Report of Research Achievements


  • K. Kitagawa, K. S. Kim, M. Iwamoto, S. Hayashi, H. Park, T. Nishiyama, N. Nakamura, Y. Fujita, S. Nakaoka, K. Aihara, A. S. Perelson, L. Allweiss, M. Dandri, K. Watashi, Y. Tanaka, S. Iwami. Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers, PLOS Computational Biology, 20(3):e1011238 (2024).
  • T. Kawahigashi†, S. Iwanami†, M. Takahashi, J. Bhadury, S. Iwami and S. Yamazaki. Age-related changes in the hematopoietic stem cell pool revealed via quantifying the balance of symmetric and asymmetric divisions, PLOS ONE, 19(1): e0292575 (2024). († Equal contribution)
  • 2023

  • S. Miyamoto†, T. Nishiyama†, A. Ueno, H. Park, T. Kanno, N. Nakamura, S. Ozono, K. Aihara, K. Takahashi, Y. Tsuchihashi, M. Ishikane, T. Arashiro, S. Saito, A. Ainai, Y. Hirata, S. Iida, H. Katano, M. Tobiume, K. Tokunaga, T. Fujimoto, M. Suzuki, M. Nakagawa, H. Nakagawa, M. Narita, Y. Kato, H. Igari, K. Fujita, T. Kato, K. Hiyama, K. Shindou, T. Adachi, K. Fukushima, F. Nakamura-Uchiyama, R. Hase, Y. Yoshimura, M. Yamato, Y. Nozaki, N. Ohmagar, M. Suzuki, T. Saito, S. Iwami# and T. Suzuki#. Infectious virus shedding duration reflects secretory IgA antibody response latency after SARS-CoV-2 infection, Proceedings of the National Academy of Sciences of the United States of America, 120(52):e2314808120 (2023). (†, # Equal contribution)
  • T. Nishiyama, Y. Miyamatsu, H. Park, N. Nakamura, R. Yokokawa Shibata, S. Iwami# and Y. Nagasaki#. Modeling COVID-19 vaccine booster-elicited antibody response and impact of infection history, Vaccine, 41:7655-7662 (2023). (, # Equal contribution).
  • J. Sunagawa, H. Park, K. S. Kim, R. Komorizono, S. Choi, L. Ramírez. Torres, J. Woo, Y. D. Jeong, W. S. Hart, R. N. Thompson, K. Aihara, S. Iwami# and R. Yamaguchi#. Isolation may select for earlier and higher peak viral load but shorter duration in SARS-CoV-2 evolution, Nature Communications, 14:7395 (2023). (, # Equal contribution)
  • W. S. Hart, H. Park, Y. D. Jeong, K. S. Kim, R. Yoshimura, R. N. Thompson and S. Iwami, Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study, Proceedings of the National Academy of Sciences of the United States of America, 120(41):e2305451120 (2023). ( Equal contribution)
  • J. Sunagawa, R. Komorizono, H. Park, WS Hart, RN Thompson, A Makino, K Tomonaga, S Iwami# and R Yamaguchi#, Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection, PLOS Computational Biology, 19(5):e1011173 (2023). (, # Equal contribution)
  • R. Suzuki, Y. Ono, K. Noshita, K.S. Kim, H. Ito, Y. Morioka, T. Tamura, D. Okuzaki, T. Tagawa, T. Takenaka, T. Yoshizumi, T. Shimamura, S. Iwami and T. Fukuhara, Smoking enhances the expression of angiotensin-converting enzyme 2 involved in the efficiency of severe acute respiratory syndrome coronavirus 2 infection, Microbiology and Immunology, 67(1):22-31 (2023).
  • D. Akazawa, H. Ohashi, T. Hishiki&, T. Morita&, S. Iwanami, K. S. Kim, Y. D. Jeong, E. S. Park, M. Kataoka, K. Shionoya, J. Mifune, K. Tsuchimoto, S. Ojima, A. H. Azam, S. Nakajima, H. Park, T. Yoshikawa, M. Shimojima, K. Kiga, S. Iwami, K. Maeda, T. Suzuki, H. Ebihara, Y. Takahashi and K. Watashi, Potential anti-monkeypox virus activity of atovaquone, mefloquine, and molnupiravir, and their potential use as treatments, Journal of the Infectious Diseases, 228(5):591-603 (2023). (, &,Equal contribution)
  • S.Torii, K.S.Kim, J.Koseki, R.Suzuki, S.Iwanami, Y.Fujita, Y.D.Jeong, J.Ito, H.Asakura, M.Nagashima, K.Sadamasu, K.Yoshimura, The Genotype to Phenotype Japan (G2P-Japan) Consortium, K.Sato, Y. Matsuura, T.Shimamura, S.Iwami, T.Fukuhara, Increased flexibility of the SARS-CoV-2 RNA-binding site causes resistance to remdesivir, PLOS Pathogens, 19(3): e1011231 (2023). (†Equal contribution).


  • K. Ikeda, T. Nakada, T. Kageyama, S. Tanaka, N. Yoshida, T. Ishikawa, Y. Goshima, N. Otaki, S. Iwami, T. Shimamura, T. Taniguchi, H. Igari, H. Hanaoka, K. Yokote, K. Tsuyuzaki, H. Nakajima, E. Kawakami, Detecting time-evolving phenotypic components of adverse reactions against BNT162b2 SARS-CoV-2 vaccine via non-negative tensor factorization, iScience, 25:105237(2022).
  • Y.D. Jeong, K. Ejima, K.S. Kim, J. Woo, S. Iwanami, Y. Fujita, IH. Jung, K. Aihara, K. Shibuya, S. Iwami, A.I. Bento and M. Ajelli, Designing isolation guidelines for COVID-19 patients with rapid antigen tests, Nature Communications, 13:4910(2022). (Equal contribution)
  • K. Ejima, K.S. Kim, A.I. Bento, S. Iwanami, Y. Fujita, K. Aihara, K. Shibuya, and S. Iwami, Estimation of timing of infection from longitudinal SARS-CoV-2 viral load data: mathematical modelling study, BMC Infectious Diseases, 22:656(2022). (Equal contribution)
  • H. Ohashi, T. Hishiki, D. Akazawa, KS. Kim, J. Woo, K. Shionoya, K. Tsuchimoto, S. Iwanami, S. Moriyama, H. Kinoshita, S. Yamada, Y. Kuroda, T. Yamamoto, N. Kishida, S. Watanabe, H. Hasegawa, H. Ebihara, T. Suzuki, M. Ken, S. Fukushi, Y. Takahashi, S. Iwami, K. Watashi, Different efficacies of neutralizing antibodies and antiviral drugs on SARS-CoV-2 Omicron subvariants, BA.1 and BA.2, Antiviral Research, 205:105372 (2022). (Equal contribution)
  • T. Nishiyama, T. Takada, H. Takeuchi, S. Iwami, Maternal embryonic leucine zipper kinase (MELK) optimally regulates the HIV-1 uncoating process, Journal of Theoretical Biology, 545:111152 (2022).
  • R. Kumata†, S. Iwanami†, K.B. Mar, Y. Kakizoe, N. Misawa, S. Nakaoka, Y. Koyanagi, A.S. Perelson, J.W. Schoggins, S. Iwami, K. Sato. Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection, PLOS Computational Biology, 18(4): e1010053 (2022). (†Equal contribution)
  • N. Yamamoto†, Y. Koizumi†, S. Tsuzuki†, K. Ejima, M. Takano, S. Iwami\*, D. Mizushima\*, S. Oka\*. Evaluating the cost-effectiveness of a pre-exposure prophylaxis program for HIV prevention for men who have sex with men in Japan, Scientific Reports, 12:3088 (2022). (†Equal contribution)
  • R. Hayashi, S. Iwami, and Y. Iwasa. Escaping stochastic extinction of mutant virus: Temporal pattern of emergence of drug resistance within a host, Journal of Theoretical Biology, 537:111029 (2022).


  • M. Akao, J. Woo, S. Iwami, and S. Iwanami. Detection of significant antiviral drug effects on COVID-19 using viral load and PCR-positive rate in randomized controlled trials, Translational and Regulatory Sciences, 3(1):8-88 (2021).
  • K. Matsuda, S. Islam, T. Takada, K. Tsuchiya, B.J. Yang Tan, S. Hattori, H. Katsuya, K. Kitagawa, K.S. Kim, M. Matsuo, K. Sugata, N.S. Delino, H. Gatanaga, K. Yoshimura, S. Matsushita, H. Mitsuya, S. Iwami, Y. Satou, and K. Maeda. A widely distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in vitro, Cell Reports Methods, 1(8):100122 (2021).
  • K. S. Kim†, S. Iwanami†, T. Oda, Y. Fujita, K. Kuba, T. Miyazaki, K. Ejima‡, S. Iwami‡. Incomplete antiviral treatment may induce longer durations of viral shedding during SARS-CoV-2 infection, Life Science Alliance, 10:e202101049 (2021). (†,‡Equal contribution)
  • Y. D. Jeong†, K. Ejima†, K. S. Kim†, S. Iwanami, A. I. Bento, Y. Fujita, I. H. Jung, K. Aihara, K. Watashi, T. Miyazaki, T. Wakita, S. Iwami, M. Ajelli. Revisiting the guidelines for ending isolation for COVID-19 patients, eLife, 10:e69340 (2021). (†Equal contribution)
  • S. Iwanami†, K. Ejima†, K.S. Kim, K. Noshita, Y. Fujita, T. Miyazaki, S. Kohno, Y. Miyazaki, S. Morimoto, S. Nakaoka, Y. Koizumi, Y. Asai, K. Aihara, K. Watashi, R. N. Thompson, K. Shibuya, K. Fujiu, A.S. Perelson‡, S. Iwami‡, T. Wakita. Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study, PLOS Medicine, 18(7):e1003660 (2021). (†,‡Equal contribution)
  • K. Shionoya, M. Yamasaki, S. Iwanami, Y. Ito, S. Fukushi, H. Ohashi, W. Saso, T. Tanaka, S. Aoki, K. Kuramochi, S. Iwami, Y. Takahashi, T. Suzuki, M. Muramatsu, M. Takeda, T. Wakita, K. Watashi. Mefloquine, a Potent anti-Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2) drug as an entry inhibitor in vitro, Frontiers in Microbiology, 12: 651403 (2021).
  • K. Ejima†, K. Su. Kim†, S. Iwanami†, Y. Fujita, M. Li, R. S. Zoh, K. Aihara, T. Miyazaki, T. Wakita and S. Iwami. Time variation in the probability of failing to detect a case of PCR testing for SARS-CoV-2 as estimated from a viral dynamics model, Journal of the Royal Society Interface, 18: 20200947 (2021). (†Equal contribution)
  • H. Ohashi†, K. Watashi†, W. Saso†, K. Shionoya, S. Iwanami, T. Hirokawa, T. Shirai, S. Kanaya, Y. Ito, K. S. Kim, T. Nomura, T. Suzuki, K. Nishioka, S. Ando, K. Ejima, Y. Koizumi, T. Tanaka, S. Aoki, K. Kuramochi, T. Suzuki, T. Hashiguchi, K. Maenaka, T. Matano, M. Muramatsu, M. Saijo, K. Aihara, S. Iwami, M. Takeda, J. A. McKeating, T. Wakita. Potential anti-COVID-19 agents, Cepharanthine and Nelfinavir, and their usage for combination treatment, iScience, 24(4):102367 (2021). (†Equal contribution)
  • K. Ejima, K.S. Kim, C. Ludema, A.I. Bento, S. Iwanami, Y. Fujita, H. Ohashi, Y. Koizumi, K. Watashi, K. Aihara, H. Nishiura, and S. Iwami. Estimation of the incubation period of COVID-19 using viral load data, Epidemics, 35:100454 (2021). (Equal contribution)
  • 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‡. 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-2, PLOS Biology, 19(3):e3001128. (2021). (†,‡Equal contribution).
  • K. Ejima†, Y. Koizumi, N. Yamamoto, M. Rosenberg, C. Ludema, A.I. Bento, D. Yoneoka, S. Ichikawa, D. Mizushima and S. Iwami†. HIV testing by public health centers and municipalities and new HIV cases during the COVID-19 pandemic in Japan, Journal of Acquired Immune Deficiency Syndromes, 87(2):e182-e187 (2021). (†Equal contribution).
  • Y. Kakizoe†, Y. Koizumi†, Y. Ikoma, H. Ohashi, T. Wakita, S. Iwami‡, K. Watashi‡. Required concentration index quantifies effective drug combinations against hepatitis C virus infection, Theoretical Biology and Medical Modelling, 18(1):4 (2021) (†,‡Equal contribution).
  • T. Oda, K.S. Kim, Y. Fujita, Y. Ito, T. Miura, S. Iwami. Quantifying antiviral effects against simian/human immunodeficiency virus induced by host immune response, Journal of Theoretical Biology, 509:110493 (2021).


  • K.S. Kim†, Y. Yamamoto, S. Nakaoka, K. Tomonaga, S. Iwami†, T. Honda. Modeling Borna disease virus in vitro spread reveals the mode of antiviral effect conferred by an endogenous bornavirus-like element, Journal of Virology, 94:e01204-20 (2020). (†Equal contribution).
  • K.S. Kim, T. Kondoh, Y. Asai, A. Takada, S. Iwami. Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule, PLOS Computational Biology, 16(9):e1007612 (2020).
  • 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†. Should a viral genome stay in the host cell or leave? A quantitative dynamics study of how hepatitis C virus deals with this dilemma, PLOS Biology, 18:e3000562 (2020). (†Equal contribution).
  • T. Kurusu, KS. Kim, Y. Koizumi, S. Nakaoka, K. Ejima, N. Misawa, Y. Koyanagi, K. Sato, S. Iwami. Quantifying the antiviral effect of APOBEC3 on HIV-1 infection in humanized mouse model, Journal of Theoretical Biology, 498:110295 (2020)