Virological characteristics of the SARS-CoV-2 BA.2.86 variant

Tomokazu Tamura¹, Keita Mizuma², Hesham Nasser³, Sayaka Deguchi⁴, Miguel Padilla-Blanco⁵, Yoshitaka Oda⁶, Keiya Uriu⁷, Jarel E M Tolentino⁸, Shuhei Tsujino⁹, Rigel Suzuki¹⁰, Isshu Kojima², Naganori Nao¹¹, Ryo Shimizu¹², Lei Wang¹³, Masumi Tsuda¹³, Michael Jonathan¹², Yusuke Kosugi⁷, Ziyi Guo¹⁴, Alfredo A Hinay Jr¹⁴, Olivia Putri¹⁵, Yoonjin Kim¹⁶, Yuri L Tanaka¹⁷, Hiroyuki Asakura¹⁸, Mami Nagashima¹⁸, Kenji Sadamasu¹⁸, Kazuhisa Yoshimura¹⁸; Genotype to Phenotype Japan (G2P-Japan) Consortium; Akatsuki Saito¹⁹, Jumpei Ito²⁰, Takashi Irie²¹, Shinya Tanaka²², Jiri Zahradnik²³, Terumasa Ikeda²⁴, Kazuo Takayama²⁵, Keita Matsuno²⁶, Takasuke Fukuhara²⁷, Kei Sato²⁸

Affiliations

¹ 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.
² Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
³ 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.
⁴ Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
⁵ First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia; Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain.
⁶ Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
⁷ 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.
⁸ 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.
⁹ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
¹⁰ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan.
¹¹ 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.
¹² Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
¹³ Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
¹⁴ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
¹⁵ 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.
¹⁶ 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.
¹⁷ Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
¹⁸ Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
¹⁹ 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.
²⁰ 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.
²¹ Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
²² Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan. Electronic address: tanaka@med.hokudai.ac.jp.
²³ First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia. Electronic address: jiri.zahradnik2@gmail.com.
²⁴ Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan. Electronic address: ikedat@kumamoto-u.ac.jp.
²⁵ Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan. Electronic address: kazuo.takayama@cira.kyoto-u.ac.jp.
²⁶ 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. Electronic address: matsuk@czc.hokudai.ac.jp.
²⁷ 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. Electronic address: fukut@pop.med.hokudai.ac.jp.
²⁸ 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. Electronic address: keisato@g.ecc.u-tokyo.ac.jp.

PMID: 38280382
DOI: 10.1016/j.chom.2024.01.001

Free article

Virological characteristics of the SARS-CoV-2 BA.2.86 variant

Tomokazu Tamura et al. Cell Host Microbe. 2024.

Free article

. 2024 Feb 14;32(2):170-180.e12.

doi: 10.1016/j.chom.2024.01.001. Epub 2024 Jan 26.

Authors

Affiliations

¹ 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.
² Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
³ 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.
⁴ Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
⁵ First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia; Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain.
⁶ Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
⁷ 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.
⁸ 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.
⁹ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
¹⁰ Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan.
¹¹ 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.
¹² Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
¹³ Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
¹⁴ Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
¹⁵ 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.
¹⁶ 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.
¹⁷ Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
¹⁸ Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
¹⁹ 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.
²⁰ 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.
²¹ Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
²² Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan. Electronic address: tanaka@med.hokudai.ac.jp.
²³ First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia. Electronic address: jiri.zahradnik2@gmail.com.
²⁴ Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan. Electronic address: ikedat@kumamoto-u.ac.jp.
²⁵ Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan. Electronic address: kazuo.takayama@cira.kyoto-u.ac.jp.
²⁶ 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. Electronic address: matsuk@czc.hokudai.ac.jp.
²⁷ 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. Electronic address: fukut@pop.med.hokudai.ac.jp.
²⁸ 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. Electronic address: keisato@g.ecc.u-tokyo.ac.jp.

PMID: 38280382
DOI: 10.1016/j.chom.2024.01.001

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.

Keywords: BA.2.86; COVID-19; SARS-CoV-2; pathogenicity.

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Conflict of interest statement

Declaration of interests J.I. has consulting fees and honoraria for lectures from Takeda Pharmaceutical Co. Ltd. K. Sato has consulting fees from Moderna Japan Co., Ltd. and Takeda Pharmaceutical Co. Ltd. and honoraria for lectures from Gilead Sciences, Inc., Moderna Japan Co., Ltd., and Shionogi & Co., Ltd.

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Virological characteristics of the SARS-CoV-2 BA.2.86 variant

Affiliations

Virological characteristics of the SARS-CoV-2 BA.2.86 variant

Authors

Affiliations

Abstract

Conflict of interest statement

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LinkOut - more resources

Full Text Sources

Medical

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