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Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants

Author

Listed:
  • Saya Moriyama

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Yuki Anraku

    (Hokkaido University; Sapporo)

  • Shunta Taminishi

    (Kyoto Prefectural University of Medicine; Kyoto)

  • Yu Adachi

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Daisuke Kuroda

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Shunsuke Kita

    (Hokkaido University; Sapporo)

  • Yusuke Higuchi

    (Kyoto Prefectural University of Medicine; Kyoto)

  • Yuhei Kirita

    (Kyoto Prefectural University of Medicine; Kyoto)

  • Ryutaro Kotaki

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Keisuke Tonouchi

    (National Institute of Infectious Diseases; Shinjuku-ku
    Waseda University; Shinjuku-ku)

  • Kohei Yumoto

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Tateki Suzuki

    (Kyoto University; Kyoto)

  • Taiyou Someya

    (Hokkaido University; Sapporo)

  • Hideo Fukuhara

    (Hokkaido University)

  • Yudai Kuroda

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Tsukasa Yamamoto

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Taishi Onodera

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Shuetsu Fukushi

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Ken Maeda

    (National Institute of Infectious Diseases; Shinjuku-ku)

  • Fukumi Nakamura-Uchiyama

    (Tokyo Metropolitan Bokutoh Hospital; Sumida-ku)

  • Takao Hashiguchi

    (Kyoto University; Kyoto)

  • Atsushi Hoshino

    (Kyoto Prefectural University of Medicine; Kyoto)

  • Katsumi Maenaka

    (Hokkaido University; Sapporo
    Hokkaido University
    Hokkaido University; Sapporo
    Hokkaido University; Sapporo)

  • Yoshimasa Takahashi

    (National Institute of Infectious Diseases; Shinjuku-ku)

Abstract

SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.

Suggested Citation

  • Saya Moriyama & Yuki Anraku & Shunta Taminishi & Yu Adachi & Daisuke Kuroda & Shunsuke Kita & Yusuke Higuchi & Yuhei Kirita & Ryutaro Kotaki & Keisuke Tonouchi & Kohei Yumoto & Tateki Suzuki & Taiyou , 2023. "Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39890-8
    DOI: 10.1038/s41467-023-39890-8
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