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, Akatsuki Saito, Keita Matsuno, Kazuo Takayama, Takao Hashiguchi (), Shinya Tanaka (), Takasuke Fukuhara (), Terumasa Ikeda () and Kei Sato ()
Additional contact information
Jumpei Ito: The University of Tokyo
Rigel Suzuki: Hokkaido University
Keiya Uriu: The University of Tokyo
Yukari Itakura: Hokkaido University
Jiri Zahradnik: Weizmann Institute of Science
Kanako Terakado Kimura: Kyoto University
Sayaka Deguchi: Kyoto University
Lei Wang: Hokkaido University
Spyros Lytras: Medical Research Council-University of Glasgow Centre for Virus Research
Tomokazu Tamura: Hokkaido University
Izumi Kida: Hokkaido University
Hesham Nasser: Kumamoto University
Maya Shofa: University of Miyazaki
Mst Monira Begum: Kumamoto University
Masumi Tsuda: Hokkaido University
Yoshitaka Oda: Hokkaido University
Tateki Suzuki: Kyoto University
Jiei Sasaki: Kyoto University
Kaori Sasaki-Tabata: Kyushu University
Shigeru Fujita: The University of Tokyo
Kumiko Yoshimatsu: Hokkaido University
Hayato Ito: Hokkaido University
Naganori Nao: 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: Weizmann Institute of Science
Akatsuki Saito: University of Miyazaki
Keita Matsuno: Hokkaido University
Kazuo Takayama: Kyoto University
Takao Hashiguchi: Kyoto University
Shinya Tanaka: Hokkaido University
Takasuke Fukuhara: Hokkaido University
Terumasa Ikeda: Kumamoto University
Kei Sato: The University of Tokyo

Nature Communications, 2023, vol. 14, issue 1, 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.

Date: 2023
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DOI: 10.1038/s41467-023-38188-z

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