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, Monira Begum Mst, 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, Takao Hashiguchi, Terumasa Ikeda, Takasuke Fukuhara, Akatsuki Saito, Shinya Tanaka (), Keita Matsuno (), Kazuo Takayama () and Kei Sato ()
Additional contact information
Tomokazu Tamura: Hokkaido University
Jumpei Ito: The University of Tokyo
Keiya Uriu: The University of Tokyo
Jiri Zahradnik: Weizmann Institute of Science
Izumi Kida: Hokkaido University
Yuki Anraku: Hokkaido University
Hesham Nasser: Kumamoto University
Maya Shofa: University of Miyazaki
Yoshitaka Oda: Hokkaido University
Spyros Lytras: Medical Research Council-University of Glasgow Centre for Virus Research
Naganori Nao: Hokkaido University
Yukari Itakura: Hokkaido University
Sayaka Deguchi: Kyoto University
Rigel Suzuki: Hokkaido University
Lei Wang: Hokkaido University
Monira Begum Mst: Kumamoto University
Shunsuke Kita: Hokkaido University
Hisano Yajima: Kyoto University
Jiei Sasaki: Kyoto University
Kaori Sasaki-Tabata: Kyushu University
Ryo Shimizu: Kumamoto University
Masumi Tsuda: Hokkaido University
Yusuke Kosugi: The University of Tokyo
Shigeru Fujita: The University of Tokyo
Lin Pan: The University of Tokyo
Daniel Sauter: The University of Tokyo
Kumiko Yoshimatsu: Hokkaido University
Saori Suzuki: 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: Weizmann Institute of Science
Katsumi Maenaka: Hokkaido University
Takao Hashiguchi: Kyoto University
Terumasa Ikeda: Kumamoto University
Takasuke Fukuhara: Hokkaido University
Akatsuki Saito: University of Miyazaki
Shinya Tanaka: Hokkaido University
Keita Matsuno: Hokkaido University
Kazuo Takayama: Kyoto University
Kei Sato: The University of Tokyo

Nature Communications, 2023, vol. 14, issue 1, 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.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (5)

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DOI: 10.1038/s41467-023-38435-3

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