Spatial-temporal virus dynamics based on reaction-diffusion model

• Project/Area Number: 16K13777
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Foundations of mathematics/Applied mathematics
• Research Institution: Kyushu University
• Principal Investigator: Iwami Shingo 九州大学, 理学研究院, 准教授 (90518119)
• Co-Investigator(Kenkyū-buntansha): 本田 知之 大阪大学, 医学系研究科, 准教授 (80402676)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2018: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 数理モデル型アプローチ / 定量的データ解析 / 時空間モデリング / 数理モデル / 時空間動態 / 反応拡散方程式 / 時空間ダイナミクス / 拡散方程式 / データ解析 / 偏微分方程式 / 実験解析 / シミュレーション

Outline of Final Research Achievements

Collaboration with theory and data analysis is establishing mainly in research using ODE. Currently, although development of measurement technology has made it possible to acquire rich spatio-temporal data, the theory based on ODE can not be applied to data including such spatial information. In this research project, we developed spatio-temporal data analysis approach using Borna virus infection experiments and numerical simulation.

Academic Significance and Societal Importance of the Research Achievements

数理モデルおよびその理論を用いたウイルス感染の時空間データ解析への適用は極めて限定的であったが、世界初となるウイルス感染の時空間データの解析が可能になった（その他ウイルス感染への応用）。また、数理科学と他分野の連携研究を通じて、特に、新規抗ウイルス薬の開発に貢献する事ができる。主に培養細胞を用いたボルナウイルス感染実験から得られる時空間データを扱ったが、提案したアプローチは、様々なウイルスを用いた時空間データ解析に応用可能である。

Research Products

• [Int'l Joint Research] INSERM(フランス)
• [Int'l Joint Research] UNSW(オーストラリア)
• [Int'l Joint Research] ICL(英国)
• [Int'l Joint Research] ロスアラモス国立研究所(米国)
• [Int'l Joint Research] ライルソン大学(カナダ)
• [Int'l Joint Research] INSERM(フランス)
• [Int'l Joint Research] ニューサウスウェールズ大学(オーストラリア)
• [Int'l Joint Research] ロスアラモス国立研究所(米国)
• [Int'l Joint Research] ユトレヒト大学(オランダ)
• [Int'l Joint Research] ライルソン大学(カナダ)
• [Int'l Joint Research] ニューサウスウェールズ大学(オーストラリア)
• [Int'l Joint Research]
• [Journal Article] Epidermal growth factor receptor is a host entry cofactor triggering hepatitis B virus internalization (2019)
  • 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
  • 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 infection (2019)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Quantitative immunology by data analysis using mathematical models (2019)
  • 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
  • Peer Reviewed
• [Journal Article] Dynamics of HIV-1 coinfection in different susceptible target cell populations during cell-free infection (2018)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A PDE multiscale model of hepatitis C virus infection can be transformed to a system of ODEs (2018)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Malaria incidences in South Africa linked to a climate mode in southwestern Indian Ocean (2018)
  • 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
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Number of infection events per cell during HIV-1 cell-free infection (2017)
  • 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
  • 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
  • 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
  • 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 culture (2017)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] A heart-brain-kidney network controls adaptation to cardiac stress through tissue macrophage activation and cellular communication (2017)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Quantifying antiviral activity optimizes drug combinations against hepatitis C virus infection (2017)
  • Author(s): Y. Koizumi, H. Ohashi, S. Nakajima, Y. Tanaka, T. Wakita, AS. Perelson, S. Iwami†, and K. Watashi†.
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Volume: 114 Pages: 1922-1927
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Duration of SHIV production by infected cells is not exponentially distributed: Implications for estimates of infection parameters and antiviral efficacy (2017)
  • Author(s): CA. Beauchemin, T. Miura, and S. Iwami.
  • Journal Title: Scientific Reports Volume: 7 Pages: 42765-42765
  • NAID: 120005997746
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A heart-brain-kidney network controls adaptation to cardiac stress through tissue macrophage activation and cellular communication (2017)
  • Author(s): K. Fujiu†, M. Shibata†, Y. Nakayama, F. Ogata, S. Matsumoto, K. Noshita, S. Iwami, S. Nakae, I. Komuro, R. Nagai, and I. Manabe.
  • Journal Title: Nature Medicine Volume: In press
  • Peer Reviewed
• [Journal Article] (In)validating experimentally-derived knowledge about influenza A defective interfering particles (2016)
  • Author(s): LE. Liao, S. Iwami, CA. Beauchemin
  • Journal Title: Journal of the Royal Society Interface Volume: 13 Pages: 2016412-2016412
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Impact of asymptomatic infections on the early spread of malaria (2016)
  • Author(s): T. Funo, H. Inaba, M. Jusup, A. Tsuzuki, N. Minakawa, and S. Iwami
  • Journal Title: Japan Journal of Industrial and Applied Mathematics Volume: 33 Pages: 671-681
  • NAID: 210000176097
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Modelling Ebola virus dynamics: Implications for therapy (2016)
  • Author(s): A. Martyushev, S. Nakanoka, K. Sato, T. Noda†, and S. Iwami†.
  • Journal Title: Antiviral Research Volume: 135 Pages: 62-73
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Quantifying the effect of Vpu on the promotion of HIV-1 replication in the humanized mouse model, (2016)
  • Author(s): H. Ikeda†, S Nakaoka†, RJ. De Boer, S. Morita, N. Misawa, Y. Koyanagi, K. Aihara, K. Sato‡, and S. Iwami‡,
  • Journal Title: Retrovirology Volume: 13 Pages: 2-2
  • NAID: 120006353849
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Dynamics of HIV infection in lymphoid tissue network (2016)
  • Author(s): S. Nakaoka, S. Iwami, and K. Sato
  • Journal Title: Journal of Mathematical Biology Volume: 72 Pages: 909-38
• [Presentation] 1.Quantifying antiviral activity optimizes drug combinations against hepatitis C virus infection (2018)
  • Author(s): Shingo Iwami
  • Organizer: ECMTB2018
  • Int'l Joint Research
• [Presentation] 2.PKPDVD modeling for multi-drug treatment on HCV infection (2018)
  • Author(s): Shingo Iwami
  • Organizer: KSIAM2018
  • Int'l Joint Research / Invited
• [Presentation] Characterizing SHIV infection in vitro and in vivo (2018)
  • Author(s): Shingo Iwami
  • Organizer: SMB&JSMB2018
  • Int'l Joint Research
• [Presentation] Modeling virus infection in cell culture (2018)
  • Author(s): Shingo Iwami
  • Organizer: Simons Semester on Mathematical Biology in Warsaw, Epi-workshop
  • Int'l Joint Research / Invited
• [Presentation] Quantification of virus infection in cell culture (2017)
  • Author(s): Shingo Iwami
  • Organizer: A3-NIMS joint workshop on mathematical biology
  • Int'l Joint Research / Invited
• [Presentation] Quantifying antiviral activity optimizes drug combinations against HCV infection (2017)
  • Author(s): Shingo Iwami
  • Organizer: The 18th RIES-HOKUDAI international symposium
  • Int'l Joint Research / Invited
• [Presentation] HCV entry inhibitors for optimally boosting direct-acting antiviral-based treatments (2017)
  • Author(s): Shingo Iwami
  • Organizer: Innovative Mathematical Modeling for the Analysis of Infectious Disease Data
  • Int'l Joint Research / Invited