Nature Communications (Feb 2024)
Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant
- Tomokazu Tamura,
- Takashi Irie,
- Sayaka Deguchi,
- Hisano Yajima,
- Masumi Tsuda,
- Hesham Nasser,
- Keita Mizuma,
- Arnon Plianchaisuk,
- Saori Suzuki,
- Keiya Uriu,
- Mst Monira Begum,
- Ryo Shimizu,
- Michael Jonathan,
- Rigel Suzuki,
- Takashi Kondo,
- Hayato Ito,
- Akifumi Kamiyama,
- Kumiko Yoshimatsu,
- Maya Shofa,
- Rina Hashimoto,
- Yuki Anraku,
- Kanako Terakado Kimura,
- Shunsuke Kita,
- Jiei Sasaki,
- Kaori Sasaki-Tabata,
- Katsumi Maenaka,
- Naganori Nao,
- Lei Wang,
- Yoshitaka Oda,
- The Genotype to Phenotype Japan (G2P-Japan) Consortium,
- Terumasa Ikeda,
- Akatsuki Saito,
- Keita Matsuno,
- Jumpei Ito,
- Shinya Tanaka,
- Kei Sato,
- Takao Hashiguchi,
- Kazuo Takayama,
- Takasuke Fukuhara
Affiliations
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University
- Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University
- Keita Mizuma
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University
- Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University
- Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University
- Michael Jonathan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University
- Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Takashi Kondo
- School of Medicine, Hokkaido University
- Hayato Ito
- Graduate School of Medicine, Hokkaido University
- Akifumi Kamiyama
- Graduate School of Medicine, Hokkaido University
- Kumiko Yoshimatsu
- Institute for Genetic Medicine, Hokkaido University
- Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Rina Hashimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University
- Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido 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
- Katsumi Maenaka
- One Health Research Center, Hokkaido University
- Naganori Nao
- Institute for Vaccine Research and Development (IVReD), Hokkaido University
- Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- The Genotype to Phenotype Japan (G2P-Japan) Consortium
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University
- Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Keita Matsuno
- Institute for Vaccine Research and Development (IVReD), Hokkaido University
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- DOI
- https://doi.org/10.1038/s41467-024-45274-3
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 1 – 17
Abstract
Abstract Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.
