ArticleNature communications2023
Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.
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Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 212 papers.
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212citing papers in PubMed
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212 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Potent type-specific de novo antibodies complement broadly reactive imprinted antibodies in immune responses to SARS-CoV-2 variants.Nature immunology · 2026Article
- GC content mismatch of transgene destabilizes RNA virus genomes.Journal of virology · 2026Article
- Human angiotensin‑converting enzyme 2‑specific benzothiazole-based allosteric inhibitor against pan‑sarbecoviruses.Nature communications · 2026Article
- Characterization of recombinant genomes of the omicron variant of SARS-CoV-2 between 2022 and 2023 in the department of Antioquia, ColombiaBiomedica : revista del Instituto Nacional de Salud · 2026Article
- Monitoring viral evolution and epidemiological characteristics of SARS-CoV-2 during 2022-2023 using Integrated Genomic Surveillance.Communications medicine · 2026Article
- A multiplexed, systems-based approach for prediction of antibody neutralization breadth for soluble human receptors.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- Epistasis and background dependence in the evolution of Omicron variants of the SARS-CoV-2 spike protein.Molecular biology and evolution · 2026Article
- Stringent selection drives convergence toward omicron-like SARS-CoV-2 receptor-binding motifs.Nature communications · 2026Article
- Broadly neutralizing monoclonal antibodies derived from mRNA LNP immunization exhibit potent neutralizing ability against JN.1, KP.3.1.1 and XEC new Omicron variants.The Journal of general virology · 2026Article
- Two years of SARS-CoV-2 genomic surveillance capacity development in Guinea.Scientific reports · 2026Article
- A comprehensive analysis of the SARS-CoV-2 omicron variant in Tocantins State, Brazil, and tracing the spread of the XBB.1.18.1 lineage.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- A bireporter recombinant SARS-CoV-2 Omicron BA.5 forbioRxiv : the preprint server for biology · 2026Article
- Polymer-lipid hybrid nanoparticle enhances mRNA delivery and T cell-mediated immunity.bioRxiv : the preprint server for biology · 2026Article
- Hidden Markov models detect recombination and ancestry of SARS-CoV-2.bioRxiv : the preprint server for biology · 2026Article
- Overview of SARS-CoV-2 genomic surveillance in Central America and the Dominican Republic from February 2020 to January 2023: the impact of PAHO and COMISCA's collaborative efforts.Frontiers in public health · 2026Article
- A tale of SARS-CoV-2 genomic surveillance in Mali: Variants introductions and transmission dynamics.PloS one · 2026Article
- The emergence of putative epistatic mutations and iSNVs in SARS-CoV-2 XBB.1.16 variants linked with alteration in immunogenic determinants.Frontiers in immunology · 2026Article
- Article
- Emergence of SARS-CoV-2 omicron subvariant NB.1.8.1 in India: Genomic evolution, transmission patterns, and public health implications.The Indian journal of medical research · 2026Review
152 more citing papers are in PubMed but not listed here.
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Authors and funding
45 authors.
Tomokazu Tamura *Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.ORCID 0000-0003-1395-6610
Jumpei Ito *Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID 0000-0003-0440-8321
Keiya Uriu *Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Jiri Zahradnik *Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.ORCID 0000-0002-8698-4236
Izumi Kida *Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.ORCID 0000-0002-6312-1454
Yuki Anraku *Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.ORCID 0000-0002-5731-0902
Hesham Nasser *Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.ORCID 0000-0001-9163-1665
Maya Shofa *Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
Yoshitaka Oda *Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Spyros Lytras *Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.ORCID 0000-0003-4202-6682
Naganori NaoDivision of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Yukari ItakuraInstitute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan.ORCID 0000-0002-3463-1834
Sayaka DeguchiCenter for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
Rigel SuzukiDepartment of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Lei WangDepartment of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.ORCID 0000-0001-6145-395X
Mst Monira BegumDivision of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
Shunsuke KitaLaboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.ORCID 0000-0003-3969-302X
Hisano YajimaLaboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Jiei SasakiLaboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Kaori Sasaki-TabataDepartment of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
Ryo ShimizuDivision of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
Masumi TsudaDepartment of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.ORCID 0000-0001-5400-5905
Yusuke KosugiDivision of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Shigeru FujitaDivision of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID 0000-0001-9008-2123
Lin PanDivision of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Daniel SauterDivision of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID 0000-0001-7665-0040
Kumiko YoshimatsuInstitute for Genetic Medicine, Hokkaido University, Sapporo, Japan.ORCID 0000-0002-0062-2753
Saori SuzukiDepartment of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.ORCID 0000-0001-5233-6604
Hiroyuki AsakuraTokyo Metropolitan Institute of Public Health, Tokyo, Japan.
Mami NagashimaTokyo Metropolitan Institute of Public Health, Tokyo, Japan.
Kenji SadamasuTokyo Metropolitan Institute of Public Health, Tokyo, Japan.
Kazuhisa YoshimuraTokyo Metropolitan Institute of Public Health, Tokyo, Japan.
Yuki YamamotoHiLung, Inc., Kyoto, Japan.
Tetsuharu NagamotoHiLung, Inc., Kyoto, Japan.
Gideon SchreiberDepartment of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.ORCID 0000-0002-2922-5882
Katsumi MaenakaInstitute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan.ORCID 0000-0002-5459-521X
Genotype to Phenotype Japan (G2P-Japan) Consortium
Takao HashiguchiLaboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.ORCID 0000-0001-7578-7571
Terumasa IkedaDivision of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.ORCID 0000-0003-2869-9450
Takasuke FukuharaDepartment of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.ORCID 0000-0001-5471-8331
Akatsuki SaitoDepartment of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.ORCID 0000-0002-2792-4399
Shinya TanakaDepartment of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. tanaka@med.hokudai.ac.jp.ORCID 0000-0001-6470-3301
Keita MatsunoInstitute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan. matsuk@czc.hokudai.ac.jp.ORCID 0000-0002-4205-6526
Kazuo TakayamaCenter for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan. kazuo.takayama@cira.kyoto-u.ac.jp.
Kei SatoDivision of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.ORCID 0000-0003-4431-1380
Funding
Medical Research Council MC_PC_19026
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.
Indexed as
COVID-19AnimalsCricetinaeHumansMalePhylogenyRecombination, GeneticSARS-CoV-2Spike Glycoprotein, CoronavirusSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2
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