29

Department of Microbiology and Immunology

Division of Systems Virology
システムウイルス学分野

Professor
Kei Sato, Ph.D.
Assistant Professor
Jumpei Ito, Ph.D., D.V.M.
Project Assistant Professor Yu Kaku, Ph.D., M.D.

教 授助 教
特任助教

博士（医学） 佐博士（理学） 伊博士（医学） 郭藤
東潤

佳平
悠The aim of our laboratory is to expand the knowledge and methodology on virology,
which were unable to shed light on by conventional experimental approach alone.
To investigate the co-evolutionary relationship between viruses and hosts, weperform bioinformatic and molecular phylogenetic analyses as well as experimental
virology. The interdisciplinary investigations based on experimental virology andother scientific fields/methods will pioneer a new science for deeply understanding
infectious diseases.

1.  Understanding the evolution of SARS-CoV-2
Yu Kaku, Keiya Uriu, Yusuke Kosugi, Shigeru Fujita, Luo Chen, Jarel Elgin Tolentino, Lin Pan, Arnon
Plianchaisuk, Ziyi Guo, Alfredo Amolong Hinay, Jr.,
Kaoru Usui, Wilaiporn Saikruang, Wenye Li, KahoOkumura, Naoko Misawa, Mai Suganami, Adam
Patrick Strange, Naomi Ohsumi, Shiho Tanaka,Mika Chiba, Ryo Yoshimura, Kyoko Yasuda, KeikoIida, Jumpei Ito, Kei Sato.
Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is a causative agent of coronavirus disease 2019 (COVID-19). SARS-CoV-2 emerged at theend of 2019 and has spread all over the world. Since
then, more than 770 million people have been infectedwith this virus and more than 7 million people havedied of COVID-19, meaning that COVID-19 is ongoing pandemic and a most urgent and crucial problem
in the current human society. To proceed and accelerate COVID-19-releated researches in Japan, welaunched a consortium, called “The Genotype to Phenotype Japan (G2P-Japan) Consortium” in January
2021. As of December 2023, more than 10 principal
investigators in Japan and Czech Republic join thisconsortium and proceed fruitful collaboration. We
aim to elucidate the virological characteristics of theSARS-CoV-2 variants continuously emerging in theworld.
2.  Predicting and understanding virus epidemics
and evolution
Jumpei Ito, Arnon Plianchaisuk, Jarel Elgin Tolentino, Mai Suganami, Adam Patrick Strange, Kaho
Okumura, Kei Sato
During the COVID-19 pandemic, extensive viralgenomic surveillance has been conducted, enabling
us to track the epidemic and evolution of SARS-CoV-2
in ultra-high resolution. Leveraging this big data, weare establishing theoretical and technical frameworks
to understand and predict the epidemic and evolution of viruses. This year, we have developed a Bayesian hierarchical model to predict the transmissibilityof SARS-CoV-2 variants based on mutation patterns
in the spike protein (Ito et al., 2023, Nat. Commun.).
Additionally, we showed that the increased transmissibility observed during the evolution of the Omicron
variant can be explained by the acquisition of a small
number of mutations in spike protein.

30Publications
Keiya Uriu, Jumpei Ito, Jiri Zahradnik, Shigeru Fujita,
Yusuke Kosugi, Gideon Schreiber, Genotype toPhenotype Japan (G2P-Japan) Consortium, Kei
Sato. Enhanced Transmissibility, Infectivity, andImmune Resistance of the SARS-CoV-2 Omicron
XBB.1.5 Variant. Lancet Infectious Diseases
23(3):280–81 (2023).
Shiho Torii, Kwang Su Kim, Jun Koseki, Rigel Suzuki,Shoya Iwanami, Yasuhisa Fujita, Yong Dam Jeong,Jumpei Ito, Hiroyuki Asakura, Mami Nagashima,Kenji Sadamasu, Kazuhisa Yoshimura, Genotype toPhenotype Japan (G2P-Japan) Consortium, Kei
Sato, Yoshiharu Matsuura, Teppei Shimamura,
Shingo Iwami, Takasuke Fukuhara. Increased Flexibility of the SARS-CoV-2 RNA-Binding Site Causes Resistance to Remdesivir. PLoS Pathogens
19(3):e1011231 (2023).
Jumpei Ito, Rigel Suzuki, Keiya Uriu, Yukari Itakura,Jiri Zahradnik, Kanako Terakado Kimura, SayakaDeguchi, Lei Wang, Spyros Lytras, Tomokazu Tamura, Izumi Kida, Hesham Nasser, Maya Shofa,
Mst Monira Begum, Masumi Tsuda, Yoshitaka Oda,Tateki Suzuki, Jiei Sasaki, Kaori Sasaki-Tabata,
Shigeru Fujita, Kumiko Yoshimatsu, Hayato Ito,
Naganori Nao, Hiroyuki Asakura, Mami Nagashima, Kenji Sadamasu, Kazuhisa Yoshimura, YukiYamamoto, Tetsuharu Nagamoto, Jin Kuramochi,
Gideon Schreiber, Genotype to Phenotype Japan(G2P-Japan) Consortium, Akatsuki Saito, KeitaMatsuno, Kazuo Takayama, Takao Hashiguchi,Shinya Tanaka, Takasuke Fukuhara, Terumasa Ikeda, Kei Sato. Convergent Evolution of SARS-CoV-2
Omicron Subvariants Leading to the Emergence ofBQ.1.1 Variant. Nature Communications 14(1):2671(2023).
Tomokazu Tamura, Jumpei Ito, Keiya Uriu, Jiri Zahradnik, Izumi Kida, Yuki Anraku, Hesham Nasser,Maya Shofa, Yoshitaka Oda, Spyros Lytras, Naganori Nao, Yukari Itakura, Sayaka Deguchi, RigelSuzuki, Lei Wang, Mst Monira Begum, Shunsuke
Kita, Hisano Yajima, Jiei Sasaki, Kaori Sasaki-Tabata, Ryo Shimizu, Masumi Tsuda, Yusuke Kosugi,Shigeru Fujita, Lin Pan, Daniel Sauter, Kumiko
Yoshimatsu, Saori Suzuki, Hiroyuki Asakura,
Mami Nagashima, Kenji Sadamasu, Kazuhisa
Yoshimura, Yuki Yamamoto, Tetsuharu Nagamoto,
Gideon Schreiber, Katsumi Maenaka, Genotype toPhenotype Japan (G2P-Japan) Consortium, Takao
Hashiguchi, Terumasa Ikeda, Takasuke Fukuhara,
Akatsuki Saito, Shinya Tanaka, Keita Matsuno, Kazuo Takayama, Kei Sato. Virological Characteristicsof the SARS-CoV-2 XBB Variant Derived from Recombination of Two Omicron Subvariants. NatureCommunications 14(1):2800 (2023).
Daichi Yamasoba, Keiya Uriu, Arnon Plianchaisuk,Yusuke Kosugi, Lin Pan, Jiri Zahradnik, Genotypeto Phenotype Japan (G2P-Japan) Consortium, Jum-pei Ito, Kei Sato. Virological Characteristics of theSARS-CoV-2 Omicron XBB.1.16 Variant. Lancet Infectious Diseases 23(6):655–56 (2023).
Tomokazu Tamura, Daichi Yamasoba, Yoshitaka Oda,
Jumpei Ito, Tomoko Kamasaki, Naganori Nao, RinaHashimoto, Yoichiro Fujioka, Rigel Suzuki, LeiWang, Hayato Ito, Yukie Kashima, Izumi Kimura,Mai Kishimoto, Masumi Tsuda, Hirofumi Sawa,Kumiko Yoshimatsu, Yuki Yamamoto, Tetsuharu
Nagamoto, Jun Kanamune, Yutaka Suzuki, Yusuke
Ohba, Genotype to Phenotype Japan (G2P-Japan)
Consortium, Isao Yokota, Keita Matsuno, Kazuo
Takayama, Shinya Tanaka, Kei Sato, Takasuke
Fukuhara. Comparative Pathogenicity of SARSCoV-2 Omicron Subvariants Including BA.1, BA.2,and BA.5. Communications Biology 6(1):772(2023).
Shigeru Fujita, Keiya Uriu, Lin Pan, Naganori Nao,Koshiro Tabata, Mai Kishimoto, Yukari Itakura, Hirofumi Sawa, Izumi Kida, Tomokazu Tamura, Genotype to Phenotype Japan (G2P-Japan) Consortium, Takasuke Fukuhara, Jumpei Ito, Keita Matsuno,Kei Sato. Impact of Imprinted Immunity Inducedby mRNA Vaccination in an Experimental Animal
Model. Journal of Infectious Diseases 228(8):1060–
65 (2023).
Shigeru Fujita, Yusuke Kosugi, Izumi Kimura, Kenzo
Tokunaga, Genotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Kei Sato. Determination of the Factors Responsible for the Tropism ofSARS-CoV-2-Related Bat Coronaviruses to Rhinolophus Bat ACE2. Journal of Virology e0099023(2023).
Izumi Kimura, Daichi Yamasoba, Hesham Nasser,
Hayato Ito, Jiri Zahradnik, Jiaqi Wu, Shigeru Fujita,Keiya Uriu, Jiei Sasaki, Tomokazu Tamura, RigelSuzuki, Sayaka Deguchi, Arnon Plianchaisuk, Kumiko Yoshimatsu, Yasuhiro Kazuma, Shuya Mitoma, Gideon Schreiber, Hiroyuki Asakura, Mami
Nagashima, Kenji Sadamasu, Kazuhisa Yoshimura,
Akifumi Takaori-Kondo, Genotype to Phenotype
Japan (G2P-Japan) Consortium, Jumpei Ito, Kotaro
Shirakawa, Kazuo Takayama, Takashi Irie, TakaoHashiguchi, So Nakagawa, Takasuke Fukuhara,Akatsuki Saito, Terumasa Ikeda, Kei Sato. Multiple
Mutations of SARS-CoV-2 Omicron BA.2 VariantOrchestrate Its Virological Characteristics. Journalof Virology e0101123 (2023).
Yu Kaku, Yusuke Kosugi, Keiya Uriu, Jumpei Ito, Alfredo A. Hinay, Jin Kuramochi, Kenji Sadamasu,Kazuhisa Yoshimura, Hiroyuki Asakura, Mami Nagashima, Genotype to Phenotype Japan (G2P-Japan) Consortium, Kei Sato. Antiviral Efficacy of theSARS-CoV-2 XBB Breakthrough Infection Sera
against Omicron Subvariants Including EG.5. Lancet Infectious Diseases 23(10):e395–96 (2023).
Hirofumi Aso, Jumpei Ito, Haruka Ozaki, Yukie

31Kashima, Yutaka Suzuki, Yoshio Koyanagi, Kei
Sato. Single-Cell Transcriptome Analysis Illuminating the Characteristics of Species-Specific Innate
Immune Responses against Viral Infections. GigaScience 12:giad086 (2022).
Keiya Uriu, Jumpei Ito, Yusuke Kosugi, Yuri L. Tanaka, Yuka Mugita, Ziyi Guo, Alfredo A. Hinay, Olivia Putri, Yoonjin Kim, Ryo Shimizu, Mst MoniraBegum, Michael Jonathan, Genotype to Phenotype
Japan (G2P-Japan) Consortium, Akatsuki Saito,Terumasa Ikeda, Kei Sato. Transmissibility, Infectivity, and Immune Evasion of the SARS-CoV-2
BA.2.86 Variant. Lancet Infectious Diseases
23(11):e460–61 (2023).
Martin Müller, Alexandra Herrmann, Shigeru Fujita,Keiya Uriu, Carolin Kruth, Adam Strange, Jan E.
Kolberg, Markus Schneider, Jumpei Ito, Marcel A.
Müller, Christian Drosten, Armin Ensser, Genotype
to Phenotype Japan (G2P-Japan) Consortium, KeiSato, Daniel Sauter. ORF3c Is Expressed in SARSCoV-2-Infected Cells and Inhibits Innate Sensingby Targeting MAVS. EMBO Reports 24(12):e57137(2023).
Yuuka Masuda, Hesham Nasser, Jiri Zahradnik,
Shuya Mitoma, Ryo Shimizu, Kayoko Nagata, Akifumi Takaori-Kondo, Gideon Schreiber, The Genotype to Phenotype Japan (G2P-Japan) Consortium,
Kotaro Shirakawa, Akatsuki Saito, Terumasa Ikeda,
Jumpei Ito, Kei Sato. Characterization of the evolutionary and virological aspects of mutations in thereceptor binding motif of the SARS-CoV-2 spike
protein. Frontiers in Virology 3:1328229 (2023).
Yusuke Kosugi, Arnon Plianchaisuk, Olivia Putri,Keiya Uriu, Yu Kaku, Alfredo A. Hinay, Luo Chen,Jin Kuramochi, Kenji Sadamasu, Kazuhisa Yoshimura, Hiroyuki Asakura, Mami Nagashima, TheGenotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Kei Sato. Virological Characteristics of the SARS-CoV-2 Omicron HK.3 Variant Harboring the FLip Substitution. Lancet Microbes2666-5247 (23):00373-7 (2024).
Yusuke Kosugi, Yu Kaku, Alfredo A. Hinay, Ziyi
Guo, Keiya Uriu, Minoru Kihara, Fumitake Saito,Yoshifumi Uwamino, Jin Kuramochi, Kotaro Shirakawa, Akifumi Takaori-Kondo, The Genotype toPhenotype Japan (G2P-Japan) Consortium, Kei
Sato. Antiviral Humoral Immunity against SARSCoV-2 Omicron Subvariants Induced by XBB.1.5
Monovalent Vaccine in Infection-Naïve and XBB-Infected Individuals. Lancet Infectious Diseases 24(3):e147-48 (2024).
Yu Kaku, Kaho Okumura, Miguel Padilla-Blanco,
Yusuke Kosugi, Keiya Uriu, Alfredo A. Hinay, LuoChen, Arnon Plianchaisuk, Kouji Kobiyama, Ken J.
Ishii, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jiri Zahradnik, Jumpei Ito, Kei
Sato. Virological Characteristics of the SARS-CoV-2
JN.1 Variant. Lancet Infectious Diseases 24 (2):e82(2024).