Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236

Shigeru Fujita; Arnon Plianchaisuk; Sayaka Deguchi; Hayato Ito; Naganori Nao; Lei Wang; Hesham Nasser; Tomokazu Tamura; Izumi Kimura; Yukie Kashima; Rigel Suzuki; Saori Suzuki; Izumi Kida; Masumi Tsuda; Yoshitaka Oda; Rina Hashimoto; Yukio Watanabe; Keiya Uriu; Daichi Yamasoba; Ziyi Guo; Alfredo A Hinay Jr; Yusuke Kosugi; Luo Chen; Lin Pan; Yu Kaku; Hin Chu; Flora Donati; Sarah Temmam; Marc Eloit; Yuki Yamamoto; Tetsuharu Nagamoto; Hiroyuki Asakura; Mami Nagashima; Kenji Sadamasu; Kazuhisa Yoshimura; Yutaka Suzuki; Genotype to Phenotype Japan (G2P-Japan) Consortium; Jumpei Ito; Terumasa Ikeda; Shinya Tanaka; Keita Matsuno; Takasuke Fukuhara; Kazuo Takayama; Kei Sato

doi:10.1016/j.ebiom.2024.105181

Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236

EBioMedicine. 2024 Jun:104:105181. doi: 10.1016/j.ebiom.2024.105181. Epub 2024 Jun 4.

Authors

Shigeru Fujita¹, Arnon Plianchaisuk², Sayaka Deguchi³, Hayato Ito⁴, Naganori Nao⁵, Lei Wang⁶, Hesham Nasser⁷, Tomokazu Tamura⁸, Izumi Kimura², Yukie Kashima⁹, Rigel Suzuki¹⁰, Saori Suzuki¹⁰, Izumi Kida¹¹, Masumi Tsuda⁶, Yoshitaka Oda¹², Rina Hashimoto³, Yukio Watanabe³, Keiya Uriu¹, Daichi Yamasoba¹³, Ziyi Guo², Alfredo A Hinay Jr², Yusuke Kosugi¹, Luo Chen¹⁴, Lin Pan¹⁴, Yu Kaku², Hin Chu¹⁵, Flora Donati¹⁶, Sarah Temmam¹⁷, Marc Eloit¹⁷, Yuki Yamamoto¹⁸, Tetsuharu Nagamoto¹⁸, Hiroyuki Asakura¹⁹, Mami Nagashima¹⁹, Kenji Sadamasu¹⁹, Kazuhisa Yoshimura¹⁹, Yutaka Suzuki⁹; Genotype to Phenotype Japan (G2P-Japan) Consortium; Jumpei Ito²⁰, Terumasa Ikeda²¹, Shinya Tanaka²², Keita Matsuno²³, Takasuke Fukuhara²⁴, Kazuo Takayama²⁵, Kei Sato²⁶

Collaborators

Genotype to Phenotype Japan (G2P-Japan) Consortium:
Hirofumi Sawa, Keita Mizuma, Jingshu Li, Yume Mimura, Yuma Ohari, Tomoya Tsubo, Zannatul Ferdous, Kenji Shishido, Hiromi Mohri, Miki Iida, Shuhei Tsujino, Naoko Misawa, Kaoru Usui, Wilaiporn Saikruang, Spyridon Lytras, Shusuke Kawakubo, Luca Nishumura, Jarel Elgin Mendoza Tolentino, Wenye Li, Maximilian Stanley Yo, Kio Horinaka, Mai Suganami, Mika Chiba, Ryo Yoshimura, Kyoko Yasuda, Keiko Iida, Adam Patrick Strange, Naomi Ohsumi, Shiho Tanaka, Eiko Ogawa, Kaho Okumura, Tsuki Fukuda, Rina Osujo, Isao Yoshida, So Nakagawa, Akifumi Takaori-Kondo, Kotaro Shirakawa, Kayoko Nagata, Ryosuke Nomura, Yoshihito Horisawa, Yusuke Tashiro, Yugo Kawai, Yoshitaka Nakata, Hiroki Futatsusako, Ayaka Sakamoto, Naoko Yasuhara, Takao Hashiguchi, Tateki Suzuki, Kanako Kimura, Jiei Sasaki, Yukari Nakajima, Hisano Yajima, Takashi Irie, Ryoko Kawabata, Kaori Sasaki-Tabata, Ryo Shimizu, M S T Monira Begum, Michael Jonathan, Yuka Mugita, Sharee Leong, Otowa Takahashi, Kimiko Ichihara, Takamasa Ueno, Chihiro Motozono, Mako Toyoda, Akatsuki Saito, Anon Kosaka, Miki Kawano, Natsumi Matsubara, Tomoko Nishiuchi, Jiri Zahradnik, Prokopios Andrikopoulos, Miguel Padilla-Blanco, Aditi Konar

Affiliations

¹ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
² Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
³ Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
⁴ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
⁵ One Health Research Center, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
⁶ Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
⁷ Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
⁸ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan.
⁹ Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
¹⁰ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan.
¹¹ Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
¹² Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
¹³ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Faculty of Medicine, Kobe University, Kobe, Japan.
¹⁴ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
¹⁵ State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
¹⁶ Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, Paris, France; Institut Pasteur, Université Paris Cité, National Reference Center for Respiratory Viruses, Paris, France.
¹⁷ Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Institut Pasteur, Université Paris Cité, The WOAH(OIE) Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France.
¹⁸ HiLung Inc., Kyoto, Japan.
¹⁹ Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
²⁰ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
²¹ Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
²² Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan. Electronic address: [email protected].
²³ One Health Research Center, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan. Electronic address: [email protected].
²⁴ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan. Electronic address: [email protected].
²⁵ Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan. Electronic address: [email protected].
²⁶ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; CREST, Japan Science and Technology Agency, Saitama, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. Electronic address: [email protected].

Abstract

Background: Although several SARS-CoV-2-related coronaviruses (SC2r-CoVs) were discovered in bats and pangolins, the differences in virological characteristics between SARS-CoV-2 and SC2r-CoVs remain poorly understood. Recently, BANAL-20-236 (B236) was isolated from a rectal swab of Malayan horseshoe bat and was found to lack a furin cleavage site (FCS) in the spike (S) protein. The comparison of its virological characteristics with FCS-deleted SARS-CoV-2 (SC2ΔFCS) has not been conducted yet.

Methods: We prepared human induced pluripotent stem cell (iPSC)-derived airway and lung epithelial cells and colon organoids as human organ-relevant models. B236, SARS-CoV-2, and artificially generated SC2ΔFCS were used for viral experiments. To investigate the pathogenicity of B236 in vivo, we conducted intranasal infection experiments in hamsters.

Findings: In human iPSC-derived airway epithelial cells, the growth of B236 was significantly lower than that of the SC2ΔFCS. A fusion assay showed that the B236 and SC2ΔFCS S proteins were less fusogenic than the SARS-CoV-2 S protein. The infection experiment in hamsters showed that B236 was less pathogenic than SARS-CoV-2 and even SC2ΔFCS. Interestingly, in human colon organoids, the growth of B236 was significantly greater than that of SARS-CoV-2.

Interpretation: Compared to SARS-CoV-2, we demonstrated that B236 exhibited a tropism toward intestinal cells rather than respiratory cells. Our results are consistent with a previous report showing that B236 is enterotropic in macaques. Altogether, our report strengthens the assumption that SC2r-CoVs in horseshoe bats replicate primarily in the intestinal tissues rather than respiratory tissues.

Funding: This study was supported in part by AMED ASPIRE (JP23jf0126002, to Keita Matsuno, Kazuo Takayama, and Kei Sato); AMED SCARDA Japan Initiative for World-leading Vaccine Research and Development Centers "UTOPIA" (JP223fa627001, to Kei Sato), AMED SCARDA Program on R&D of new generation vaccine including new modality application (JP223fa727002, to Kei Sato); AMED SCARDA Hokkaido University Institute for Vaccine Research and Development (HU-IVReD) (JP223fa627005h0001, to Takasuke Fukuhara, and Keita Matsuno); AMED Research Program on Emerging and Re-emerging Infectious Diseases (JP21fk0108574, to Hesham Nasser; JP21fk0108493, to Takasuke Fukuhara; JP22fk0108617 to Takasuke Fukuhara; JP22fk0108146, to Kei Sato; JP21fk0108494 to G2P-Japan Consortium, Keita Matsuno, Shinya Tanaka, Terumasa Ikeda, Takasuke Fukuhara, and Kei Sato; JP21fk0108425, to Kazuo Takayama and Kei Sato; JP21fk0108432, to Kazuo Takayama, Takasuke Fukuhara and Kei Sato; JP22fk0108534, Terumasa Ikeda, and Kei Sato; JP22fk0108511, to Yuki Yamamoto, Terumasa Ikeda, Keita Matsuno, Shinya Tanaka, Kazuo Takayama, Takasuke Fukuhara, and Kei Sato; JP22fk0108506, to Kazuo Takayama and Kei Sato); AMED Research Program on HIV/AIDS (JP22fk0410055, to Terumasa Ikeda; and JP22fk0410039, to Kei Sato); AMED Japan Program for Infectious Diseases Research and Infrastructure (JP22wm0125008 to Keita Matsuno); AMED CREST (JP21gm1610005, to Kazuo Takayama; JP22gm1610008, to Takasuke Fukuhara; JST PRESTO (JPMJPR22R1, to Jumpei Ito); JST CREST (JPMJCR20H4, to Kei Sato); JSPS KAKENHI Fund for the Promotion of Joint International Research (International Leading Research) (JP23K20041, to G2P-Japan Consortium, Keita Matsuno, Takasuke Fukuhara and Kei Sato); JST SPRING (JPMJSP2108 to Shigeru Fujita); JSPS KAKENHI Grant-in-Aid for Scientific Research C (22K07103, to Terumasa Ikeda); JSPS KAKENHI Grant-in-Aid for Scientific Research B (21H02736, to Takasuke Fukuhara); JSPS KAKENHI Grant-in-Aid for Early-Career Scientists (22K16375, to Hesham Nasser; 20K15767, to Jumpei Ito); JSPS Core-to-Core Program (A. Advanced Research Networks) (JPJSCCA20190008, to Kei Sato); JSPS Research Fellow DC2 (22J11578, to Keiya Uriu); JSPS Research Fellow DC1 (23KJ0710, to Yusuke Kosugi); JSPS Leading Initiative for Excellent Young Researchers (LEADER) (to Terumasa Ikeda); World-leading Innovative and Smart Education (WISE) Program 1801 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (to Naganori Nao); Ministry of Health, Labour and Welfare (MHLW) under grant 23HA2010 (to Naganori Nao and Keita Matsuno); The Cooperative Research Program (Joint Usage/Research Center program) of Institute for Life and Medical Sciences, Kyoto University (to Kei Sato); International Joint Research Project of the Institute of Medical Science, the University of Tokyo (to Terumasa Ikeda and Takasuke Fukuhara); The Tokyo Biochemical Research Foundation (to Kei Sato); Takeda Science Foundation (to Terumasa Ikeda and Takasuke Fukuhara); Mochida Memorial Foundation for Medical and Pharmaceutical Research (to Terumasa Ikeda); The Naito Foundation (to Terumasa Ikeda); Hokuto Foundation for Bioscience (to Tomokazu Tamura); Hirose Foundation (to Tomokazu Tamura); and Mitsubishi Foundation (to Kei Sato).

Keywords: BANAL-20-236; Bat coronavirus; SARS-CoV-2; Spillover.

MeSH terms

Animals
COVID-19* / virology
Chiroptera* / virology
Chlorocebus aethiops
Cricetinae
Epithelial Cells / virology
Furin / metabolism
Humans
Induced Pluripotent Stem Cells / cytology
Induced Pluripotent Stem Cells / metabolism
Induced Pluripotent Stem Cells / virology
Organoids / metabolism
Organoids / virology
SARS-CoV-2* / genetics
SARS-CoV-2* / physiology
Spike Glycoprotein, Coronavirus / genetics
Spike Glycoprotein, Coronavirus / metabolism
Vero Cells

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2
Furin