A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron

DOI HANDLE PDF Web Site 4 Citations 104 References Open Access
  • Maeda, Ryota
    Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University; COGNANO Inc.
  • Fujita, Junso
    Graduate School of Frontier Biosciences, Osaka University; Graduate School of Pharmaceutical Sciences, Osaka University
  • Konishi, Yoshinobu
    Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University
  • Kazuma, Yasuhiro
    Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University
  • Yamazaki, Hiroyuki
    COGNANO Inc.; Shizuoka City Shizuoka Hospital
  • Anzai, Itsuki
    Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University
  • Watanabe, Tokiko
    Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University
  • Yamaguchi, Keishi
    Graduate School of Pharmaceutical Sciences, Osaka University
  • Kasai, Kazuki
    COGNANO Inc.
  • Nagata, Kayoko
    Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University
  • Yamaoka, Yutaro
    Department of Microbiology and Molecular Biodefense Research, Yokohama City University Graduate School of Medicine
  • Miyakawa, Kei
    Department of Microbiology and Molecular Biodefense Research, Yokohama City University Graduate School of Medicine
  • Ryo, Akihide
    Department of Microbiology and Molecular Biodefense Research, Yokohama City University Graduate School of Medicine
  • Shirakawa, Kotaro
    Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University
  • Sato, Kei
    Division of System Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo; Graduate School of Medicine, The University of Tokyo; CREST, Japan Science and Technology Agency
  • Makino, Fumiaki
    Graduate School of Frontier Biosciences, Osaka University; JEOL Ltd.
  • Matsuura, Yoshiharu
    Centre for Infectious Disease Education and Research, Osaka University; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University
  • Inoue, Tsuyoshi
    Graduate School of Pharmaceutical Sciences, Osaka University
  • Imura, Akihiro
    COGNANO Inc.
  • Namba, Keiichi
    Graduate School of Frontier Biosciences, Osaka University; JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University; RIKEN Centre for Biosystems Dynamics Research and SPring-8 Centre
  • Takaori-Kondo, Akifumi
    Department of Haematology and Oncology, Graduate School of Medicine, Kyoto University

Abstract

We are amid the historic coronavirus infectious disease 2019 (COVID-19) pandemic. Imbalances in the accessibility of vaccines, medicines, and diagnostics among countries, regions, and populations, and those in war crises, have been problematic. Nanobodies are small, stable, customizable, and inexpensive to produce. Herein, we present a panel of nanobodies that can detect the spike proteins of five SARS-CoV-2 variants of concern (VOCs) including Omicron. Here we show via ELISA, lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays that our nanobodies can quantify the spike variants. This panel of nanobodies broadly neutralizes viral infection caused by pseudotyped and authentic SARS-CoV-2 VOCs. Structural analyses show that the P86 clone targets epitopes that are conserved yet unclassified on the receptor-binding domain (RBD) and contacts the N-terminal domain (NTD). Human antibodies rarely access both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins that go undetected by conventional antibodies.

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