Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.

Animals Cricetinae COVID-19 Phylogeny SARS-CoV-2 / genetics Amino Acid Substitution Biological Assay Antibodies, Neutralizing Antibodies, Viral

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
11 05 2023
Historique:
received: 09 12 2022
accepted: 18 04 2023
medline: 15 5 2023
pubmed: 12 5 2023
entrez: 11 5 2023
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-023-38188-z PMID: 37169744 PMC: PMC10175283
pubmed: 37169744
doi: 10.1038/s41467-023-38188-z
pii: 10.1038/s41467-023-38188-z
pmc: PMC10175283
doi:

Substances chimiques

Antibodies, Neutralizing 0
Antibodies, Viral 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

2671

Investigateurs

Saori Suzuki (S)
Marie Kato (M)
Zannatul Ferdous (Z)
Hiromi Mouri (H)
Kenji Shishido (K)
Naoko Misawa (N)
Izumi Kimura (I)
Yusuke Kosugi (Y)
Pan Lin (P)
Mai Suganami (M)
Mika Chiba (M)
Ryo Yoshimura (R)
Kyoko Yasuda (K)
Keiko Iida (K)
Naomi Ohsumi (N)
Adam P Strange (AP)
Daniel Sauter (D)
So Nakagawa (S)
Jiaqi Wu (J)
Yukio Watanabe (Y)
Ayaka Sakamoto (A)
Naoko Yasuhara (N)
Yukari Nakajima (Y)
Hisano Yajima (H)
Kotaro Shirakawa (K)
Akifumi Takaori-Kondo (A)
Kayoko Nagata (K)
Yasuhiro Kazuma (Y)
Ryosuke Nomura (R)
Yoshihito Horisawa (Y)
Yusuke Tashiro (Y)
Yugo Kawa (Y)
Takashi Irie (T)
Ryoko Kawabata (R)
Ryo Shimizu (R)
Otowa Takahashi (O)
Kimiko Ichihara (K)
Chihiro Motozono (C)
Mako Toyoda (M)
Takamasa Ueno (T)
Yuki Shibatani (Y)
Tomoko Nishiuchi (T)

Informations de copyright

© 2023. The Author(s).

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Auteurs

Jumpei Ito (J)

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
ORCID: 0000-0003-0440-8321

Rigel Suzuki (R)

Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.

Keiya Uriu (K)

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 (Y)

Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
ORCID: 0000-0002-3463-1834

Jiri Zahradnik (J)

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia.
ORCID: 0000-0002-8698-4236

Kanako Terakado Kimura (KT)

Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.

Sayaka Deguchi (S)

Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.

Lei Wang (L)

Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
ORCID: 0000-0001-6145-395X

Spyros Lytras (S)

Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.
ORCID: 0000-0003-4202-6682

Tomokazu Tamura (T)

Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.

Izumi Kida (I)

Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
ORCID: 0000-0002-6312-1454

Hesham Nasser (H)

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.
ORCID: 0000-0001-9163-1665

Maya Shofa (M)

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 (MM)

Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.

Masumi Tsuda (M)

Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
ORCID: 0000-0001-5400-5905

Yoshitaka Oda (Y)

Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.

Tateki Suzuki (T)

Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
ORCID: 0000-0002-6946-3850

Jiei Sasaki (J)

Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.

Kaori Sasaki-Tabata (K)

Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.

Shigeru Fujita (S)

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.
ORCID: 0000-0001-9008-2123

Kumiko Yoshimatsu (K)

Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
ORCID: 0000-0002-0062-2753

Hayato Ito (H)

Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.

Naganori Nao (N)

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.

Hiroyuki Asakura (H)

Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.

Mami Nagashima (M)

Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.

Kenji Sadamasu (K)

Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.

Kazuhisa Yoshimura (K)

Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.

Yuki Yamamoto (Y)

HiLung, Inc, Kyoto, Japan.

Tetsuharu Nagamoto (T)

HiLung, Inc, Kyoto, Japan.

Jin Kuramochi (J)

Interpark Kuramochi Clinic, Utsunomiya, Japan.
Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan.
ORCID: 0000-0002-9078-0527

Gideon Schreiber (G)

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
ORCID: 0000-0002-2922-5882

Akatsuki Saito (A)

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.
ORCID: 0000-0002-2792-4399

Keita Matsuno (K)

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.
ORCID: 0000-0002-4205-6526

Kazuo Takayama (K)

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 (T)

Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan. hashiguchi.takao.1a@kyoto-u.ac.jp.
ORCID: 0000-0001-7578-7571

Shinya Tanaka (S)

Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. tanaka@med.hokudai.ac.jp.
Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan. tanaka@med.hokudai.ac.jp.
ORCID: 0000-0001-6470-3301

Takasuke Fukuhara (T)

Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan. fukut@pop.med.hokudai.ac.jp.
AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan. fukut@pop.med.hokudai.ac.jp.
Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan. fukut@pop.med.hokudai.ac.jp.
ORCID: 0000-0001-5471-8331

Terumasa Ikeda (T)

Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan. ikedat@kumamoto-u.ac.jp.
ORCID: 0000-0003-2869-9450

Kei Sato (K)

Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
CREST, Japan Science and Technology Agency, Kawaguchi, Japan. KeiSato@g.ecc.u-tokyo.ac.jp.
ORCID: 0000-0003-4431-1380

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Arvicolinae › Cricetinae › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Phénomènes génétiques › Mutagenèse › Substitution d'acide aminé › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Techniques d'investigation › Dosage biologique › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Globulines › Sérum-globulines › Immunoglobulines › Anticorps › Anticorps neutralisants › Convergent evolution of SARS-CoV-2 Omicron...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Globulines › Sérum-globulines › Immunoglobulines › Anticorps › Anticorps antiviraux › Convergent evolution of SARS-CoV-2 Omicron...