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Multi-omics analysis and comprehensive understanding of viral perturbation of pathogenesis principles

Research Project

Project/Area Number 18KK0447
Research Category

Fund for the Promotion of Joint International Research (Fostering Joint International Research (A))

Allocation TypeMulti-year Fund
Review Section Basic Section 49060:Virology-related
Research InstitutionThe University of Tokyo

Principal Investigator

Sato Kei  東京大学, 医科学研究所, 教授 (10593684)

Project Period (FY) 2019 – 2023
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥15,600,000 (Direct Cost: ¥12,000,000、Indirect Cost: ¥3,600,000)
Keywordsウイルス / ウイルス学 / システムウイルス学 / バイオインフォマティクス
Outline of Final Research Achievements

The main objective of this project was to elucidate the mechanisms of disease expression by viruses (Project 1) and virus-derived elements (Project 2) from an interdisciplinary approach combining experimental virology (wet research) and bioinformatics analysis (dry research). In this study, international joint research with four overseas research institutes (Germany, Switzerland, the Netherlands, and the United Kingdom) was planned for each of the above plans 1 and 2. Immediately after the start of the research project, COVID pandemic broke out, making it extremely difficult to travel to the planned overseas research institutes. In light of the social situation of the new coronavirus pandemic, we changed our original plan and started a research project on SARS-CoV-2. To promote this project, Vietnam was added to the list of overseas research institutions, and efforts were made to promote international joint research.

Academic Significance and Societal Importance of the Research Achievements

社会的情勢を鑑み、研究の方向性を変更した。具体的には、本研究を通して構築した解析方法を駆使し、新型コロナウイルスに関する研究も実施し、複数の学術論文をcorresponding authorとして発表した。出現が続く新型コロナウイルスの変異株(デルタ株、ラムダ株、ミュー株、オミクロン株)のウイルス学的性状を包括的に解析し、それらを世界に先駆けて解明した。これらの研究成果は、NatureやNew England Journal of Medicine、Cell姉妹誌などに、corresponding authorとして発表した。

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (34 results)

All 2023 2022 2021 2020 2019

All Int'l Joint Research (1 results) Journal Article (31 results) (of which Int'l Joint Research: 24 results,  Peer Reviewed: 31 results,  Open Access: 30 results) Presentation (1 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Book (1 results)

  • [Int'l Joint Research] VietNam Academy Of Science And Technology(ベトナム)2022

    • Year and Date
      2022-06-05
    • Related Report
      2023 Annual Research Report
  • [Journal Article] ORF3c is expressed in SARS‐CoV‐2‐infected cells and inhibits innate sensing by targeting MAVS2023

    • Author(s)
      M?ller Martin、Herrmann Alexandra、Fujita Shigeru、Uriu Keiya、Kruth Carolin、Strange Adam、Kolberg Jan E、Schneider Markus、Ito Jumpei、M?ller Marcel A、Drosten Christian、Ensser Armin、Sato Kei、Sauter Daniel、The Genotype to Phenotype Japan (G2P‐Japan) Consortium
    • Journal Title

      EMBO reports

      Volume: 24 Issue: 12 Pages: 57137-57137

    • DOI

      10.15252/embr.202357137

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike2022

    • Author(s)
      Yamasoba Daichi、Kimura Izumi、Nasser Hesham他
    • Journal Title

      Cell

      Volume: 未定 Issue: 12 Pages: 2103-2115

    • DOI

      10.1016/j.cell.2022.04.035

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies2022

    • Author(s)
      Yamasoba Daichi、Kosugi Yusuke、Kimura Izumi、Fujita Shigeru、Uriu Keiya、Ito Jumpei、Sato Kei
    • Journal Title

      The Lancet Infectious Diseases

      Volume: 22 Issue: 7 Pages: 942-943

    • DOI

      10.1016/s1473-3099(22)00365-6

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.52022

    • Author(s)
      Kimura et al.
    • Journal Title

      Cell

      Volume: 185 Issue: 21 Pages: 3992-4007

    • DOI

      10.1016/j.cell.2022.09.018

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant2022

    • Author(s)
      Saito et al.
    • Journal Title

      Cell Host & Microbe

      Volume: 30 Issue: 11 Pages: 1540-1540

    • DOI

      10.1016/j.chom.2022.10.003

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance2022

    • Author(s)
      Kimura Izumi、Kosugi Yusuke、Wu Jiaqi、other 17 authors、Saito Akatsuki、Nakagawa So、Sato Kei
    • Journal Title

      Cell Reports

      Volume: 38 Issue: 2 Pages: 110218-110218

    • DOI

      10.1016/j.celrep.2021.110218

    • NAID

      120007183813

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity2022

    • Author(s)
      Meng Bo、Abdullahi Adam、Ferreira Isabella A. T. M.、Goonawardane Niluka、Saito Akatsuki、Kimura Izumi、Yamasoba Daichi、Other 48 authors、Sato Kei、Gupta Ravindra K.
    • Journal Title

      Nature

      Volume: 603 Issue: 7902 Pages: 706-714

    • DOI

      10.1038/s41586-022-04474-x

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant2022

    • Author(s)
      Suzuki Rigel、Yamasoba Daichi、Kimura Izumi、Wang Lei他
    • Journal Title

      Nature

      Volume: 603 Issue: 7902 Pages: 700-705

    • DOI

      10.1038/s41586-022-04462-1

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Characterization of the Immune Resistance of Severe Acute Respiratory Syndrome Coronavirus 2 Mu Variant and the Robust Immunity Induced by Mu Infection2022

    • Author(s)
      Uriu Keiya et al.
    • Journal Title

      The Journal of Infectious Diseases

      Volume: 00 Issue: 7 Pages: 00-00

    • DOI

      10.1093/infdis/jiac053

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Sarbecovirus ORF6 proteins hamper the induction of interferon signaling2021

    • Author(s)
      Kimura I, Konno Y, Uriu K, Hopfensperge K, Sauter D, Nakagawa S, Sato K
    • Journal Title

      Cell Reports

      Volume: 34 Issue: 13 Pages: 108916-108916

    • DOI

      10.1016/j.celrep.2021.108916

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A comprehensive investigation on the interplay between feline APOBEC3Z3 proteins and feline immunodeficiency virus Vif proteins. Journal of Virology.2021

    • Author(s)
      Yusuke Kosugi‡, Keiya Uriu‡, Narumi Suzuki‡, Keisuke Yamamoto‡, Shumpei Nagaoka‡, Izumi Kimura‡, Yoriyuki Konno‡, Hirofumi Aso‡, Brian J Willett, Tomoko Kobayashi, Yoshio Koyanagi, Mahoko Takahashi Ueda, Jumpei Ito and Kei Sato. ‡Equal contribution.
    • Journal Title

      Journal of Virology

      Volume: 00178-21 Issue: 13 Pages: 00-00

    • DOI

      10.1128/jvi.00178-21

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Elucidation of the Complicated Scenario of Primate APOBEC3 Gene Evolution2021

    • Author(s)
      Uriu Keiya、Kosugi Yusuke、Suzuki Narumi、Ito Jumpei、Sato Kei
    • Journal Title

      Journal of Virology

      Volume: 95 Issue: 12 Pages: 00-00

    • DOI

      10.1128/jvi.00144-21

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity2021

    • Author(s)
      Motozono Chihiro、Toyoda Mako、Zahradnik Jiri、Saito Akatsuki、Other 19 authors、Ikeda Terumasa、Nakagawa So、Ueno Takamasa、Sato Kei
    • Journal Title

      Cell Host & Microbe

      Volume: 29 Issue: 7 Pages: 1124-1136

    • DOI

      10.1016/j.chom.2021.06.006

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion2021

    • Author(s)
      Ferreira IATM, Kemp SA, Datir R, Saito A, Meng B, Rakshit P, Takaori-Kondo A, Kosugi Y, Uriu K, Kimura I, Shirakawa K, Abdullahi A, Agarwal A, Ozono S, Tokunaga K, Sato K, Gupta RK
    • Journal Title

      The Journal of Infectious Diseases

      Volume: 224 Issue: 6 Pages: 989-994

    • DOI

      10.1093/infdis/jiab368

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] IFITM proteins promote SARS-CoV-2 infection and are targets for virus inhibition in vitro2021

    • Author(s)
      Prelli Bozzo Caterina et al.
    • Journal Title

      Nature Communications

      Volume: 12 Issue: 1 Pages: 00-00

    • DOI

      10.1038/s41467-021-24817-y

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion2021

    • Author(s)
      Mlcochova Petra、Kemp Steven A.、Dhar Mahesh Shanker他
    • Journal Title

      Nature

      Volume: 599 Issue: 7883 Pages: 114-119

    • DOI

      10.1038/s41586-021-03944-y

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An additional NF-κB site allows HIV-1 subtype C to evade restriction by nuclear PYHIN proteins2021

    • Author(s)
      Bosso Matteo、Sturzel Christina M.、Kmiec Dorota、Badarinarayan Smitha Srinivasachar、Braun Elisabeth、Ito Jumpei、Sato Kei、Hahn Beatrice H.、Sparrer Konstantin M.J.、Sauter Daniel、Kirchhoff Frank
    • Journal Title

      Cell Reports

      Volume: 36 Issue: 12 Pages: 109735-109735

    • DOI

      10.1016/j.celrep.2021.109735

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Neutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum2021

    • Author(s)
      Uriu Keiya、Kimura Izumi、Shirakawa Kotaro、Takaori-Kondo Akifumi、Nakada Taka-aki、Kaneda Atsushi、Nakagawa So、Sato Kei
    • Journal Title

      New England Journal of Medicine

      Volume: 385 Issue: 25 Pages: 2397-2399

    • DOI

      10.1056/nejmc2114706

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation2021

    • Author(s)
      Saito Akatsuki、Irie Takashi、Suzuki Rigel、Maemura Tadashi、Nasser Hesham、Uriu Keiya、Kosugi Yusuke、Other 43 authors、Tanaka Shinya、Nakagawa So、Ikeda Terumasa、Fukuhara Takasuke、Kawaoka Yoshihiro、Sato Kei、The Genotype to Phenotype Japan (G2P-Japan) Consortium
    • Journal Title

      Nature

      Volume: 602 Issue: 7896 Pages: 300-306

    • DOI

      10.1038/s41586-021-04266-9

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage2021

    • Author(s)
      Zhao Zhe、Fagerlund Riku、Tossavainen Helena、Hopfensperger Kristina、Lotke Rishikesh、Srinivasachar Badarinarayan Smitha、Kirchhoff Frank、Permi Perttu、Sato Kei、Sauter Daniel、Saksela Kalle
    • Journal Title

      PLOS Pathogens

      Volume: 17 Issue: 11 Pages: 1009728-1009728

    • DOI

      10.1371/journal.ppat.1009728

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The True Nature of Viruses Elucidated by Systems Virology2021

    • Author(s)
      Sato Kei
    • Journal Title

      Frontiers in Virology

      Volume: 1 Pages: 00-00

    • DOI

      10.3389/fviro.2021.808865

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inherited chromosomally integrated HHV-6 possibly modulates human gene expression2020

    • Author(s)
      Kumata Ryuichi、Ito Jumpei、Sato Kei
    • Journal Title

      Virus Genes

      Volume: 56 Issue: 3 Pages: 386-389

    • DOI

      10.1007/s11262-020-01745-5

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] A tissue level atlas of the healthy human virome2020

    • Author(s)
      Kumata Ryuichi、Ito Jumpei、Takahashi Kenta、Suzuki Tadaki、Sato Kei
    • Journal Title

      BMC Biology

      Volume: 18 Issue: 1 Pages: 1-15

    • DOI

      10.1186/s12915-020-00785-5

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In?Vivo2020

    • Author(s)
      Aso Hirofumi、Nagaoka Shumpei、Kawakami Eiryo、Ito Jumpei、Islam Saiful、Tan Benjy Jek Yang、Nakaoka Shinji、Ashizaki Koichi、Shiroguchi Katsuyuki、Suzuki Yutaka、Satou Yorifumi、Koyanagi Yoshio、Sato Kei
    • Journal Title

      Cell Reports

      Volume: 32 Issue: 2 Pages: 107887-107887

    • DOI

      10.1016/j.celrep.2020.107887

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans2020

    • Author(s)
      Nakano Yusuke、Yamamoto Keisuke、Ueda Mahoko Takahashi、Soper Andrew、Konno Yoriyuki、Kimura Izumi、Uriu Keiya、Kumata Ryuichi、Aso Hirofumi、Misawa Naoko、Nagaoka Shumpei、Shimizu Soma、Mitsumune Keito、Kosugi Yusuke、Juarez-Fernandez Guillermo、Ito Jumpei、...、Koyanagi Yoshio、Harris Reuben S.、Sato Kei
    • Journal Title

      PLOS Pathogens

      Volume: 16 Issue: 9 Pages: 1008812-1008812

    • DOI

      10.1371/journal.ppat.1008812

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression2020

    • Author(s)
      Ito Jumpei、Kimura Izumi、Soper Andrew、Coudray Alexandre、Koyanagi Yoshio、Nakaoka Hirofumi、Inoue Ituro、Turelli Priscilla、Trono Didier、Sato Kei
    • Journal Title

      Science Advances

      Volume: 6 Issue: 43 Pages: 3020-3020

    • DOI

      10.1126/sciadv.abc3020

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Reconstitution of prospermatogonial specification in vitro from human induced pluripotent stem cells2020

    • Author(s)
      Hwang Young Sun、Suzuki Shinnosuke、Seita Yasunari、Ito Jumpei、Sakata Yuka、Aso Hirofumi、Sato Kei、Hermann Brian P.、Sasaki Kotaro
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 5656-5656

    • DOI

      10.1038/s41467-020-19350-3

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant2020

    • Author(s)
      Konno Yoriyuki、Kimura Izumi、Uriu Keiya、Fukushi Masaya、Irie Takashi、Koyanagi Yoshio、Sauter Daniel、Gifford Robert J.、Nakagawa So、Sato Kei
    • Journal Title

      Cell Reports

      Volume: 32 Issue: 12 Pages: 108185-108185

    • DOI

      10.1016/j.celrep.2020.108185

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Retroviruses drive the rapid evolution of mammalian APOBEC3 genes2020

    • Author(s)
      Jumpei Ito, Robert J. Gifford, Kei Sato
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 117 Issue: 1 Pages: 610-618

    • DOI

      10.1073/pnas.1914183116

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Comparative description of the expression profile of interferon-stimulated genes in multiple cell lineages targeted by HIV-1 infection2019

    • Author(s)
      Hirofumi Aso, Jumpei Ito, Yoshio Koyanagi & Kei Sato
    • Journal Title

      Front Microbiol

      Volume: 10 Pages: 429-429

    • DOI

      10.3389/fmicb.2019.00429

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation.2019

    • Author(s)
      Yamasoba D, Sato K, Ichinose T, Imamura T, Koepke L, Joas S, Reith E, Hotter D, Misawa N, Akaki K, Uehata T, Mino T, Miyamoto S, Noda T, Yamashita A, Standley DM, Kirchhoff F, Sauter D, Koyanagi Y, Takeuchi O.
    • Journal Title

      Nat Microbiol

      Volume: 4 Issue: 9 Pages: 1532-1544

    • DOI

      10.1038/s41564-019-0460-3

    • NAID

      120006731123

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Human-specific adaptations in Vpu conferring anti-tetherin activity are critical for efficient early HIV-1 replication in vivo2019

    • Author(s)
      Kei Sato
    • Organizer
      Highlights in Basic andClinical Research in HIV/AIDS
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Book] ネオウイルス学2021

    • Author(s)
      河岡 義裕、岩見 真吾、大場 靖子、川口 寧、佐藤 佳、澤 洋文、鈴木 信弘、高橋 英樹、朝長 啓造、中川 草、長崎 慶三、西浦 博、野田 岳志、古瀬 祐気、堀江 真行、牧野 晶子、松浦 善治、松野 啓太、村田 和義、望月 智弘、渡辺 登喜子
    • Total Pages
      320
    • Publisher
      集英社
    • ISBN
      4087211592
    • Related Report
      2020 Research-status Report

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Published: 2019-02-06   Modified: 2026-01-16  

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