Nature Communications (May 2023)
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
- Jumpei Ito,
- Rigel Suzuki,
- Keiya Uriu,
- Yukari Itakura,
- Jiri Zahradnik,
- Kanako Terakado Kimura,
- Sayaka Deguchi,
- Lei Wang,
- Spyros Lytras,
- Tomokazu Tamura,
- Izumi Kida,
- Hesham Nasser,
- Maya Shofa,
- Mst Monira Begum,
- Masumi Tsuda,
- Yoshitaka Oda,
- Tateki Suzuki,
- Jiei Sasaki,
- Kaori Sasaki-Tabata,
- Shigeru Fujita,
- Kumiko Yoshimatsu,
- Hayato Ito,
- Naganori Nao,
- Hiroyuki Asakura,
- Mami Nagashima,
- Kenji Sadamasu,
- Kazuhisa Yoshimura,
- Yuki Yamamoto,
- Tetsuharu Nagamoto,
- Jin Kuramochi,
- Gideon Schreiber,
- The Genotype to Phenotype Japan (G2P-Japan) Consortium,
- Akatsuki Saito,
- Keita Matsuno,
- Kazuo Takayama,
- Takao Hashiguchi,
- Shinya Tanaka,
- Takasuke Fukuhara,
- Terumasa Ikeda,
- Kei Sato
Affiliations
- Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Yukari Itakura
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University
- Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science
- Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Lei Wang
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Spyros Lytras
- Medical Research Council-University of Glasgow Centre for Virus Research
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Izumi Kida
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University
- Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Masumi Tsuda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Yoshitaka Oda
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Kaori Sasaki-Tabata
- Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University
- Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Kumiko Yoshimatsu
- Institute for Genetic Medicine, Hokkaido University
- Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University
- Hiroyuki Asakura
- Tokyo Metropolitan Institute of Public Health
- Mami Nagashima
- Tokyo Metropolitan Institute of Public Health
- Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health
- Kazuhisa Yoshimura
- Tokyo Metropolitan Institute of Public Health
- Yuki Yamamoto
- HiLung, Inc
- Tetsuharu Nagamoto
- HiLung, Inc
- Jin Kuramochi
- Interpark Kuramochi Clinic
- Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science
- The Genotype to Phenotype Japan (G2P-Japan) Consortium
- Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University
- Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University
- Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University
- Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University
- Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University
- Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- DOI
- https://doi.org/10.1038/s41467-023-38188-z
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 20
Abstract
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.
