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Begum MSTM, Bokani A, Rajib SA, Soleimanpour M, Maeda Y, Yoshimura K, Satou Y, Ebrahimi D, Ikeda T. Potential Role of APOBEC3 Family Proteins in SARS-CoV-2 Replication. Viruses 2024; 16:1141. [PMID: 39066304 PMCID: PMC11281575 DOI: 10.3390/v16071141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has acquired multiple mutations since its emergence. Analyses of the SARS-CoV-2 genomes from infected patients exhibit a bias toward C-to-U mutations, which are suggested to be caused by the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) cytosine deaminase proteins. However, the role of A3 enzymes in SARS-CoV-2 replication remains unclear. To address this question, we investigated the effect of A3 family proteins on SARS-CoV-2 replication in the myeloid leukemia cell line THP-1 lacking A3A to A3G genes. The Wuhan, BA.1, and BA.5 variants had comparable viral replication in parent and A3A-to-A3G-null THP-1 cells stably expressing angiotensin-converting enzyme 2 (ACE2) protein. On the other hand, the replication and infectivity of these variants were abolished in A3A-to-A3G-null THP-1-ACE2 cells in a series of passage experiments over 20 days. In contrast to previous reports, we observed no evidence of A3-induced SARS-CoV-2 mutagenesis in the passage experiments. Furthermore, our analysis of a large number of publicly available SARS-CoV-2 genomes did not reveal conclusive evidence for A3-induced mutagenesis. Our studies suggest that A3 family proteins can positively contribute to SARS-CoV-2 replication; however, this effect is deaminase-independent.
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Affiliation(s)
- MST Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ayub Bokani
- School of Engineering and Technology, CQ University, Sydney, NSW 2000, Australia
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | | | - Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Nursing, Kibi International University, Takahashi 716-8508, Japan
| | | | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
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2
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Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H, Sasaki-Tabata K, Guo Z, Hinay AA, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant. Microbiol Immunol 2024. [PMID: 38961765 DOI: 10.1111/1348-0421.13165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.
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Affiliation(s)
- Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomo Nomai
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Miguel Padilla-Blanco
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Keiya Uriu
- 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
| | - Keita Mizuma
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Isshu Kojima
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tomoya Tsubo
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jingshu Li
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ziyi Guo
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Alfredo A Hinay
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | | | | | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Hesham Nasser
- 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
| | - Michael Jonathan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Olivia Putri
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Yoonjin Kim
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Life Sciences, Faculty of Natural Science, Imperial College London, London, UK
| | - Luo Chen
- 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, Kashiwa, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Tomokazu Tamura
- 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
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- 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
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Jiri Zahradnik
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Takasuke Fukuhara
- 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
| | - Kei Sato
- 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, Kashiwa, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, 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
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3
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Shen J, Xu X, Fan J, Chen H, Zhao Y, Huang W, Liu W, Zhang Z, Cui Q, Li Q, Niu Z, Jiang D, Cao G. APOBEC3-related mutations in the spike protein-encoding region facilitate SARS-CoV-2 evolution. Heliyon 2024; 10:e32139. [PMID: 38868014 PMCID: PMC11168432 DOI: 10.1016/j.heliyon.2024.e32139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
SARS-CoV-2 evolves gradually to cause COVID-19 epidemic. One of driving forces of SARS-CoV-2 evolution might be activation of apolipoprotein B mRNA editing catalytic subunit-like protein 3 (APOBEC3) by inflammatory factors. Here, we aimed to elucidate the effect of the APOBEC3-related viral mutations on the infectivity and immune evasion of SARS-CoV-2. The APOBEC3-related C > U mutations ranked as the second most common mutation types in the SARS-CoV-2 genome. mRNA expression of APOBEC3A (A3A), APOBEC3B (A3B), and APOBEC3G (A3G) in peripheral blood cells increased with disease severity. A3B, a critical member of the APOBEC3 family, was significantly upregulated in both severe and moderate COVID-19 patients and positively associated with neutrophil proportion and COVID-19 severity. We identified USP18 protein, a key molecule centralizing the protein-protein interaction network of key APOBEC3 proteins. Furthermore, mRNA expression of USP18 was significantly correlated to ACE2 and TMPRSS2 expression in the tissue of upper airways. Knockdown of USP18 mRNA significantly decreased A3B expression. Ectopic expression of A3B gene increased SARS-CoV-2 infectivity. C > U mutations at S371F, S373L, and S375F significantly conferred with the immune escape of SARS-CoV-2. Thus, APOBEC3, whose expression are upregulated by inflammatory factors, might promote SARS-CoV-2 evolution and spread via upregulating USP18 level and facilitating the immune escape. A3B and USP18 might be therapeutic targets for interfering with SARS-CoV-2 evolution.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Xinxin Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongsen Chen
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Weijin Huang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Qianqian Cui
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Qianqian Li
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Dongming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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4
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Fujita S, Plianchaisuk A, Deguchi S, Ito H, Nao N, Wang L, Nasser H, Tamura T, Kimura I, Kashima Y, Suzuki R, Suzuki S, Kida I, Tsuda M, Oda Y, Hashimoto R, Watanabe Y, Uriu K, Yamasoba D, Guo Z, Hinay AA, Kosugi Y, Chen L, Pan L, Kaku Y, Chu H, Donati F, Temmam S, Eloit M, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Suzuki Y, Ito J, Ikeda T, Tanaka S, Matsuno K, Fukuhara T, Takayama K, Sato K. Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236. EBioMedicine 2024; 104:105181. [PMID: 38838469 PMCID: PMC11215962 DOI: 10.1016/j.ebiom.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/18/2024] [Accepted: 05/18/2024] [Indexed: 06/07/2024] Open
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).
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Affiliation(s)
- Shigeru Fujita
- 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
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- 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
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- 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
| | - Tomokazu Tamura
- 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
| | - Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukie Kashima
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Rina Hashimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yukio Watanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Keiya Uriu
- 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
| | - Daichi Yamasoba
- 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
| | - Ziyi Guo
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Alfredo A Hinay
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kosugi
- 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
| | - Luo Chen
- 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
| | - Lin Pan
- 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
| | - Yu Kaku
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hin Chu
- 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
| | - Flora Donati
- 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
| | - Sarah Temmam
- 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
| | - Marc Eloit
- 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
| | | | | | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Jumpei Ito
- 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
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- 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.
| | - Takasuke Fukuhara
- 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.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
| | - Kei Sato
- 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.
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5
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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6
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Tamura T, Mizuma K, Nasser H, Deguchi S, Padilla-Blanco M, Oda Y, Uriu K, Tolentino JEM, Tsujino S, Suzuki R, Kojima I, Nao N, Shimizu R, Wang L, Tsuda M, Jonathan M, Kosugi Y, Guo Z, Hinay AA, Putri O, Kim Y, Tanaka YL, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Saito A, Ito J, Irie T, Tanaka S, Zahradnik J, Ikeda T, Takayama K, Matsuno K, Fukuhara T, Sato K. Virological characteristics of the SARS-CoV-2 BA.2.86 variant. Cell Host Microbe 2024; 32:170-180.e12. [PMID: 38280382 DOI: 10.1016/j.chom.2024.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/05/2023] [Accepted: 01/04/2024] [Indexed: 01/29/2024]
Abstract
In late 2023, several SARS-CoV-2 XBB descendants, notably EG.5.1, were predominant worldwide. However, a distinct SARS-CoV-2 lineage, the BA.2.86 variant, also emerged. BA.2.86 is phylogenetically distinct from other Omicron sublineages, accumulating over 30 amino acid mutations in its spike protein. Here, we examined the virological characteristics of the BA.2.86 variant. Our epidemic dynamics modeling suggested that the relative reproduction number of BA.2.86 is significantly higher than that of EG.5.1. Additionally, four clinically available antivirals were effective against BA.2.86. Although the fusogenicity of BA.2.86 spike is similar to that of the parental BA.2 spike, the intrinsic pathogenicity of BA.2.86 in hamsters was significantly lower than that of BA.2. Since the growth kinetics of BA.2.86 are significantly lower than those of BA.2 both in vitro and in vivo, the attenuated pathogenicity of BA.2.86 is likely due to its decreased replication capacity. These findings uncover the features of BA.2.86, providing insights for control and treatment.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Graduate School of Medicine, Hokkaido University, Sapporo, Japan; School of Medicine, Hokkaido University, Sapporo, Japan; Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan
| | - Keita Mizuma
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan; Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Miguel Padilla-Blanco
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia; Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Keiya Uriu
- 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
| | - Jarel E M Tolentino
- 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, Kashiwa, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Isshu Kojima
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Michael Jonathan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Yusuke Kosugi
- 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
| | - Ziyi Guo
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Alfredo A Hinay
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Olivia Putri
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Yoonjin Kim
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Faculty of Natural Science, Imperial College London, London, UK
| | - Yuri L Tanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Jiri Zahradnik
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.
| | - Keita Matsuno
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; One Health Research Center, 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.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan; Graduate School of Medicine, Hokkaido University, Sapporo, Japan; School of Medicine, Hokkaido University, Sapporo, Japan; Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
| | - Kei Sato
- 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, Kashiwa, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan; International Research Center for Infectious Diseases, 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.
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7
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Müller M, Herrmann A, Fujita S, Uriu K, Kruth C, Strange A, Kolberg JE, Schneider M, Ito J, Müller MA, Drosten C, Ensser A, Sato K, Sauter D. ORF3c is expressed in SARS-CoV-2-infected cells and inhibits innate sensing by targeting MAVS. EMBO Rep 2023; 24:e57137. [PMID: 37870297 DOI: 10.15252/embr.202357137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Most SARS-CoV-2 proteins are translated from subgenomic RNAs (sgRNAs). While the majority of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. One example is the ORF3a sgRNA that also encodes ORF3c, an enigmatic 41-amino-acid peptide. Here, we show that ORF3c is expressed in SARS-CoV-2-infected cells and suppresses RIG-I- and MDA5-mediated IFN-β induction. ORF3c interacts with the signaling adaptor MAVS, induces its C-terminal cleavage, and inhibits the interaction of RIG-I with MAVS. The immunosuppressive activity of ORF3c is conserved among members of the subgenus sarbecovirus, including SARS-CoV and coronaviruses isolated from bats. Notably, however, the SARS-CoV-2 delta and kappa variants harbor premature stop codons in ORF3c, demonstrating that this reading frame is not essential for efficient viral replication in vivo and is likely compensated by other viral proteins. In agreement with this, disruption of ORF3c does not significantly affect SARS-CoV-2 replication in CaCo-2, CaLu-3, or Rhinolophus alcyone cells. In summary, we here identify ORF3c as an immune evasion factor of SARS-CoV-2 that suppresses innate sensing in infected cells.
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Affiliation(s)
- Martin Müller
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Alexandra Herrmann
- Institute for Clinical and Molecular Virology, University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Shigeru Fujita
- 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
| | - Keiya Uriu
- 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
| | - Carolin Kruth
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Adam Strange
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jan E Kolberg
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Markus Schneider
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Marcel A Müller
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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8
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Kumar S, Delipan R, Chakraborty D, Kanjo K, Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. J Virol 2023; 97:e0092223. [PMID: 37861334 PMCID: PMC10688319 DOI: 10.1128/jvi.00922-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE The Omicron subvariants have substantially evaded host-neutralizing antibodies and adopted an endosomal route of entry. The virus has acquired several mutations in the receptor binding domain and N-terminal domain of S1 subunit, but remarkably, also incorporated mutations in S2 which are fixed in Omicron sub-lineage. Here, we found that the mutations in the S2 subunit affect the structural and biological properties such as neutralization escape, entry route, fusogenicity, and protease requirement. In vivo, these mutations may have significant roles in tropism and replication. A detailed understanding of the effects of S2 mutations on Spike function, immune evasion, and viral entry would inform the vaccine design, as well as therapeutic interventions aiming to block the essential proteases for virus entry. Thus, our study has identified the crucial role of S2 mutations in stabilizing the Omicron spike and modulating neutralization resistance to antibodies targeting the S1 subunit.
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Affiliation(s)
- Sahil Kumar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rathina Delipan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | | | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | - Nittu Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Samreen Siddiqui
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Vinitaa Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Krishan G. Thakur
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Rajesh P. Ringe
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
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9
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Fujita S, Kosugi Y, Kimura I, Tokunaga K, Ito J, Sato K. Determination of the factors responsible for the tropism of SARS-CoV-2-related bat coronaviruses to Rhinolophus bat ACE2. J Virol 2023; 97:e0099023. [PMID: 37724881 PMCID: PMC10779674 DOI: 10.1128/jvi.00990-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE The efficiency of infection receptor use is the first step in determining the species tropism of viruses. After the coronavirus disease 2019 pandemic, a number of SARS-CoV-2-related coronaviruses (SC2r-CoVs) were identified in Rhinolophus bats, and some of them can use human angiotensin converting enzyme 2 (ACE2) for the infection receptor without acquiring additional mutations. This means that the potential of certain SC2r-CoVs to cause spillover from bats to humans is "off-the-shelf." However, both SC2r-CoVs and Rhinolophus bat species are highly diversified, and the host tropism of SC2r-CoVs remains unclear. Here, we focus on two Laotian SC2r-CoVs, BANAL-20-236 and BANAL-20-52, and determine how the tropism of SC2r-CoVs to Rhinolophus bat ACE2 is determined at the amino acid resolution level.
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Affiliation(s)
- Shigeru Fujita
- 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
| | - Yusuke Kosugi
- 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
| | - Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
MatsunoKeita1NaoNaganori1SawaHirofumi1TanakaShinya1TsudaMasumi1WangLei1OdaYoshikata1FerdousZannatul1ShishidoKenji1FukuharaTakasuke1TamuraTomokazu1SuzukiRigel1SuzukiSaori1ItoHayato1KakuYuMisawaNaokoPlianchaisukArnonGuoZiyiHinayAlfredo A.UriuKeiyaTolentinoJarel Elgin M.ChenLuoPanLinSuganamiMaiChibaMikaYoshimuraRyoYasudaKyokoIidaKeikoOhsumiNaomiStrangeAdam P.TanakaShihoYoshimuraKazuhisa2SadamasuKenji2NagashimaMami2AsakuraHiroyuki2YoshidaIsao2NakagawaSo3Takaori-KondoAkifumi4NagataKayoko4NomuraRyosuke4HorisawaYoshihito4TashiroYusuke4KawaiYugo4TakayamaKazuo4HashimotoRina4DeguchiSayaka4WatanabeYukio4SakamotoAyaka4YasuharaNaokoHashiguchiTakao4SuzukiTateki4KimuraKanako4SasakiJiei4NakajimaYukari4YajimaHisano4IrieTakashi5KawabataRyoko5TabataKaori6IkedaTerumasa7NasserHesham7ShimizuRyo7Monira BegumM. S. T.7JonathanMichael7MugitaYuka7TakahashiOtowa7IchiharaKimiko7MotozonoChihiro7UenoTakamasa7ToyodaMako7SaitoAkatsuki8ShofaMaya8ShibataniYuki8NishiuchiTomoko8ShirakawaKotaro4Hokkaido University, Sapporo, JapanTokyo Metropolitan Institute of Public Health, Shinjuku City, JapanTokai University, Shibuya City, JapanKyoto University, Kyoto, JapanHiroshima University, Hiroshima, JapanKyushu University, Fukuoka, JapanKumamoto University, Kumamoto, JapanUniversity of Miyazaki, Miyazaki, Japan
- 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
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Jumpei Ito
- 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
| | - Kei Sato
- 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
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
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10
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Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, Sato K. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. J Virol 2023; 97:e0101123. [PMID: 37796123 PMCID: PMC10781145 DOI: 10.1128/jvi.01011-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- 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
| | - Hesham Nasser
- 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
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shigeru Fujita
- 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
| | - Keiya Uriu
- 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
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
MisawaNaoko1KosugiYusuke1PanLin1SuganamiMai1ChibaMika1YoshimuraRyo1YasudaKyoko1IidaKeiko1OhsumiNaomi1StrangeAdam P.1KakuYu1PlianchaisukArnon1GuoZiyi1HinayAlfredo Jr. Amolong1Mendoza TolentinoJarel Elgin1ChenLuo1ShimizuRyo2Monira BegumM. S. T.2TakahashiOtowa2IchiharaKimiko2JonathanMichael2MugitaYuka2SuzukiSaori3SuzukiTateki4KimuraKanako4NakajimaYukari4YajimaHisano4HashimotoRina4WatanabeYukio4SakamotoAyaka4YasuharaNaoko4NagataKayoko4NomuraRyosuke4HorisawaYoshihito4TashiroYusuke4KawaiYugo4ShibataniYuki5NishiuchiTomoko5YoshidaIsao6KawabataRyoko7MatsunoKeita8NaoNaganori9SawaHirofumi9TanakaShinya10TsudaMasumi10WangLei10OdaYoshikata10FerdousZannatul10ShishidoKenji10MotozonoChihiro11ToyodaMako11UenoTakamasa11TabataKaori12Institute of Medical Science, University of Tokyo, Tokyo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, JapanHokkaido University, Sapporo, JapanKyoto University, Kyoto, JapanUniversity of Miyazaki, Miyazaki, JapanTokyo Metropolitan Institute of Public Health, Tokyo, JapanHiroshima University, Hiroshima, JapanOne Health Research Center, Hokkaido University, Sapporo, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo, JapanHokkaido University, Sapporo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto, JapanKyushu University, Fukuoka, Japan
- 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
- 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
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- 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
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-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
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Kei Sato
- 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
- 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
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
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11
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Qing E, Gallagher T. Adaptive variations in SARS-CoV-2 spike proteins: effects on distinct virus-cell entry stages. mBio 2023; 14:e0017123. [PMID: 37382441 PMCID: PMC10470846 DOI: 10.1128/mbio.00171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/14/2023] [Indexed: 06/30/2023] Open
Abstract
Evolved SARS-CoV-2 variants of concern (VOCs) spread through human populations in succession. Major virus variations are in the entry-facilitating viral spike (S) proteins; Omicron VOCs have 29-40 S mutations relative to ancestral D614G viruses. The impacts of this Omicron divergence on S protein structure, antigenicity, cell entry pathways, and pathogenicity have been extensively evaluated, yet gaps remain in correlating specific alterations with S protein functions. In this study, we compared the functions of ancestral D614G and Omicron VOCs using cell-free assays that can reveal differences in several distinct steps of the S-directed virus entry process. Relative to ancestral D614G, Omicron BA.1 S proteins were hypersensitized to receptor activation, to conversion into intermediate conformational states, and to membrane fusion-activating proteases. We identified mutations conferring these changes in S protein character by evaluating domain-exchanged D614G/Omicron recombinants in the cell-free assays. Each of the three functional alterations was mapped to specific S protein domains, with the recombinants providing insights on inter-domain interactions that fine-tune S-directed virus entry. Our results provide a structure-function atlas of the S protein variations that may promote the transmissibility and infectivity of current and future SARS-CoV-2 VOCs. IMPORTANCE Continuous SARS-CoV-2 adaptations generate increasingly transmissible variants. These succeeding variants show ever-increasing evasion of suppressive antibodies and host factors, as well as increasing invasion of susceptible host cells. Here, we evaluated the adaptations enhancing invasion. We used reductionist cell-free assays to compare the entry steps of ancestral (D614G) and Omicron (BA.1) variants. Relative to D614G, Omicron entry was distinguished by heightened responsiveness to entry-facilitating receptors and proteases and by enhanced formation of intermediate states that execute virus-cell membrane fusion. We found that these Omicron-specific characteristics arose from mutations in specific S protein domains and subdomains. The results reveal the inter-domain networks controlling S protein dynamics and efficiencies of entry steps, and they offer insights on the evolution of SARS-CoV-2 variants that arise and ultimately dominate infections worldwide.
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Affiliation(s)
- Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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12
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Park SB, Khan M, Chiliveri SC, Hu X, Irvin P, Leek M, Grieshaber A, Hu Z, Jang ES, Bax A, Liang TJ. SARS-CoV-2 omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype. Commun Biol 2023; 6:556. [PMID: 37225764 DOI: 10.1038/s42003-023-04923-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/08/2023] [Indexed: 05/26/2023] Open
Abstract
Since the emergence of the Omicron variants at the end of 2021, they quickly became the dominant variants globally. The Omicron variants may be more easily transmitted compared to the earlier Wuhan and the other variants. In this study, we aimed to elucidate mechanisms of the altered infectivity associated with the Omicron variants. We systemically evaluated mutations located in the S2 sequence of spike and identified mutations that are responsible for altered viral fusion. We demonstrated that mutations near the S1/S2 cleavage site decrease S1/S2 cleavage, resulting in reduced fusogenicity. Mutations in the HR1 and other S2 sequences also affect cell-cell fusion. Based on nuclear magnetic resonance (NMR) studies and in silico modeling, these mutations affect fusogenicity possibly at multiple steps of the viral fusion. Our findings reveal that the Omicron variants have accumulated mutations that contribute to reduced syncytial formation and hence an attenuated pathogenicity.
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Affiliation(s)
- Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Mohsin Khan
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, 20850, USA
| | - Parker Irvin
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Madeleine Leek
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ailis Grieshaber
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eun Sun Jang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, 13620, Republic of Korea
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, 20892, USA.
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13
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Tamura T, Ito J, Uriu K, Zahradnik J, Kida I, Anraku Y, Nasser H, Shofa M, Oda Y, Lytras S, Nao N, Itakura Y, Deguchi S, Suzuki R, Wang L, Begum MM, Kita S, Yajima H, Sasaki J, Sasaki-Tabata K, Shimizu R, Tsuda M, Kosugi Y, Fujita S, Pan L, Sauter D, Yoshimatsu K, Suzuki S, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Schreiber G, Maenaka K, Hashiguchi T, Ikeda T, Fukuhara T, Saito A, Tanaka S, Matsuno K, Takayama K, Sato K. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun 2023; 14:2800. [PMID: 37193706 DOI: 10.1038/s41467-023-38435-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023] Open
Abstract
In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- 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
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- 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
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Yukari Itakura
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yusuke Kosugi
- 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
| | - Shigeru Fujita
- 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
| | - Lin Pan
- 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, Kashiwa, Japan
| | - Daniel Sauter
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | | | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katsumi Maenaka
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-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
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan.
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Kei Sato
- 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, Kashiwa, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, 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.
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14
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Ito J, Suzuki R, Uriu K, Itakura Y, Zahradnik J, Kimura KT, Deguchi S, Wang L, Lytras S, Tamura T, Kida I, Nasser H, Shofa M, Begum MM, Tsuda M, Oda Y, Suzuki T, Sasaki J, Sasaki-Tabata K, Fujita S, Yoshimatsu K, Ito H, Nao N, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Yamamoto Y, Nagamoto T, Kuramochi J, Schreiber G, Saito A, Matsuno K, Takayama K, Hashiguchi T, Tanaka S, Fukuhara T, Ikeda T, Sato K. Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant. Nat Commun 2023; 14:2671. [PMID: 37169744 PMCID: PMC10175283 DOI: 10.1038/s41467-023-38188-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/18/2023] [Indexed: 05/13/2023] Open
Abstract
In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.
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Affiliation(s)
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Keiya Uriu
- 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
| | - Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hesham Nasser
- 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
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigeru Fujita
- 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
| | | | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | | | | | - Jin Kuramochi
- Interpark Kuramochi Clinic, Utsunomiya, Japan
- Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, 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.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Kei Sato
- 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.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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15
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Kimura I, Yamasoba D, Tamura T, Nao N, Suzuki T, Oda Y, Mitoma S, Ito J, Nasser H, Zahradnik J, Uriu K, Fujita S, Kosugi Y, Wang L, Tsuda M, Kishimoto M, Ito H, Suzuki R, Shimizu R, Begum MM, Yoshimatsu K, Kimura KT, Sasaki J, Sasaki-Tabata K, Yamamoto Y, Nagamoto T, Kanamune J, Kobiyama K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Shirakawa K, Takaori-Kondo A, Kuramochi J, Schreiber G, Ishii KJ, Hashiguchi T, Ikeda T, Saito A, Fukuhara T, Tanaka S, Matsuno K, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell 2022; 185:3992-4007.e16. [PMID: 36198317 PMCID: PMC9472642 DOI: 10.1016/j.cell.2022.09.018] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/20/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- 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
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hesham Nasser
- 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
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Keiya Uriu
- 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
| | - Shigeru Fujita
- 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
| | - Yusuke Kosugi
- 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
| | - Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Mai Kishimoto
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | | | - Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | | | | | | | - Kouji Kobiyama
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jin Kuramochi
- Interpark Kuramochi Clinic, Utsunomiya, Japan; Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Keita Matsuno
- One Health Research Center, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Kei Sato
- 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; International Vaccine Design Center, 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; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
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