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TitleVirological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 2800, Year 2023
Publish dateMay 16, 2023
AuthorsTomokazu 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 / / Takao Hashiguchi / Terumasa Ikeda / Takasuke Fukuhara / Akatsuki Saito / Shinya Tanaka / Keita Matsuno / Kazuo Takayama / Kei Sato /
PubMed AbstractIn 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 ...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.
External linksNat Commun / PubMed:37193706 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 3.29 Å
Structure data

35622

8ios

EMDB-35622: SARS-CoV-2 XBB.1 spike glycoprotein (closed-1 state)
PDB-8ios: Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-1 state)
Method: EM (single particle) / Resolution: 2.5 Å

35623

8iot

EMDB-35623: SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state)
PDB-8iot: Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state)
Method: EM (single particle) / Resolution: 2.51 Å

35624

8iou

EMDB-35624: SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (1-up state)
PDB-8iou: Structure of SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (1-up state)
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-35625: SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (2-up state)
Method: EM (single particle) / Resolution: 2.99 Å

35626

8iov

EMDB-35626: SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 focused on RBD-ACE2 interface
PDB-8iov: Structure of SARS-CoV-2 XBB.1 spike RBD in complex with ACE2
Method: EM (single particle) / Resolution: 3.29 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / spike glycoprotein / VIRAL PROTEIN/PROTEIN BINDING / VIRAL PROTEIN-PROTEIN BINDING complex

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