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Big data ecology for understanding host-pathogen interaction from sequence data

Research Project

Project/Area Number 16H04845
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Ecology/Environment
Research InstitutionNagoya University (2020, 2022)
Kyushu University (2016-2019)

Principal Investigator

Iwami Shingo  名古屋大学, 理学研究科, 教授 (90518119)

Co-Investigator(Kenkyū-buntansha) 立木 佑弥  東京都立大学, 理学研究科, 助教 (40741799)
Project Period (FY) 2016-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2020: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2019: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2018: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2017: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Keywords数理モデル / シミュレーション / データ解析 / 進化シミュレーション / 数理モデリング / 配列進化シミュレータ / 配列データ / 数理モデル型アプローチ / 進化シミュレータ / 定量的データ解析 / ウイルス進化 / コンピュータシミュレーション / バイオインフォマティクス / ハイブリッド力学系 / インフルエンザ / 遺伝子配列 / 進化動態 / ビックデータ
Outline of Final Research Achievements

We conducted a study to predict the prevalence of infectious diseases by combining a mathematical model and its theory (theoretical ecology) described by a hybrid dynamical system with gene sequence information of pathogens (infectious disease epidemiology), which is accumulating as information worthy of big data, using a data assimilation method (computer science). Using a mathematical model and computer simulation based on the developed hybrid dynamical system, we analyzed the gene sequence data of seasonal influenza A that have been accumulated up to the present day. The complementary fusion of the theory of population dynamics and data assimilation methods historically used in ecology suggested the possibility of making breakthroughs in both data reproducibility and future prediction.

Translated with www.DeepL.com/Translator (free version)

Academic Significance and Societal Importance of the Research Achievements

課題実施期間中に、COVID-19が出現したことを受け、開発したアプローチを発展させて、SARS-CoV-2の進化動態を予測する進化シミュレータの開発にも着手した。早期の流行予測により、医療体制の整備、個人保護具・抗ウイルス薬の最適分配、被害規模の推定等が可能になれば、感染症対策を大きく改善する事に貢献できる。

Report

(6 results)
  • 2022 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (50 results)

All 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (18 results) Journal Article (22 results) (of which Int'l Joint Research: 14 results,  Peer Reviewed: 22 results,  Open Access: 14 results,  Acknowledgement Compliant: 1 results) Presentation (10 results) (of which Int'l Joint Research: 9 results,  Invited: 7 results)

  • [Int'l Joint Research] オックスフォード大学(英国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] ロスアラモス国立研究所(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] ニューサウスウェールズ大学(オーストリア)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] INSERM(フランス)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Oxford University/Imperial College of London(英国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] UNSW(オーストラリア)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Pusan University(韓国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Los Alamos National Laboratory/Indiana University/Stanford University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] INSERM(フランス)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] UNSW(オーストラリア)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] ICL(英国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] INSERM(フランス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] UNSW(オーストラリア)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ICL(英国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ロスアラモス国立研究所(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] INSERM(フランス)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] ライルソン大学(カナダ)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] ニューサウスウェールズ大学(オーストラリア)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Quantifying antiviral effects against simian/human immunodeficiency virus induced by host immune response2021

    • Author(s)
      T. Oda, K.S. Kim, Y. Fujita, Y. Ito, T. Miura, S. Iwami.
    • Journal Title

      Journal of Theoretical Biology

      Volume: 509 Pages: 110493-110493

    • DOI

      10.1016/j.jtbi.2020.110493

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Required concentration index quantifies effective drug combinations against hepatitis C virus infection2021

    • Author(s)
      Kakizoe Yusuke、Koizumi Yoshiki、Ikoma Yukino、Ohashi Hirofumi、Wakita Takaji、Iwami Shingo、Watashi Koichi
    • Journal Title

      Theoretical Biology and Medical Modelling

      Volume: 18 Issue: 1 Pages: 4-4

    • DOI

      10.1186/s12976-020-00135-6

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-22021

    • Author(s)
      K.S. Kim, K. Ejima, S. Iwanami, Y. Fujita, H. Ohashi, Y. Koizumi, Y. Asai, S. Nakaoka, K. Watashi, K. Aihara, R.N. Thompson, R. Ke, A.S. Perelson and S. Iwami.
    • Journal Title

      PLOS Biology

      Volume: 19 Issue: 3 Pages: 3001128-3001128

    • DOI

      10.1371/journal.pbio.3001128

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantifying the antiviral effect of APOBEC3 on HIV-1 infection in humanized mouse model2020

    • Author(s)
      Tatsuya Kurusu, Kwang Su Kim, Yoshiki Koizumi, Shinji Nakaoka, Keisuke Ejima, Naoko Misawa, Yoshio Koyanagi, Kei Sato, Shingo Iwami
    • Journal Title

      Journal of Theoretical Biology

      Volume: 498 Pages: 110295-110295

    • DOI

      10.1016/j.jtbi.2020.110295

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Should a viral genome stay in the host cell or leave? A quantitative dynamics study of how hepatitis C virus deals with this dilemma2020

    • Author(s)
      S. Iwanami, K. Kitagawa, H. Ohashi, Y. Asai, K. Shionoya, W. Saso, K. Nishioka, H. Inaba, S. Nakaoka, T. Wakita, O. Diekmann, S. Iwami and K. Watashi
    • Journal Title

      PLoS Biology

      Volume: 18(7) Issue: 7 Pages: 3000562-3000562

    • DOI

      10.1371/journal.pbio.3000562

    • NAID

      120006872724

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule2020

    • Author(s)
      K.S. Kim, T. Kondoh, Y. Asai, A. Takada, S. Iwami.
    • Journal Title

      PLOS Computational Biology

      Volume: 16 Issue: 9 Pages: e1007612-e1007612

    • DOI

      10.1371/journal.pcbi.1007612

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] T. Honda. Modeling Borna disease virus in vitro spread reveals the mode of antiviral effect conferred by an endogenous bornavirus-like element2020

    • Author(s)
      K.S. Kim, Y. Yamamoto, S. Nakaoka, K. Tomonaga, S. Iwami,
    • Journal Title

      Journal of Virology

      Volume: - Issue: 21

    • DOI

      10.1128/jvi.01204-20

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The machinery for endocytosis of epidermal growth factor receptor coordinates the transport of incoming hepatitis B virus to the endosomal network.2020

    • Author(s)
      Iwamoto M, Saso W, Nishioka K, Ohashi H, Sugiyama R, Ryo A, Ohki M, Yun JH, Park SY, Ohshima T, Suzuki R, Aizaki H, Muramatsu M, Matano T, Iwami S, Sureau C, Wakita T, Watashi K
    • Journal Title

      J Biol Chem

      Volume: 295 Issue: 3 Pages: 800-807

    • DOI

      10.1074/jbc.ac119.010366

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Revealing uninfected and infected target cell dynamics from peripheral blood data in highly and less pathogenic simian/human immunodeficiency virus infected Rhesus macaque2019

    • Author(s)
      A. Hara, S. Iwanami, Y. Ito, T. Miura, S. Nakaoka and S. Iwami
    • Journal Title

      Journal of Theoretical Biology

      Volume: 479 Pages: 29-36

    • DOI

      10.1016/j.jtbi.2019.07.005

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Epidermal growth factor receptor is a host entry cofactor triggering hepatitis B virus internalization2019

    • Author(s)
      M. Iwamoto, W. Saso, R. Sugiyama, K. Ishii, M. Ohki, S. Nagamori, R. Suzuki, H. Aizaki, A. Ryo, J-H Yun, S-Y Park, N. Ohtani, M. Muramatsu, S. Iwami, Y. Tanaka, C. Sureau, T. Wakita and K. Watashi
    • Journal Title

      Proc. Natl. Acad. Sci. USA

      Volume: 116 Issue: 17 Pages: 8487-8492

    • DOI

      10.1073/pnas.1811064116

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mathematical analysis of a transformed ODE from a PDE multiscale model of hepatitis C virus infection2019

    • Author(s)
      Kitagawa K., Kuniya T., Nakaoka S., Asai Y., Watashi K. and Iwami S.
    • Journal Title

      Bulletin of Mathematical Biology

      Volume: 81(5) Issue: 5 Pages: 1427-1441

    • DOI

      10.1007/s11538-018-00564-y

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantitative immunology by data analysis using mathematical models2019

    • Author(s)
      S. Iwanami and S. Iwami
    • Journal Title

      Encyclopedia of Bioinformatics and Computational Biology

      Volume: 2 Pages: 984-992

    • DOI

      10.1016/b978-0-12-809633-8.20250-1

    • ISBN
      9780128114322
    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of HIV-1 coinfection in different susceptible target cell populations during cell-free infection2018

    • Author(s)
      Y. Ito, A. Tauzin, A. Remion, K. Ejima, F. Mammano and S. Iwami
    • Journal Title

      Journal of Theoretical Biology

      Volume: 455 Pages: 39-46

    • DOI

      10.1016/j.jtbi.2018.06.025

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A PDE multiscale model of hepatitis C virus infection can be transformed to a system of ODEs2018

    • Author(s)
      K. Kitagawa, S. Nakaoka, Y. Asai, K. Watashi, S. Iwami
    • Journal Title

      Journal of Theoretical Biology

      Volume: 48 Pages: 80-85

    • DOI

      10.1016/j.jtbi.2018.04.006

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Malaria incidences in South Africa linked to a climate mode in southwestern Indian Ocean2018

    • Author(s)
      SK. Behera, Y. Morioka, T. Ikeda, T. Doi, JV. Ratnam, M. Nonaka, A. Tsuzuki, C. Imai, Y. Kim, M. Hashizume, S. Iwami, P. Kruger, R. Maharaj, N. Sweijd and N. Minakawa
    • Journal Title

      Environmental Development

      Volume: 27 Pages: 47-57

    • DOI

      10.1016/j.envdev.2018.07.002

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells.2018

    • Author(s)
      Mahgoub M, Yasunaga JI, Iwami S, Nakaoka S, Koizumi Y, Shimura K, Matsuoka M.
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 115 Issue: 6 Pages: 529-538

    • DOI

      10.1073/pnas.1715724115

    • NAID

      120006697286

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Human-specific adaptations in Vpu conferring anti-tetherin activity are critical for efficient early HIV-1 replication in vivo.2017

    • Author(s)
      Eri Yamada, Shinji Nakaoka, Lukas Klein, Elisabeth Reith, Simon Langer, Kristina Hopfensperger, Shingo Iwami, Gideon Schreiber, Frank Kirchhoff, Yoshio Koyanagi, Daniel Sauter & Kei Sato
    • Journal Title

      Cell Host & Microbe

      Volume: 23 Issue: 1 Pages: 110-120

    • DOI

      10.1016/j.chom.2017.12.009

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Number of infection events per cell during HIV-1 cell-free infection2017

    • Author(s)
      Ito Y, Remion A, Tauzin A, Ejima K, Nakaoka S, Iwasa Y, Iwami S, Mammano F
    • Journal Title

      Sci Rep

      Volume: 7 Issue: 1 Pages: 6559-6559

    • DOI

      10.1038/s41598-017-03954-9

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Reply to Padmanabhan and Dixit: Hepatitis C virus entry inhibitors for optimally boosting direct-acting antiviral-based treatments.2017

    • Author(s)
      Ohashi HK, Koizumi Y, Fukano K, Wakita T, Perelson AS, Iwami S, Watashi K
    • Journal Title

      Proc Acad Natl Acad USA

      Volume: 114 Issue: 23

    • DOI

      10.1073/pnas.1705234114

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation.2017

    • Author(s)
      Yusuke Nakano, Naoko Misawa, Guillermo Juarez-Fernandez, Miyu Moriwaki, Shinji Nakaoka, Takaaki Funo, Eri Yamada, Andrew Soper, Rokusuke Yoshikawa, Diako Ebrahimi, Yuuya Tachiki, Shingo Iwami, Reuben S. Harris, Yoshio Koyanagi & Kei Sato
    • Journal Title

      PLOS Pathogens

      Volume: 13 Issue: 5 Pages: 31-31

    • DOI

      10.1371/journal.ppat.1006348

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A highly pathogenic simian/human immunodeficiency virus effectively produces infectious virions compared with a less pathogenic virus in cell culture2017

    • Author(s)
      Iwanami S, Kakizoe Y, Morita S, Miura T, Nakaoka S, Iwami S
    • Journal Title

      Theor Biol Med Model

      Volume: 14 Issue: 1 Pages: 9-9

    • DOI

      10.1186/s12976-017-0055-8

    • NAID

      120006305768

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A heart-brain-kidney network controls adaptation to cardiac stress through tissue macrophage activation and cellular communication2017

    • Author(s)
      Fujiu K, Shibata M, Nakayama Y, Ogata F, Matsumoto S, Noshita K, Iwami S, Nakae S, Komuro I, Nagai R, Manabe I
    • Journal Title

      Nature Medicine

      Volume: 印刷中 Issue: 5 Pages: 611-622

    • DOI

      10.1038/nm.4326

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] How IFN-α changes cccDNA decay rate in HBV infection2019

    • Author(s)
      Shingo Iwami
    • Organizer
      The 4th Workshop on Virus Dynamics in Paris
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Mathematical modeling and quantifying virus dynamics in cell culture2019

    • Author(s)
      Shingo Iwami
    • Organizer
      ICIAM 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 1造血幹細胞移植実験の数理モデル型定量的データ解析アプローチ2019

    • Author(s)
      岩見真吾
    • Organizer
      日本生化学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Quantifying antiviral activity optimizes drug combinations against hepatitis C virus infection2018

    • Author(s)
      Shingo Iwami
    • Organizer
      ECMTB2018
    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] PKPDVD modeling for multi-drug treatment on HCV infection2018

    • Author(s)
      Shingo Iwami
    • Organizer
      KSIAM2018
    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Characterizing SHIV infection in vitro and in vivo2018

    • Author(s)
      Shingo Iwami
    • Organizer
      SMB&JSMB2018
    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Modeling virus infection in cell culture2018

    • Author(s)
      Shingo Iwami
    • Organizer
      Simons Semester on Mathematical Biology in Warsaw, Epi-workshop
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Quantification of virus infection in cell culture2017

    • Author(s)
      Shingo Iwami
    • Organizer
      A3-NIMS joint workshop on mathematical biology
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Quantifying antiviral activity optimizes drug combinations against HCV infection2017

    • Author(s)
      Shingo Iwami
    • Organizer
      The 18th RIES-HOKUDAI international symposium
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] HCV entry inhibitors for optimally boosting direct-acting antiviral-based treatments2017

    • Author(s)
      Shingo Iwami
    • Organizer
      Innovative Mathematical Modeling for the Analysis of Infectious Disease Data
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited

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Published: 2016-04-21   Modified: 2024-01-30  

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