更なる免疫逃避能力の獲得--. 京都大学プレスリリース. 2023-05-22.	ja
dc.description.abstract	In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.	en
dc.language.iso	eng	-
dc.publisher	Springer Nature	en
dc.rights	© The Author(s) 2023	en
dc.rights	This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	-
dc.subject	SARS-CoV-2	en
dc.subject	Viral evolution	en
dc.subject	Virus–host interactions	en
dc.title	Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants	en
dc.type	journal article	-
dc.type.niitype	Journal Article	-
dc.identifier.jtitle	Nature Communications	en
dc.identifier.volume	14	-
dc.relation.doi	10.1038/s41467-023-38435-3	-
dc.textversion	publisher	-
dc.identifier.artnum	2800	-
dc.address	Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University; Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo; Graduate School of Medicine, The University of Tokyo	en
dc.address	Department of Biomolecular Sciences, Weizmann Institute of Science; First Medical Faculty at Biocev, Charles University	en
dc.address	Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University	en
dc.address	Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University	en
dc.address	Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University	en
dc.address	Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki	en
dc.address	Department of Cancer Pathology, Faculty of Medicine, Hokkaido University	en
dc.address	Medical Research Council-University of Glasgow Centre for Virus Research	en
dc.address	Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University; One Health Research Center, Hokkaido University	en
dc.address	Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University; Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University	en
dc.address	Center for iPS Cell Research and Application (CiRA), Kyoto University	en
dc.address	Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University; Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University	en
dc.address	Department of Cancer Pathology, Faculty of Medicine, Hokkaido University; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University	en
dc.address	Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University	en
dc.address	Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University	en
dc.address	Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University	en
dc.address	Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University	en
dc.address	Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University	en
dc.address	Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University	en
dc.address	Department of Cancer Pathology, Faculty of Medicine, Hokkaido University; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo; Graduate School of Medicine, The University of Tokyo	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo; Graduate School of Medicine, The University of Tokyo	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo; Graduate School of Frontier Sciences, The University of Tokyo	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen	en
dc.address	Institute for Genetic Medicine, Hokkaido University	en
dc.address	Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University; Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University	en
dc.address	Tokyo Metropolitan Institute of Public Health	en
dc.address	Tokyo Metropolitan Institute of Public Health	en
dc.address	Tokyo Metropolitan Institute of Public Health	en
dc.address	Tokyo Metropolitan Institute of Public Health	en
dc.address	HiLung, Inc.	en
dc.address	HiLung, Inc.	en
dc.address	Department of Biomolecular Sciences, Weizmann Institute of Science	en
dc.address	Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University; Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University; Global Station for Biosurfaces and Drug Discovery, Hokkaido University; Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University	en
dc.address	Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University; CREST, Japan Science and Technology Agency	en
dc.address	Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University	en
dc.address	Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University; Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University; AMED-CREST, Japan Agency for Medical Research and Development (AMED); Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University	en
dc.address	Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki; Center for Animal Disease Control, University of Miyazaki	en
dc.address	Department of Cancer Pathology, Faculty of Medicine, Hokkaido University; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University	en
dc.address	Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University; One Health Research Center, Hokkaido University; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University	en
dc.address	Center for iPS Cell Research and Application (CiRA), Kyoto University; CREST, Japan Science and Technology Agency	en
dc.address	Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo; Graduate School of Medicine, The University of Tokyo; Graduate School of Frontier Sciences, The University of Tokyo; CREST, Japan Science and Technology Agency; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University	en
dc.identifier.pmid	37193706	-
dc.relation.url	https://www.kyoto-u.ac.jp/ja/research-news/2023-05-22-1	-
dcterms.accessRights	open access	-
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dc.identifier.eissn	2041-1723	-
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jpcoar.awardTitle	高速リバースジェネティクス系を駆使した新興再興ウイルス研究の推進	ja
jpcoar.awardTitle	APOBEC3 family proteins mediate HIV-1 restriction in myeloid cells	en
jpcoar.awardTitle	内在性レトロウイルスが駆動する遺伝子発現制御ネットワークの生理機能の解明	ja
jpcoar.awardTitle	新型コロナウイルス変異株の形質予測・進化予測手法の開発	ja
jpcoar.awardTitle	ウイルスのPLAMP生成機構とPLAMPを介した病原性制御機構の解明	ja
jpcoar.awardTitle	細胞表面蛋白質の弱い分子認識の定量化・構造解析	ja
jpcoar.awardTitle	新興ウイルスの誕生原理と、コウモリがその自然宿主たり得る原理の解明	ja
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