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

• Project/Area Number: 18KK0447
• Research Category: Fund for the Promotion of Joint International Research (Fostering Joint International Research (A))
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 49060:Virology-related
• Research Institution: The University of Tokyo
• Principal Investigator: 佐藤 佳 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: ¥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 Annual Research Achievements

新型コロナウイルスパンデミックの影響によって、予定していた海外渡航を実現することはできなかった。しかし、オンライン会議やメールなどを駆使し、国際共同研究を遂行するよう努め、期待していた研究成果をあげることはできた。特に、イギリス、ドイツとは、すでに共同研究成果となる学術論文を発表している。また、ベトナムとは、今後につながる国際共同研究が発展している。

Research Products

• [Int'l Joint Research] VietNam Academy Of Science And Technology(ベトナム) (2022)
  • Year and Date: 2022-06-05
• [Journal Article] ORF3c is expressed in SARS‐CoV‐2‐infected cells and inhibits innate sensing by targeting MAVS (2023)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies (2022)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5 (2022)
  • Author(s): Kimura et al.
  • Journal Title: Cell Volume: 185 Issue: 21 Pages: 3992-4007
  • DOI: 10.1016/j.cell.2022.09.018
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant (2022)
  • 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
  • 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 Infection (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Sarbecovirus ORF6 proteins hamper the induction of interferon signaling (2021)
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Elucidation of the Complicated Scenario of Primate APOBEC3 Gene Evolution (2021)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity (2021)
  • 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
  • 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 Evasion (2021)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] IFITM proteins promote SARS-CoV-2 infection and are targets for virus inhibition in vitro (2021)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion (2021)
  • 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
  • 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 proteins (2021)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Neutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum (2021)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation (2021)
  • 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
  • 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 lineage (2021)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The True Nature of Viruses Elucidated by Systems Virology (2021)
  • Author(s): Sato Kei
  • Journal Title: Frontiers in Virology Volume: 1 Pages: 00-00
  • DOI: 10.3389/fviro.2021.808865
  • Peer Reviewed / Open Access
• [Journal Article] Inherited chromosomally integrated HHV-6 possibly modulates human gene expression (2020)
  • 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
  • Peer Reviewed
• [Journal Article] A tissue level atlas of the healthy human virome (2020)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In?Vivo (2020)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans (2020)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression (2020)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Reconstitution of prospermatogonial specification in vitro from human induced pluripotent stem cells (2020)
  • 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
  • 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 Variant (2020)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Retroviruses drive the rapid evolution of mammalian APOBEC3 genes (2020)
  • 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
  • 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 infection (2019)
  • 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
  • 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
  • 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 vivo (2019)
  • Author(s): Kei Sato
  • Organizer: Highlights in Basic andClinical Research in HIV/AIDS
  • 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