Nature Communications (May 2023)
Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants
- Tomokazu Tamura,
- Jumpei Ito,
- Keiya Uriu,
- Jiri Zahradnik,
- Izumi Kida,
- Yuki Anraku,
- Hesham Nasser,
- Maya Shofa,
- Yoshitaka Oda,
- Spyros Lytras,
- Naganori Nao,
- Yukari Itakura,
- Sayaka Deguchi,
- Rigel Suzuki,
- Lei Wang,
- MST Monira Begum,
- Shunsuke Kita,
- Hisano Yajima,
- Jiei Sasaki,
- Kaori Sasaki-Tabata,
- Ryo Shimizu,
- Masumi Tsuda,
- Yusuke Kosugi,
- Shigeru Fujita,
- Lin Pan,
- Daniel Sauter,
- Kumiko Yoshimatsu,
- Saori Suzuki,
- Hiroyuki Asakura,
- Mami Nagashima,
- Kenji Sadamasu,
- Kazuhisa Yoshimura,
- Yuki Yamamoto,
- Tetsuharu Nagamoto,
- Gideon Schreiber,
- Katsumi Maenaka,
- The Genotype to Phenotype Japan (G2P-Japan) Consortium,
- Takao Hashiguchi,
- Terumasa Ikeda,
- Takasuke Fukuhara,
- Akatsuki Saito,
- Shinya Tanaka,
- Keita Matsuno,
- Kazuo Takayama,
- Kei Sato
Affiliations
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science
- Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University
- Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University
- Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research
- Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University
- Yukari Itakura
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University
- Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- MST Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University
- Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University
- Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Yusuke Kosugi
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Lin Pan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Daniel Sauter
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Kumiko Yoshimatsu
- Institute for Genetic Medicine, Hokkaido University
- Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Hiroyuki Asakura
- Tokyo Metropolitan Institute of Public Health
- Mami Nagashima
- Tokyo Metropolitan Institute of Public Health
- Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health
- Kazuhisa Yoshimura
- Tokyo Metropolitan Institute of Public Health
- Yuki Yamamoto
- HiLung, Inc.
- Tetsuharu Nagamoto
- HiLung, Inc.
- Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science
- Katsumi Maenaka
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University
- The Genotype to Phenotype Japan (G2P-Japan) Consortium
- Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Keita Matsuno
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University
- Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- DOI
- https://doi.org/10.1038/s41467-023-38435-3
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 20
Abstract
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.
