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.

A panel of nanobodies are presented that can detect the spike proteins of five SARS-CoV-2 variants of concern and structural analyses show that one clone targets conserved epitopes on the receptor-binding domain and contacts the N-terminal domain.

Details

Title
A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron
Author
Maeda, Ryota 1   VIAFID ORCID Logo  ; Fujita, Junso 2   VIAFID ORCID Logo  ; Konishi, Yoshinobu 3   VIAFID ORCID Logo  ; Kazuma, Yasuhiro 3   VIAFID ORCID Logo  ; Yamazaki, Hiroyuki 4 ; Anzai, Itsuki 5 ; Watanabe, Tokiko 5 ; Yamaguchi, Keishi 6 ; Kasai, Kazuki 7   VIAFID ORCID Logo  ; Nagata, Kayoko 3 ; Yamaoka, Yutaro 8 ; Miyakawa, Kei 8 ; Ryo, Akihide 8 ; Shirakawa, Kotaro 3   VIAFID ORCID Logo  ; Sato, Kei 9   VIAFID ORCID Logo  ; Makino, Fumiaki 10   VIAFID ORCID Logo  ; Matsuura, Yoshiharu 11   VIAFID ORCID Logo  ; Inoue, Tsuyoshi 6 ; Imura, Akihiro 7   VIAFID ORCID Logo  ; Namba, Keiichi 12   VIAFID ORCID Logo  ; Takaori-Kondo, Akifumi 3   VIAFID ORCID Logo 

1  Kyoto University, Department of Haematology and Oncology, Graduate School of Medicine, Kyoto, Japan (GRID:grid.258799.8) (ISNI:0000 0004 0372 2033); COGNANO Inc., Kyoto, Japan (GRID:grid.258799.8) 
2  Osaka University, Graduate School of Frontier Biosciences, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971); Osaka University, Graduate School of Pharmaceutical Sciences, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971) 
3  Kyoto University, Department of Haematology and Oncology, Graduate School of Medicine, Kyoto, Japan (GRID:grid.258799.8) (ISNI:0000 0004 0372 2033) 
4  COGNANO Inc., Kyoto, Japan (GRID:grid.258799.8); Shizuoka City Shizuoka Hospital, Shizuoka, Japan (GRID:grid.258799.8) 
5  Osaka University, Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971) 
6  Osaka University, Graduate School of Pharmaceutical Sciences, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971) 
7  COGNANO Inc., Kyoto, Japan (GRID:grid.136593.b) 
8  Yokohama City University Graduate School of Medicine, Department of Microbiology and Molecular Biodefense Research, Yokohama, Japan (GRID:grid.268441.d) (ISNI:0000 0001 1033 6139) 
9  The University of Tokyo, Division of System Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X); The University of Tokyo, Graduate School of Medicine, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X); CREST, Japan Science and Technology Agency, Saitama, Japan (GRID:grid.419082.6) (ISNI:0000 0004 1754 9200) 
10  Osaka University, Graduate School of Frontier Biosciences, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971); JEOL Ltd., Tokyo, Japan (GRID:grid.410892.6) (ISNI:0000 0001 2284 8430) 
11  Osaka University, Centre for Infectious Disease Education and Research, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971); Osaka University, Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971) 
12  Osaka University, Graduate School of Frontier Biosciences, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971); Osaka University, JEOL YOKOGUSHI Research Alliance Laboratories, Osaka, Japan (GRID:grid.136593.b) (ISNI:0000 0004 0373 3971); RIKEN Centre for Biosystems Dynamics Research and SPring-8 Centre, Osaka, Japan (GRID:grid.136593.b) 
Publication year
2022
Publication date
2022
Publisher
Nature Publishing Group
e-ISSN
23993642
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s42003-022-03630-3
ProQuest document ID
2685241988
Copyright
© The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.