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Acknowledgements
The authors would like to thank all members belonging to The Genotype
to Phenotype Japan (G2P-Japan) Consortium. We thank Dr. Kenzo
Tokunaga (National Institute for Infectious Diseases, Japan) and Dr. Jin
Gohda (The University of Tokyo, Japan) for providing reagents. We also
thank the National Institute for Infectious Diseases, Japan, for providing
clinical isolates of BQ.1.1 (strain TY41-796-P1; GISAID ID:
EPI_ISL_15579783) and BA.2 (strain TY40-385; GISAID ID:
EPI_ISL_9595859). We appreciate the technical assistance to the BL32XU
beamline staff at SPring-8 and from The Research Support Center,
Research Center for Human Disease Modeling, Kyushu University
Graduate School of Medical Sciences. We gratefully acknowledge all
data contributors, i.e., the Authors and their Originating laboratories
responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via
the GISAID Initiative, on which this research is based. The supercomputing resource was provided by the Human Genome Center at The
University of Tokyo. This study was supported in part by AMED SCARDA
Japan Initiative for World-leading Vaccine Research and Development
Centers “UTOPIA” (JP223fa627001, to K.S.), AMED SCARDA Program on
R&D of new generation vaccine including new modality application
(JP223fa727002, to K.S.); AMED SCRADA Kyoto University Immunomonitoring Center (KIC) (JP223fa627009, to T.H.); AMED SCARDA Worldleading institutes for vaccine research and development Hokkaido
18
Article
Synergy Campus (223fa627005h0001, to K.M., and T.F.); AMED
Research Program on Emerging and Re-emerging Infectious Diseases
(JP21fk0108574, to H.N.; JP21fk0108465, to A.S.; JP22fk0108516, to T.F.;
JP21fk0108493, to Takasuke Fukuhara; JP22fk0108617 to T.F.;
JP22fk0108146, to K.S.; JP21fk0108494 to G2P-Japan Consortium, K.M.,
S.T., T.I., T.F., and K.S.; JP21fk0108425, to K.T., A.S., and K.S.;
22fk0108506, to K.T., A.S., and K.S.; JP21fk0108432, to K.T., T.F., and
K.S.); AMED Research Program on HIV/AIDS (JP22fk0410033, to A.S.;
JP22fk0410047, to A.S.; JP22fk0410055, to T.I.; and JP22fk0410039, to
K.S.); AMED CRDF Global Grant (JP22jk0210039 to A.S.); AMED Japan
Program for Infectious Diseases Research and Infrastructure
(JP22wm0325009, to A.S.; JP22wm0125008 to K.M.); AMED CREST
(JP21gm1610005, to K.T.; JP22gm1610008, to T.F.); JST PRESTO
(JPMJPR22R1, to J.I.); JST CREST (JPMJCR20H4, to K.S.; JPMJCR20H8, to
T.H.); JSPS KAKENHI Grant-in-Aid for Scientific Research C (22K07103, to
T.I.); JSPS KAKENHI Grant-in-Aid for Scientific Research B (21H02736, to
T.F.); JSPS KAKENHI Grant-in-Aid for Early-Career Scientists (22K16375,
to H.N.; 20K15767 and 23K14526, J.I.); JSPS KAKENHI grant 20H05773 (to
T.H.); JSPS Core-to-Core Program (A. Advanced Research Networks)
(JPJSCCA20190008, to K.S.); JSPS Research Fellow DC2 (22J11578, to
K.U.); JSPS Leading Initiative for Excellent Young Researchers (LEADER)
(to T.I.); World-leading Innovative and Smart Education (WISE) Program
1801 from the Ministry of Education, Culture, Sports, Science and
Technology (MEXT) (to N.N.); Research Support Project for Life Science
and Drug Discovery [Basis for Supporting Innovative Drug Discovery and
Life Science Research (BINDS)] from AMED under the Grant
JP22ama121001 (to T.H.); The Cooperative Research Program (Joint
Usage/Research Center program) of Institute for Life and Medical Sciences, Kyoto University (to K.S.); The Tokyo Biochemical Research
Foundation (to K.S.); Takeda Science Foundation (to T.I.); Mochida
Memorial Foundation for Medical and Pharmaceutical Research (to T.I.);
The Naito Foundation (to T.I.); Shin-Nihon Foundation of Advanced
Medical Research (to T.I.); Waksman Foundation of Japan (to T.I.); an
intramural grant from Kumamoto University COVID-19 Research Projects
(AMABIE) (to T.I.); the Ito Foundation Research Grant (to A.S.); International Joint Research Project of the Institute of Medical Science, the
University of Tokyo (to T.I., T.F., and A.S.); the UK’s Medical Research
Council (to S.L.); and the project of National Institute of Virology and
Bacteriology, Programme EXCELES, funded by the European Union,
Next Generation EU (LX22NPO5103, to J.Z.).
Author contributions
J.I. and S.L. performed phylogenetic analyses. J.I. performed statistical,
modeling, and bioinformatics analyses. K.U., S.D., H.N., M.S., M.S.T.M.B.,
S.F., A.S., K.T., and T.I. performed the cell culture experiments. R.S., Y.I.,
T.T., I.K., K.Y., H.I., N.N., K.M., and T.F. performed animal experiments.
L.W., M.T., Y.O., and S.T. performed histopathological analysis. J.Z. and
G.S. performed the yeast surface display assay. S.D. and K.T. prepared
AO-ALI and airway-on-a-chip systems. Y.Y. and T.N. performed the
generation and provision of human iPSC-derived airway and alveolar
epithelial cells. J.S., K.S.-T., and T.H. prepared BQ.1.1 S RBD and human
https://doi.org/10.1038/s41467-023-38188-z
ACE2. K.T.K., T.S., and T.H. determined the structure of the BQ.1.1 RBD
and human ACE2 complex. H.A., M.N., K.S., and K.Y. performed viral
genome sequencing analysis. J.K. contributed to clinical sample collection. J.I., A.S., K.M., K.T., S.T., T.F., T.I., and K.S. designed the experiments and interpreted the results. J.I. and K.S. wrote the original
manuscript. All authors reviewed and proofread the manuscript. The
Genotype to Phenotype Japan (G2P-Japan) Consortium contributed to
the project administration.
Competing interests
Y.Y. and T.N. are founders and shareholders of HiLung, Inc. Y.Y. is a
coinventor of patents (PCT/JP2016/057254; “Method for inducing differentiation of alveolar epithelial cells”, PCT/JP2016/059786, “Method of
producing airway epithelial cells”). The other authors declare that no
competing interests exist.
Additional information
Supplementary information The online version contains supplementary
material available at
https://doi.org/10.1038/s41467-023-38188-z.
Correspondence and requests for materials should be addressed to
Takao Hashiguchi, Shinya Tanaka, Takasuke Fukuhara, Terumasa Ikeda or
Kei Sato.
Peer review information Nature Communications thanks Jason Kindrachuk and the other, anonymous, reviewer(s) for their contribution to
the peer review of this work. A peer review file is available.
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© The Author(s) 2023
Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. 3Graduate School of Medicine, The University of
Tokyo, Tokyo, Japan. 4Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan. 5Department of
Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel. 6First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia.
Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan. 8Center for iPS Cell Research and Application (CiRA),
Kyoto University, Kyoto, Japan. 9Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. 10Institute for Chemical Reaction
Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan. 11Medical Research Council-University of Glasgow Centre for Virus Research,
Glasgow, UK. 12Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan. 13Division of
Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan. 14Department of Clinical
Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt. 15Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki,
Miyazaki, Japan. 16Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan. 17Department of Medicinal Sciences,
Nature Communications | (2023)14:2671
19
Article
https://doi.org/10.1038/s41467-023-38188-z
Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan. 18Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
19
Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan. 20Tokyo Metropolitan
Institute of Public Health, Tokyo, Japan. 21HiLung, Inc, Kyoto, Japan. 22Interpark Kuramochi Clinic, Utsunomiya, Japan. 23Department of Global Health
Promotion, Tokyo Medical and Dental University, Tokyo, Japan. 24Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan. 25One Health
Research Center, Hokkaido University, Sapporo, Japan. 26Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan.
27
International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan. 28AMED-CREST, Japan Agency for
Medical Research and Development (AMED), Tokyo, Japan. 29Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University,
Suita, Japan. 30International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. 31International
Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. 32Graduate School of Frontier Sciences, The University of
Tokyo, Kashiwa, Japan. 33Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
34
CREST, Japan Science and Technology Agency, Kawaguchi, Japan. 40These authors contributed equally: Jumpei Ito, Rigel Suzuki, Keiya Uriu, Yukari Itakura,
e-mail: hashiguchi.takao.1a@kyoto-u.ac.jp; tanaka@med.hokudai.ac.jp;
Jiri Zahradnik, Kanako Terakado Kimura, Sayaka Deguchi, Lei Wang, Spyros Lytras.
fukut@pop.med.hokudai.ac.jp; ikedat@kumamoto-u.ac.jp; KeiSato@g.ecc.u-tokyo.ac.jp
The Genotype to Phenotype Japan (G2P-Japan) Consortium
Saori Suzuki2, Marie Kato9, Zannatul Ferdous9, Hiromi Mouri9, Kenji Shishido9, Naoko Misawa1, Izumi Kimura1,
Yusuke Kosugi1, Pan Lin1, Mai Suganami1, Mika Chiba1, Ryo Yoshimura1, Kyoko Yasuda1, Keiko Iida1, Naomi Ohsumi1,
Adam P. Strange1, Daniel Sauter1,35, So Nakagawa36, Jiaqi Wu36, Yukio Watanabe8, Ayaka Sakamoto8, Naoko Yasuhara8,
Yukari Nakajima37, Hisano Yajima37, Kotaro Shirakawa37, Akifumi Takaori-Kondo37, Kayoko Nagata37, Yasuhiro Kazuma37,
Ryosuke Nomura37, Yoshihito Horisawa37, Yusuke Tashiro37, Yugo Kawa37, Takashi Irie38, Ryoko Kawabata38, Ryo Shimizu13,
Otowa Takahashi13, Kimiko Ichihara13, Chihiro Motozono39, Mako Toyoda39, Takamasa Ueno39, Yuki Shibatani15 &
Tomoko Nishiuchi15
35
University Hospital Tübingen, Tübingen, Germany. 36Tokai University School of Medicine, Isehara, Japan. 37Kyoto University, Kyoto, Japan. 38Hiroshima
University, Hiroshima, Japan. 39Kumamoto University, Kumamoto, Japan.
Nature Communications | (2023)14:2671
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