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Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Ito, Jumpei; Suzuki, Rigel; Uriu, Keiya; Itakura, Yukari; Zahradnik, Jiri; Kimura, Kanako Terakado; Deguchi, Sayaka; Wang, Lei; Lytras, Spyros; Tamura, Tomokazu; Kida, Izumi; Nasser, Hesham; Shofa, Maya; Begum, Mst Monira; Tsuda, Masumi; Oda, Yoshitaka; Suzuki, Tateki; Sasaki, Jiei; Sasaki-Tabata, Kaori; Fujita, Shigeru; Yoshimatsu, Kumiko; Ito, Hayato; Nao, Naganori; Asakura, Hiroyuki; Nagashima, Mami; Sadamasu, Kenji; Yoshimura, Kazuhisa; Yamamoto, Yuki; Nagamoto, Tetsuharu; Kuramochi, Jin; Schreiber, Gideon; Saito, Akatsuki; Matsuno, Keita; Takayama, Kazuo; Hashiguchi, Takao; Tanaka, Shinya; Fukuhara, Takasuke; Ikeda, Terumasa; Sato, Kei.
  • Ito J; Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
  • Suzuki R; Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
  • Uriu K; Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
  • Itakura Y; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
  • Zahradnik J; Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
  • Kimura KT; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
  • Deguchi S; First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia.
  • Wang L; Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
  • Lytras S; Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
  • Tamura T; Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
  • Kida I; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
  • Nasser H; Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.
  • Shofa M; Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
  • Begum MM; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
  • Tsuda M; Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
  • Oda Y; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
  • Suzuki T; Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
  • Sasaki J; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.
  • Sasaki-Tabata K; Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
  • Fujita S; Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
  • Yoshimatsu K; Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
  • Ito H; Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
  • Nao N; Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
  • Asakura H; Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
  • Nagashima M; Department of Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
  • Sadamasu K; Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
  • Yoshimura K; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
  • Yamamoto Y; Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
  • Nagamoto T; Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
  • Kuramochi J; Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
  • Schreiber G; One Health Research Center, Hokkaido University, Sapporo, Japan.
  • Saito A; Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
  • Matsuno K; Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
  • Takayama K; Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
  • Hashiguchi T; Tokyo Metropolitan Institute of Public Health, Tokyo, Japan.
  • Tanaka S; HiLung, Inc, Kyoto, Japan.
  • Fukuhara T; HiLung, Inc, Kyoto, Japan.
  • Ikeda T; Interpark Kuramochi Clinic, Utsunomiya, Japan.
  • Sato K; Department of Global Health Promotion, Tokyo Medical and Dental University, Tokyo, Japan.
Nat Commun ; 14(1): 2671, 2023 05 11.
Article in English | MEDLINE | ID: covidwho-2315617
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Randomized controlled trials Topics: Variants Limits: Animals Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2023 Document Type: Article Affiliation country: S41467-023-38188-z

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Randomized controlled trials Topics: Variants Limits: Animals Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2023 Document Type: Article Affiliation country: S41467-023-38188-z