Induction of IGHV3-53 public antibodies with broadly neutralising activity against SARS-CoV-2 including Omicron subvariants in a Delta breakthrough infection caseResearch in context

Authors: Takeo Kuwata, Yu Kaku, Shashwata Biswas, Kaho Matsumoto, Mikiko Shimizu, Yoko Kawanami, Ryuta Uraki, Kyo Okazaki, Rumi Minami, Yoji Nagasaki, Mami Nagashima, Isao Yoshida, Kenji Sadamasu, Kazuhisa Yoshimura, Mutsumi Ito, Maki Kiso, Seiya Yamayoshi, Masaki Imai, Terumasa Ikeda, Kei Sato, Mako Toyoda, Takamasa Ueno, Takako Inoue, Yasuhito Tanaka, Kanako Tarakado Kimura, Takao Hashiguchi, Yukihiko Sugita, Takeshi Noda, Hiroshi Morioka, Yoshihiro Kawaoka, Shuzo Matsushita, Jumpei Ito, Naoko Misawa, Arnon Plianchaisuk, Ziyi Guo, Alfredo Hina, Jr., Keiya Uriu, Kaoru Usui, Wilaiporn Saikruang, Spyridon Lytras, Ryo Yoshimura, Shusuke Kawakubo, Luca Nishimura, Yusuke Kosugi, Shigeru Fujita, Luo Chen, Jarel Elgin M. Tolentino, Lin Pan, Wenye Li, Maximilian Stanley Yo, Kio Horinaka, Mai Suganami, Adam P. Strange, Mika Chiba, Keiko Iida, Naomi Ohsumi, Kaho Okumura, Shiho Tanaka, Eiko Ogawa, Kyoko Yasuda, Tsuki Fukuda, Rina Osujo, Takasuke Fukuhara, Tomokazu Tamura, Rigel Suzuki, Saori Suzuki, Hayato Ito, Keita Matsuno, Hirofumi Sawa, Naganori Nao, Shinya Tanaka, Masumi Tsuda, Lei Wang, Yoshikata Oda, Zannatul Ferdous, Kenji Shishido, Keita Mizuma, Isshu Kojima, Jingshu Li, Tomoya Tsubo, Shuhei Tsujino, So Nakagawa, Kotaro Shirakawa, Akifumi Takaori-Kondo, Kayoko Nagata, Ryosuke Nomura, Yoshihito Horisawa, Yusuke Tashiro, Yugo Kawai, Kazuo Takayama, Rina Hashimoto, Sayaka Deguchi, Yukio Watanabe, Ayaka Sakamoto, Naoko Yasuhara, Tateki Suzuki, Kanako Kimura, Jiei Sasaki, Yukari Nakajima, Hisano Yajima, Yoshitaka Nakata, Hiroki Futatsusako, Takashi Irie, Ryoko Kawabata, Kaori Tabata, Hesham Nasser, Ryo Shimizu, MST Monira Begum, Michael Jonathan, Yuka Mugita, Otowa Takahashi, Kimiko Ichihara, Chihiro Motozono, Sharee Leong, Akatsuki Saito, Maya Shofa, Yuki Shibatani, Tomoko Nishiuchi, Hiroyuki Asakura, Jiri Zahradnik, Prokopios Andrikopoulos, Miguel Padilla-Blanco, Aditi Konar

Source: EBioMedicine, Vol 110, Iss , Pp 105439- (2024)

Subject Terms: SARS-CoV-2, Neutralising antibody, Variant, Public antibody, Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396424004754; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/e91f95c836a440f4825df3e5b712b6d7

Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant

Authors: Tomokazu Tamura, Takashi Irie, Sayaka Deguchi, Hisano Yajima, Masumi Tsuda, Hesham Nasser, Keita Mizuma, Arnon Plianchaisuk, Saori Suzuki, Keiya Uriu, Mst Monira Begum, Ryo Shimizu, Michael Jonathan, Rigel Suzuki, Takashi Kondo, Hayato Ito, Akifumi Kamiyama, Kumiko Yoshimatsu, Maya Shofa, Rina Hashimoto, Yuki Anraku, Kanako Terakado Kimura, Shunsuke Kita, Jiei Sasaki, Kaori Sasaki-Tabata, Katsumi Maenaka, Naganori Nao, Lei Wang, Yoshitaka Oda, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Terumasa Ikeda, Akatsuki Saito, Keita Matsuno, Jumpei Ito, Shinya Tanaka, Kei Sato, Takao Hashiguchi, Kazuo Takayama, Takasuke Fukuhara

Source: Nature Communications, Vol 15, Iss 1, Pp 1-17 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b5a5c3770f4043cdb31e4db8570c052a

Potential Role of APOBEC3 Family Proteins in SARS-CoV-2 Replication

Authors: MST Monira Begum, Ayub Bokani, Samiul Alam Rajib, Mohadeseh Soleimanpour, Yosuke Maeda, Kazuhisa Yoshimura, Yorifumi Satou, Diako Ebrahimi, Terumasa Ikeda

Source: Viruses, Vol 16, Iss 7, p 1141 (2024)

Subject Terms: APOBEC3 family proteins, SARS-CoV-2, deaminase-independent mechanism, THP-1, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/16/7/1141; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/1ee127e91c944350a970a5e9d6cd01ea

Virological characteristics correlating with SARS-CoV-2 spike protein fusogenicity

Authors: MST Monira Begum, Kimiko Ichihara, Otowa Takahashi, Hesham Nasser, Michael Jonathan, Kenzo Tokunaga, Isao Yoshida, Mami Nagashima, Kenji Sadamasu, Kazuhisa Yoshimura, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Kei Sato, Terumasa Ikeda, Keita Matsuno, Naganori Nao, Hirofumi Sawa, Shinya Tanaka, Masumi Tsuda, Lei Wang, Yoshikata Oda, Zannatul Ferdous, Kenji Shishido, Takasuke Fukuhara, Tomokazu Tamura, Rigel Suzuki, Saori Suzuki, Hayato Ito, Jumpei Ito, Yu Kaku, Naoko Misawa, Arnon Plianchaisuk, Ziyi Guo, Alfredo Jr. Hinay, Keiya Uriu, Yusuke Kosugi, Shigeru Fujita, Jarel Elgin Mendoza Tolentino, Luo Chen, Lin Pan, Mai Suganami, Mika Chiba, Ryo Yoshimura, Kyoko Yasuda, Keiko Iida, Naomi Ohsumi, Adam Patrick Strange, Hiroyuki Asakura, So Nakagawa, Akifumi Takaori-Kondo, Kotaro Shirakawa, Kayoko Nagata, Ryosuke Nomura, Yoshihito Horisawa, Yusuke Tashiro, Yugo Kawai, Kazuo Takayama, Rina Hashimoto, Sayaka Deguchi, Yukio Watanabe, Ayaka Sakamoto, Naoko Yasuhara, Takao Hashiguchi, Tateki Suzuki, Kanako Kimura, Jiei Sasaki, Yukari Nakajima, Hisano Yajima, Takashi Irie, Ryoko Kawabata, Kaori Tabata, Ryo Shimizu, Yuka Mugita, Takamasa Ueno, Chihiro Motozono, Mako Toyoda, Akatsuki Saito, Maya Shofa, Yuki Shibatani, Tomoko Nishiuchi

Source: Frontiers in Virology, Vol 4 (2024)

Subject Terms: SARS-CoV-2, fusogenicity, pathogenicity, S1/S2 cleavage efficiency, plaque size, pseudoviral infectivity, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fviro.2024.1353661/full; https://doaj.org/toc/2673-818X

Access URL: https://doaj.org/article/5d2678f123154258a7ff9b66e6f6851e

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

Authors: Jumpei Ito, Rigel Suzuki, Keiya Uriu, Yukari Itakura, Jiri Zahradnik, Kanako Terakado Kimura, Sayaka Deguchi, 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, Yuki Yamamoto, Tetsuharu Nagamoto, Jin Kuramochi, Gideon Schreiber, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Akatsuki Saito, Keita Matsuno, Kazuo Takayama, Takao Hashiguchi, Shinya Tanaka, Takasuke Fukuhara, Terumasa Ikeda, Kei Sato

Source: Nature Communications, Vol 14, Iss 1, Pp 1-20 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/3a5b69cf1c574de1a780fa1122cc5cad

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Authors: 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, Rigel Suzuki, 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, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Takao Hashiguchi, Terumasa Ikeda, Takasuke Fukuhara, Akatsuki Saito, Shinya Tanaka, Keita Matsuno, Kazuo Takayama, Kei Sato

Source: Nature Communications, Vol 14, Iss 1, Pp 1-20 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/dfbe0e4be21c40ac852c2c02d183fb39

Usefulness of K-line in predicting prognosis of laminoplasty for cervical spondylotic myelopathy

Authors: Terumasa Ikeda, Hiroshi Miyamoto, Masao Akagi

Source: BMC Musculoskeletal Disorders, Vol 24, Iss 1, Pp 1-6 (2023)

Subject Terms: Cervical spondylotic myelopathy, K-line, Cervical spinal kyphosis, Diseases of the musculoskeletal system, RC925-935

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2474

Access URL: https://doaj.org/article/6d092e3ce7cb440487d03661149ae03b

APOBEC3 family proteins as drivers of virus evolution

Authors: Michael Jonathan, Terumasa Ikeda

Source: Frontiers in Virology, Vol 3 (2023)

Subject Terms: APOBEC3, C-to-U/G-to-A mutations, deamination, retroviruses, DNA viruses, RNA viruses, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fviro.2023.1332010/full; https://doaj.org/toc/2673-818X

Access URL: https://doaj.org/article/cec99a4848714854b29c4790ee1fba4c

Characterization of the evolutionary and virological aspects of mutations in the receptor binding motif of the SARS-CoV-2 spike protein

Authors: 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

Source: Frontiers in Virology, Vol 3 (2023)

Subject Terms: SARS-CoV-2, evolution, receptor binding motif, variants of concerns, epidemic dynamics modeling, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fviro.2023.1328229/full; https://doaj.org/toc/2673-818X

Access URL: https://doaj.org/article/ba57fdf08fff498fb71144b8613e9fd2

APOBEC3 degradation is the primary function of HIV-1 Vif determining virion infectivity in the myeloid cell line THP-1

Authors: Terumasa Ikeda, Ryo Shimizu, Hesham Nasser, Michael A. Carpenter, Adam Z. Cheng, William L. Brown, Daniel Sauter, Reuben S. Harris

Source: mBio, Vol 14, Iss 4 (2023)

Subject Terms: HIV-1, APOBEC3, G-to-A mutations, deaminase-dependent mechanism, deaminase-independent mechanism, Vif, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/3cc59ec71ecd4139a30a3d0bbeed458b

Monitoring fusion kinetics of viral and target cell membranes in living cells using a SARS-CoV-2 spike-protein-mediated membrane fusion assay

Authors: Hesham Nasser, Ryo Shimizu, Jumpei Ito, Akatsuki Saito, Kei Sato, Terumasa Ikeda, Keita Matsuno, Naganori Nao, Hirofumi Sawa, Mai Kishimoto, Shinya Tanaka, Masumi Tsuda, Lei Wang, Yoshikata Oda, Marie Kato, Zannatul Ferdous, Hiromi Mouri, Kenji Shishido, Takasuke Fukuhara, Tomokazu Tamura, Rigel Suzuki, Hayato Ito, Daichi Yamasoba, Izumi Kimura, Naoko Misawa, Keiya Uriu, Yusuke Kosugi, Shigeru Fujita, Mai Suganami, Mika Chiba, Ryo Yoshimura, So Nakagawa, Jiaqi Wu, Akifumi Takaori-Kondo, Kotaro Shirakawa, Kayoko Nagata, Yasuhiro Kazuma, Ryosuke Nomura, Yoshihito Horisawa, Yusuke Tashiro, Yugo Kawai, Takashi Irie, Ryoko Kawabata, MST Monira Begum, Otowa Takahashi, Kimiko Ichihara, Takamasa Ueno, Chihiro Motozono, Mako Toyoda, Yuri L. Tanaka, Erika P. Butlertanaka, Maya Shofa, Kazuo Takayama, Rina Hashimoto, Sayaka Deguchi, Takao Hashiguchi, Tateki Suzuki, Kanako Kimura, Jiei Sasaki, Yukari Nakajima, Kaori Tabata

Source: STAR Protocols, Vol 3, Iss 4, Pp 101773- (2022)

Subject Terms: Cell-based Assays, Microbiology, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166722006530; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/29370f9faa774a2b998e2833a7d82fe9

The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant

Authors: Izumi Kimura, Daichi Yamasoba, Hesham Nasser, Jiri Zahradnik, Yusuke Kosugi, Jiaqi Wu, Kayoko Nagata, Keiya Uriu, Yuri L. Tanaka, Jumpei Ito, Ryo Shimizu, Toong Seng Tan, Erika P. Butlertanaka, Hiroyuki Asakura, Kenji Sadamasu, Kazuhisa Yoshimura, Takamasa Ueno, Akifumi Takaori-Kondo, Gideon Schreiber, Mako Toyoda, Kotaro Shirakawa, Takashi Irie, Akatsuki Saito, So Nakagawa, Terumasa Ikeda, Kei Sato

Source: iScience, Vol 25, Iss 12, Pp 105720- (2022)

Subject Terms: Molecular biology, Virology, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004222019939; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/68c61f21418441b58860e4f5398388dc

Radiation-Induced Osteosarcoma in the Cervical Spine after Definitive Radiotherapy for Esophageal Cancer: A Case Report

Authors: Kensuke Toriumi, Hiroshi Miyamoto, Terumasa Ikeda, Masao Akagi

Source: Spine Surgery and Related Research, Vol 4, Iss 4, Pp 374-376 (2020)

Subject Terms: radiation-induced osteosarcoma, cervical spine, definitive radiotherapy, Surgery, RD1-811

File Description: electronic resource

Relation: https://www.jstage.jst.go.jp/article/ssrr/4/4/4_2019-0127/_pdf/-char/en; https://doaj.org/toc/2432-261X

Access URL: https://doaj.org/article/1d51831bd3454bd692fd64ca03399be9

Resistance of SARS-CoV-2 variants to neutralization by antibodies induced in convalescent patients with COVID-19

Authors: Yu Kaku, Takeo Kuwata, Hasan Md Zahid, Takao Hashiguchi, Takeshi Noda, Noriko Kuramoto, Shashwata Biswas, Kaho Matsumoto, Mikiko Shimizu, Yoko Kawanami, Kazuya Shimura, Chiho Onishi, Yukiko Muramoto, Tateki Suzuki, Jiei Sasaki, Yoji Nagasaki, Rumi Minami, Chihiro Motozono, Mako Toyoda, Hiroshi Takahashi, Hiroto Kishi, Kazuhiko Fujii, Tsuneyuki Tatsuke, Terumasa Ikeda, Yosuke Maeda, Takamasa Ueno, Yoshio Koyanagi, Hajime Iwagoe, Shuzo Matsushita

Source: Cell Reports, Vol 36, Iss 2, Pp 109385- (2021)

Subject Terms: COVID-19, SARS-CoV-2, neutralizing antibody, mAb, variant, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S221112472100783X; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/f1a9d41ea6c74255acbd2cbf6031a0bf

Potential Utilization of APOBEC3-Mediated Mutagenesis for an HIV-1 Functional Cure

Authors: Terumasa Ikeda, Yuan Yue, Ryo Shimizu, Hesham Nasser

Source: Frontiers in Microbiology, Vol 12 (2021)

Subject Terms: APOBEC3-mediated mutagenesis, genetic factors, A3 expression, A3-interacting proteins, adaptive immunity, Vif inhibitors, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2021.686357/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/feff802e382648b491bedb363c0fec5f

A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans.

Authors: Yusuke Nakano, Keisuke Yamamoto, Mahoko Takahashi Ueda, Andrew Soper, Yoriyuki Konno, Izumi Kimura, Keiya Uriu, Ryuichi Kumata, Hirofumi Aso, Naoko Misawa, Shumpei Nagaoka, Soma Shimizu, Keito Mitsumune, Yusuke Kosugi, Guillermo Juarez-Fernandez, Jumpei Ito, So Nakagawa, Terumasa Ikeda, Yoshio Koyanagi, Reuben S Harris, Kei Sato

Source: PLoS Pathogens, Vol 16, Iss 9, p e1008812 (2020)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/d550843508e54cdeb238ee8a7ee1d1a4

Natural APOBEC3C variants can elicit differential HIV-1 restriction activity

Authors: Brett D. Anderson, Terumasa Ikeda, Seyed Arad Moghadasi, Amber St. Martin, William L. Brown, Reuben S. Harris

Source: Retrovirology, Vol 15, Iss 1, Pp 1-11 (2018)

Subject Terms: APOBEC3C, DNA cytosine deaminase, HIV-1, Human genetic variation, Innate immunity, Retrovirus restriction factor, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12977-018-0459-5; https://doaj.org/toc/1742-4690

Access URL: https://doaj.org/article/7f8c1f7bd80544c3a7e4d7d3c3f3ac67

Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease

Authors: Diako Ebrahimi, Christopher M. Richards, Michael A. Carpenter, Jiayi Wang, Terumasa Ikeda, Jordan T. Becker, Adam Z. Cheng, Jennifer L. McCann, Nadine M. Shaban, Daniel J. Salamango, Gabriel J. Starrett, Jairam R. Lingappa, Jeongsik Yong, William L. Brown, Reuben S. Harris

Source: Nature Communications, Vol 9, Iss 1, Pp 1-11 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ea3b48a2ed974a7c8e6b38190a93470e

HIV-1 Vif Triggers Cell Cycle Arrest by Degrading Cellular PPP2R5 Phospho-regulators

Authors: Daniel J. Salamango, Terumasa Ikeda, Seyed Arad Moghadasi, Jiayi Wang, Jennifer L. McCann, Artur A. Serebrenik, Diako Ebrahimi, Matthew C. Jarvis, William L. Brown, Reuben S. Harris

Source: Cell Reports, Vol 29, Iss 5, Pp 1057-1065.e4 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124719312549; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/c1e98fbb6c6d4901afc605ca1d57b854

HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G.

Authors: Terumasa Ikeda, Menelaos Symeonides, John S Albin, Ming Li, Markus Thali, Reuben S Harris

Source: PLoS Pathogens, Vol 14, Iss 4, p e1007010 (2018)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5931688?pdf=render; https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/08693200b7e74366a9587add3def27ac