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3. Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5

Author

Tamura, Tomokazu, Yamasoba, Daichi, Oda, Yoshitaka, Ito, Jumpei, Kamasaki, Tomoko, Nao, Naganori, Hashimoto, Rina, Fujioka, Yoichiro, Suzuki, Rigel, Wang, Lei, Ito, Hayato, Kashima, Yukie, Kimura, Izumi, Kishimoto, Mai, Tsuda, Masumi, Sawa, Hirofumi, Yoshimatsu, Kumiko, Yamamoto, Yuki, Nagamoto, Tetsuharu, Kanamune, Jun, Suzuki, Yutaka, Ohba, Yusuke, Yokota, Isao, Matsuno, Keita, Takayama, Kazuo, Tanaka, Shinya, Sato, Kei, and Fukuhara, Takasuke

Published
2023
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4. Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

Author

Ito, Jumpei, Suzuki, Rigel, Uriu, Keiya, Itakura, Yukari, Zahradnik, Jiri, Kimura, Kanako Terakado, Deguchi, Sayaka, Wang, Lei, Lytras, Spyros, Tamura, Tomokazu, Kida, Izumi, Nasser, Hesham, Shofa, Maya, Begum, Mst Monira, Tsuda, Masumi, Oda, Yoshitaka, Suzuki, Tateki, Sasaki, Jiei, Sasaki-Tabata, Kaori, Fujita, Shigeru, Yoshimatsu, Kumiko, Ito, Hayato, Nao, Naganori, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Yamamoto, Yuki, Nagamoto, Tetsuharu, Kuramochi, Jin, Schreiber, Gideon, Saito, Akatsuki, Matsuno, Keita, Takayama, Kazuo, Hashiguchi, Takao, Tanaka, Shinya, Fukuhara, Takasuke, Ikeda, Terumasa, and Sato, Kei

Published
2023
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5. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Author

Tamura, Tomokazu, Ito, Jumpei, Uriu, Keiya, Zahradnik, Jiri, Kida, Izumi, Anraku, Yuki, Nasser, Hesham, Shofa, Maya, Oda, Yoshitaka, Lytras, Spyros, Nao, Naganori, Itakura, Yukari, Deguchi, Sayaka, Suzuki, Rigel, Wang, Lei, Begum, MST Monira, Kita, Shunsuke, Yajima, Hisano, Sasaki, Jiei, Sasaki-Tabata, Kaori, Shimizu, Ryo, Tsuda, Masumi, Kosugi, Yusuke, Fujita, Shigeru, Pan, Lin, Sauter, Daniel, Yoshimatsu, Kumiko, Suzuki, Saori, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Yamamoto, Yuki, Nagamoto, Tetsuharu, Schreiber, Gideon, Maenaka, Katsumi, Hashiguchi, Takao, Ikeda, Terumasa, Fukuhara, Takasuke, Saito, Akatsuki, Tanaka, Shinya, Matsuno, Keita, Takayama, Kazuo, and Sato, Kei

Published
2023
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7. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

Author

Suzuki, Rigel, Yamasoba, Daichi, Kimura, Izumi, Wang, Lei, Kishimoto, Mai, Ito, Jumpei, Morioka, Yuhei, Nao, Naganori, Nasser, Hesham, Uriu, Keiya, Kosugi, Yusuke, Tsuda, Masumi, Orba, Yasuko, Sasaki, Michihito, Shimizu, Ryo, Kawabata, Ryoko, Yoshimatsu, Kumiko, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Sawa, Hirofumi, Ikeda, Terumasa, Irie, Takashi, Matsuno, Keita, Tanaka, Shinya, Fukuhara, Takasuke, and Sato, Kei

Published
2022
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8. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation

Author

Saito, Akatsuki, Irie, Takashi, Suzuki, Rigel, Maemura, Tadashi, Nasser, Hesham, Uriu, Keiya, Kosugi, Yusuke, Shirakawa, Kotaro, Sadamasu, Kenji, Kimura, Izumi, Ito, Jumpei, Wu, Jiaqi, Iwatsuki-Horimoto, Kiyoko, Ito, Mutsumi, Yamayoshi, Seiya, Loeber, Samantha, Tsuda, Masumi, Wang, Lei, Ozono, Seiya, Butlertanaka, Erika P., Tanaka, Yuri L., Shimizu, Ryo, Shimizu, Kenta, Yoshimatsu, Kumiko, Kawabata, Ryoko, Sakaguchi, Takemasa, Tokunaga, Kenzo, Yoshida, Isao, Asakura, Hiroyuki, Nagashima, Mami, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Yoshimura, Kazuhisa, Takaori-Kondo, Akifumi, Imai, Masaki, Tanaka, Shinya, Nakagawa, So, Ikeda, Terumasa, Fukuhara, Takasuke, Kawaoka, Yoshihiro, and Sato, Kei

Published
2022
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11. Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection

Author

Tamura, Tomokazu, primary, Ito, Hayato, additional, Torii, Shiho, additional, Wang, Lei, additional, Tsujino, Shuhei, additional, Kamiyama, Akifumi, additional, Oda, Yoshitaka, additional, Morioka, Yuhei, additional, Suzuki, Saori, additional, Shirakawa, Kotaro, additional, Sato, Kei, additional, Yoshimatsu, Kumiko, additional, Matsuura, Yoshiharu, additional, Iwano, Satoshi, additional, Tanaka, Shinya, additional, and Fukuhara, Takasuke, additional

Published
2023
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14. Hantavirus infection as a risk factor for chronic kidney disease of unknown aetiology (CKDu) and its prevalence in endemic areas of Sri Lanka since 2010 according to a retrospective serological analysis

Author

Gamage, Chandika D., primary, Nanayakkara, Shanika, additional, Sarathkumara, Yomani D., additional, Muthusinghe, Devinda S., additional, Shimizu, Kenta, additional, Arikawa, Jiro, additional, Lokupathirage, Sithumini M. W., additional, Nanayakkara, Nishantha, additional, Gunarathne, Lishanthe, additional, Chandrajith, Rohana, additional, Harada, Kouji H., additional, Koizumi, Akio, additional, and Yoshimatsu, Kumiko, additional

Published
2022
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15. Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant

Author

Saito, Akatsuki, primary, Tamura, Tomokazu, additional, Zahradnik, Jiri, additional, Deguchi, Sayaka, additional, Tabata, Koshiro, additional, Anraku, Yuki, additional, Kimura, Izumi, additional, Ito, Jumpei, additional, Yamasoba, Daichi, additional, Nasser, Hesham, additional, Toyoda, Mako, additional, Nagata, Kayoko, additional, Uriu, Keiya, additional, Kosugi, Yusuke, additional, Fujita, Shigeru, additional, Shofa, Maya, additional, Monira Begum, MST, additional, Shimizu, Ryo, additional, Oda, Yoshitaka, additional, Suzuki, Rigel, additional, Ito, Hayato, additional, Nao, Naganori, additional, Wang, Lei, additional, Tsuda, Masumi, additional, Yoshimatsu, Kumiko, additional, Kuramochi, Jin, additional, Kita, Shunsuke, additional, Sasaki-Tabata, Kaori, additional, Fukuhara, Hideo, additional, Maenaka, Katsumi, additional, Yamamoto, Yuki, additional, Nagamoto, Tetsuharu, additional, Asakura, Hiroyuki, additional, Nagashima, Mami, additional, Sadamasu, Kenji, additional, Yoshimura, Kazuhisa, additional, Ueno, Takamasa, additional, Schreiber, Gideon, additional, Takaori-Kondo, Akifumi, additional, Shirakawa, Kotaro, additional, Sawa, Hirofumi, additional, Irie, Takashi, additional, Hashiguchi, Takao, additional, Takayama, Kazuo, additional, Matsuno, Keita, additional, Tanaka, Shinya, additional, Ikeda, Terumasa, additional, Fukuhara, Takasuke, additional, and Sato, Kei, additional

Published
2022
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17. Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5

Author

Kimura, Izumi, primary, Yamasoba, Daichi, additional, Tamura, Tomokazu, additional, Nao, Naganori, additional, Suzuki, Tateki, additional, Oda, Yoshitaka, additional, Mitoma, Shuya, additional, Ito, Jumpei, additional, Nasser, Hesham, additional, Zahradnik, Jiri, additional, Uriu, Keiya, additional, Fujita, Shigeru, additional, Kosugi, Yusuke, additional, Wang, Lei, additional, Tsuda, Masumi, additional, Kishimoto, Mai, additional, Ito, Hayato, additional, Suzuki, Rigel, additional, Shimizu, Ryo, additional, Begum, MST Monira, additional, Yoshimatsu, Kumiko, additional, Kimura, Kanako Terakado, additional, Sasaki, Jiei, additional, Sasaki-Tabata, Kaori, additional, Yamamoto, Yuki, additional, Nagamoto, Tetsuharu, additional, Kanamune, Jun, additional, Kobiyama, Kouji, additional, Asakura, Hiroyuki, additional, Nagashima, Mami, additional, Sadamasu, Kenji, additional, Yoshimura, Kazuhisa, additional, Shirakawa, Kotaro, additional, Takaori-Kondo, Akifumi, additional, Kuramochi, Jin, additional, Schreiber, Gideon, additional, Ishii, Ken J., additional, Hashiguchi, Takao, additional, Ikeda, Terumasa, additional, Saito, Akatsuki, additional, Fukuhara, Takasuke, additional, Tanaka, Shinya, additional, Matsuno, Keita, additional, and Sato, Kei, additional

Published
2022
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18. Identification of cap-dependent endonuclease inhibitors with broad-spectrum activity against bunyaviruses

Author

Toba, Shinsuke, primary, Sato, Akihiko, additional, Kawai, Makoto, additional, Taoda, Yoshiyuki, additional, Unoh, Yuto, additional, Kusakabe, Shinji, additional, Nobori, Haruaki, additional, Uehara, Shota, additional, Uemura, Kentaro, additional, Taniguchi, Keiichi, additional, Kobayashi, Masanori, additional, Noshi, Takeshi, additional, Yoshida, Ryu, additional, Naito, Akira, additional, Shishido, Takao, additional, Maruyama, Junki, additional, Paessler, Slobodan, additional, Carr, Michael J., additional, Hall, William W., additional, Yoshimatsu, Kumiko, additional, Arikawa, Jiro, additional, Matsuno, Keita, additional, Sakoda, Yoshihiro, additional, Sasaki, Michihito, additional, Orba, Yasuko, additional, Sawa, Hirofumi, additional, and Kida, Hiroshi, additional

Published
2022
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19. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike

Author

Yamasoba, Daichi, primary, Kimura, Izumi, additional, Nasser, Hesham, additional, Morioka, Yuhei, additional, Nao, Naganori, additional, Ito, Jumpei, additional, Uriu, Keiya, additional, Tsuda, Masumi, additional, Zahradnik, Jiri, additional, Shirakawa, Kotaro, additional, Suzuki, Rigel, additional, Kishimoto, Mai, additional, Kosugi, Yusuke, additional, Kobiyama, Kouji, additional, Hara, Teppei, additional, Toyoda, Mako, additional, Tanaka, Yuri L., additional, Butlertanaka, Erika P., additional, Shimizu, Ryo, additional, Ito, Hayato, additional, Wang, Lei, additional, Oda, Yoshitaka, additional, Orba, Yasuko, additional, Sasaki, Michihito, additional, Nagata, Kayoko, additional, Yoshimatsu, Kumiko, additional, Asakura, Hiroyuki, additional, Nagashima, Mami, additional, Sadamasu, Kenji, additional, Yoshimura, Kazuhisa, additional, Kuramochi, Jin, additional, Seki, Motoaki, additional, Fujiki, Ryoji, additional, Kaneda, Atsushi, additional, Shimada, Tadanaga, additional, Nakada, Taka-aki, additional, Sakao, Seiichiro, additional, Suzuki, Takuji, additional, Ueno, Takamasa, additional, Takaori-Kondo, Akifumi, additional, Ishii, Ken J., additional, Schreiber, Gideon, additional, Sawa, Hirofumi, additional, Saito, Akatsuki, additional, Irie, Takashi, additional, Tanaka, Shinya, additional, Matsuno, Keita, additional, Fukuhara, Takasuke, additional, Ikeda, Terumasa, additional, and Sato, Kei, additional

Published
2022
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20. Pathological Studies on Hantaan Virus-Infected Mice Simulating Severe Hemorrhagic Fever with Renal Syndrome

Author

Wei, Zhouoxing, Shimizu, Kenta, Sarii, Rakiiya S., Muthusinghe, Devinda S., Lokupathirage, Sithumini M. W., Nio-Kobayashi, Junko, Yoshimatsu, Kumiko, Wei, Zhouoxing, Shimizu, Kenta, Sarii, Rakiiya S., Muthusinghe, Devinda S., Lokupathirage, Sithumini M. W., Nio-Kobayashi, Junko, and Yoshimatsu, Kumiko

Abstract

Hantaan virus is the causative agent of hemorrhagic fever with renal syndrome (HFRS). The Hantaan virus strain, Korean hemorrhagic fever virus clone-5 (KHF5), causes weight loss and renal hemorrhage in laboratory mice. Clone-4 (KHF4), which has a single E417K amino acid change in its glycoprotein, is an avirulent variant. In this study, KHF4 and KHF5 were compared to evaluate pathological differences in mice in vitro and in vivo. The characteristics of the two glycoproteins were not significantly different in vitro. However, the virulent KHF5 strain targeted the lungs and caused pneumonia and edema in vivo. Both strains induced high infectivity levels in the liver and caused hepatitis; however, petechial hemorrhage and glycogen storage reduction were observed in KHF5-infected mice alone. Renal hemorrhage was observed using viral antigens in the tubular region of KHF5-infected mice. In addition, an increase in white blood cell levels and neutrophilia were found in KHF5-infected mice. Microarray analysis of liver cells showed that CD8+ T cell activation, acute-phase protein production, and neutrophil activation was induced by KHF5 infection. KHF5 infectivity was significantly increased in vivo and the histological and clinicopathological findings were similar to those in patients with HFRS.

Published
2022

21. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

Author

Sato, Kei, primary, Suzuki, Rigel, additional, Yamasoba, Daichi, additional, Kimura, Izumi, additional, Wang, Lei, additional, Kishimoto, Mai, additional, Ito, Jumpei, additional, Morioka, Yuhei, additional, Nao, Naganori, additional, Nasser, Hesham, additional, Uriu, Keiya, additional, Kosugi, Yusuke, additional, Tsuda, Masumi, additional, Orba, Yasuko, additional, Sasaki, Michihito, additional, Shimizu, Ryo, additional, Kawabata, Ryoko, additional, Yoshimatsu, Kumiko, additional, Asakura, Hiroyuki, additional, Nagashima, Mami, additional, Sadamasu, Kenji, additional, Yoshimura, Kazuhisa, additional, Sawa, Hirofumi, additional, Ikeda, Terumasa, additional, Irie, Takashi, additional, Matsuno, Keita, additional, Tanaka, Shinya, additional, and Fukuhara, Takasuke, additional

Published
2022
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22. Identification of Novel Rodent-Borne Orthohantaviruses in an Endemic Area of Chronic Kidney Disease of Unknown Etiology (CKDu) in Sri Lanka

Author

Muthusinghe, Devinda S., primary, Shimizu, Kenta, additional, Lokupathirage, Sithumini M. W., additional, Wei, Zhouoxing, additional, Sarathkumara, Yomani D., additional, Fonseka, G. R. Amanda, additional, Senarathne, Pavani, additional, Koizumi, Nobuo, additional, Kawakami, Tomonori, additional, Koizumi, Akio, additional, Wickramasinghe, Chaminda, additional, Ebihara, Hideki, additional, Matsuno, Keita, additional, Tsuda, Yoshimi, additional, Arikawa, Jiro, additional, Gamage, Chandika D., additional, and Yoshimatsu, Kumiko, additional

Published
2021
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23. Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.

Author

Tsujino S, Deguchi S, Nomai T, Padilla-Blanco M, Plianchaisuk A, Wang L, Begum MM, Uriu K, Mizuma K, Nao N, Kojima I, Tsubo T, Li J, Matsumura Y, Nagao M, Oda Y, Tsuda M, Anraku Y, Kita S, Yajima H, Sasaki-Tabata K, Guo Z, Hinay AA Jr, Yoshimatsu K, Yamamoto Y, Nagamoto T, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Nasser H, Jonathan M, Putri O, Kim Y, Chen L, Suzuki R, Tamura T, Maenaka K, Irie T, Matsuno K, Tanaka S, Ito J, Ikeda T, Takayama K, Zahradnik J, Hashiguchi T, Fukuhara T, and Sato K

Subjects
Humans, Animals, Antiviral Agents pharmacology, Chlorocebus aethiops, Vero Cells, Cryoelectron Microscopy, Mice, SARS-CoV-2 genetics, Phylogeny, COVID-19 virology, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus chemistry
Abstract

In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population., (© 2024 The Author(s). Microbiology and Immunology published by The Societies and John Wiley & Sons Australia, Ltd.)

Published
2024
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24. Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.

Author

Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, and Fukuhara T

Subjects
Animals, Cricetinae, Humans, Codon, Nonsense, Phylogeny, SARS-CoV-2 genetics, Biological Assay, COVID-19
Abstract

Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5., (© 2024. The Author(s).)

Published
2024
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25. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics.

Author

Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, and Sato K

Subjects
Humans, COVID-19 virology, Mutation, SARS-CoV-2 genetics, SARS-CoV-2 pathogenicity, SARS-CoV-2 physiology, Spike Glycoprotein, Coronavirus genetics, Genome, Viral genetics
Abstract

Importance: Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non- spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein., Competing Interests: The authors declare no conflict of interest.

Published
2023
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