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

Author

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

Published
2024
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5. Multicolor and multi-spot observations of Starlink's Visorsat

Author

Horiuchi, Takashi, Hanayama, Hidekazu, Ohishi, Masatoshi, Nakaoka, Tatsuya, Imazawa, Ryo, Kawabata, Koji S., Takahashi, Jun, Onozato, Hiroki, Saito, Tomoki, Yamanaka, Masayuki, Nogami, Daisaku, Tampo, Yusuke, Kojiguchi, Naoto, Ito, Jumpei, Shibata, Masaaki, Schramm, Malte, Oasa, Yumiko, Kanai, Takahiro, Oide, Kohei, Murata, Katsuhiro L., Hosokawa, Ryohei, Takamatsu, Yutaka, Imai, Yuri, Ito, Naohiro, Niwano, Masafumi, Takagi, Seiko, Ono, Tatsuharu, and Kouprianov, Vladimir V.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

This study provides the results of simultaneous multicolor observations for the first Visorsat (STARLINK-1436) and the ordinary Starlink satellite, STARLINK-1113 in the $U$, $B$, $V$, $g'$, $r$, $i$, $R_{\rm C}$, $I_{\rm C}$, $z$, $J$, $H$, and $K_s$ bands to quantitatively investigate the extent to which Visorsat reduces its reflected light. Our results are as follows: (1) in most cases, Virorsat is fainter than STARLINK-1113, and the sunshade on Visorsat, therefore, contributes to the reduction of the reflected sunlight; (2) the magnitude at 550 km altitude (normalized magnitude) of both satellites often reaches the naked-eye limiting magnitude ($<$ 6.0); (3) from a blackbody radiation model of the reflected flux, the peak of the reflected components of both satellites is around the $z$ band; and (4) the albedo of the near infrared range is larger than that of the optical range. Under the assumption that Visorsat and STARLINK-1113 have the same reflectivity, we estimate the covering factor, $C_{\rm f}$, of the sunshade on Visorsat, using the blackbody radiation model: the covering factor ranges from $0.18 \leq C_{\rm f} \leq 0.92$. From the multivariable analysis of the solar phase angle (Sun-target-observer), the normalized magnitude, and the covering factor, the phase angle versus covering factor distribution presents a moderate anti-correlation between them, suggesting that the magnitudes of Visorsat depend not only on the phase angle but also on the orientation of the sunshade along our line of sight. However, the impact on astronomical observations from Visorsat-designed satellites remains serious. Thus, new countermeasures are necessary for the Starlink satellites to further reduce reflected sunlight., Comment: 31 pages, 9 figures, published in PASJ

Published
2023
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6. Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236

Author

Sawa, Hirofumi, Mizuma, Keita, Li, Jingshu, Mimura, Yume, Ohari, Yuma, Tsubo, Tomoya, Ferdous, Zannatul, Shishido, Kenji, Mohri, Hiromi, Iida, Miki, Tsujino, Shuhei, Misawa, Naoko, Usui, Kaoru, Saikruang, Wilaiporn, Lytras, Spyridon, Kawakubo, Shusuke, Nishumura, Luca, Mendoza Tolentino, Jarel Elgin, Li, Wenye, Yo, Maximilian Stanley, Horinaka, Kio, Suganami, Mai, Chiba, Mika, Yoshimura, Ryo, Yasuda, Kyoko, Iida, Keiko, Strange, Adam Patrick, Ohsumi, Naomi, Tanaka, Shiho, Ogawa, Eiko, Okumura, Kaho, Fukuda, Tsuki, Osujo, Rina, Yoshida, Isao, Nakagawa, So, Takaori-Kondo, Akifumi, Shirakawa, Kotaro, Nagata, Kayoko, Nomura, Ryosuke, Horisawa, Yoshihito, Tashiro, Yusuke, Kawai, Yugo, Nakata, Yoshitaka, Futatsusako, Hiroki, Sakamoto, Ayaka, Yasuhara, Naoko, Hashiguchi, Takao, Suzuki, Tateki, Kimura, Kanako, Sasaki, Jiei, Nakajima, Yukari, Yajima, Hisano, Irie, Takashi, Kawabata, Ryoko, Sasaki-Tabata, Kaori, Shimizu, Ryo, Monira Begum, M.S.T., Jonathan, Michael, Mugita, Yuka, Leong, Sharee, Takahashi, Otowa, Ichihara, Kimiko, Ueno, Takamasa, Motozono, Chihiro, Toyoda, Mako, Saito, Akatsuki, Kosaka, Anon, Kawano, Miki, Matsubara, Natsumi, Nishiuchi, Tomoko, Zahradnik, Jiri, Andrikopoulos, Prokopios, Padilla-Blanco, Miguel, Konar, Aditi, Fujita, Shigeru, Plianchaisuk, Arnon, Deguchi, Sayaka, Ito, Hayato, Nao, Naganori, Wang, Lei, Nasser, Hesham, Tamura, Tomokazu, Kimura, Izumi, Kashima, Yukie, Suzuki, Rigel, Suzuki, Saori, Kida, Izumi, Tsuda, Masumi, Oda, Yoshitaka, Hashimoto, Rina, Watanabe, Yukio, Uriu, Keiya, Yamasoba, Daichi, Guo, Ziyi, Hinay, Alfredo A., Jr., Kosugi, Yusuke, Chen, Luo, Pan, Lin, Kaku, Yu, Chu, Hin, Donati, Flora, Temmam, Sarah, Eloit, Marc, Yamamoto, Yuki, Nagamoto, Tetsuharu, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Suzuki, Yutaka, Ito, Jumpei, Ikeda, Terumasa, Tanaka, Shinya, Matsuno, Keita, Fukuhara, Takasuke, Takayama, Kazuo, and Sato, Kei

Published
2024
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9. 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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10. 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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11. 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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13. The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant

Author

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

Published
2022
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14. 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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15. 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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16. Virological characteristics of a SARS-CoV-2-related bat coronavirus, BANAL-20-236

Author

Fujita, Shigeru, primary, Plianchaisuk, Arnon, additional, Deguchi, Sayaka, additional, Ito, Hayato, additional, Nao, Naganori, additional, Wang, Lei, additional, Nasser, Hesham, additional, Tamura, Tomokazu, additional, Kimura, Izumi, additional, Kashima, Yukie, additional, Suzuki, Rigel, additional, Suzuki, Saori, additional, Kida, Izumi, additional, Tsuda, Masumi, additional, Oda, Yoshitaka, additional, Hashimoto, Rina, additional, Watanabe, Yukio, additional, Uriu, Keiya, additional, Yamasoba, Daichi, additional, Guo, Ziyi, additional, Hinay, Alfredo A., additional, Kosugi, Yusuke, additional, Chen, Luo, additional, Pan, Lin, additional, Kaku, Yu, additional, Chu, Hin, additional, Donati, Flora, additional, Temmam, Sarah, additional, Eloit, Marc, additional, Yamamoto, Yuki, additional, Nagamoto, Tetsuharu, additional, Asakura, Hiroyuki, additional, Nagashima, Mami, additional, Sadamasu, Kenji, additional, Yoshimura, Kazuhisa, additional, Suzuki, Yutaka, additional, Sawa, Hirofumi, additional, Mizuma, Keita, additional, Li, Jingshu, additional, Mimura, Yume, additional, Ohari, Yuma, additional, Tsubo, Tomoya, additional, Ferdous, Zannatul, additional, Shishido, Kenji, additional, Mohri, Hiromi, additional, Iida, Miki, additional, Tsujino, Shuhei, additional, Misawa, Naoko, additional, Usui, Kaoru, additional, Saikruang, Wilaiporn, additional, Lytras, Spyridon, additional, Kawakubo, Shusuke, additional, Nishumura, Luca, additional, Mendoza Tolentino, Jarel Elgin, additional, Li, Wenye, additional, Yo, Maximilian Stanley, additional, Horinaka, Kio, additional, Suganami, Mai, additional, Chiba, Mika, additional, Yoshimura, Ryo, additional, Yasuda, Kyoko, additional, Iida, Keiko, additional, Strange, Adam Patrick, additional, Ohsumi, Naomi, additional, Tanaka, Shiho, additional, Ogawa, Eiko, additional, Okumura, Kaho, additional, Fukuda, Tsuki, additional, Osujo, Rina, additional, Yoshida, Isao, additional, Nakagawa, So, additional, Takaori-Kondo, Akifumi, additional, Shirakawa, Kotaro, additional, Nagata, Kayoko, additional, Nomura, Ryosuke, additional, Horisawa, Yoshihito, additional, Tashiro, Yusuke, additional, Kawai, Yugo, additional, Nakata, Yoshitaka, additional, Futatsusako, Hiroki, additional, Sakamoto, Ayaka, additional, Yasuhara, Naoko, additional, Hashiguchi, Takao, additional, Suzuki, Tateki, additional, Kimura, Kanako, additional, Sasaki, Jiei, additional, Nakajima, Yukari, additional, Yajima, Hisano, additional, Irie, Takashi, additional, Kawabata, Ryoko, additional, Sasaki-Tabata, Kaori, additional, Shimizu, Ryo, additional, Monira Begum, M.S.T., additional, Jonathan, Michael, additional, Mugita, Yuka, additional, Leong, Sharee, additional, Takahashi, Otowa, additional, Ichihara, Kimiko, additional, Ueno, Takamasa, additional, Motozono, Chihiro, additional, Toyoda, Mako, additional, Saito, Akatsuki, additional, Kosaka, Anon, additional, Kawano, Miki, additional, Matsubara, Natsumi, additional, Nishiuchi, Tomoko, additional, Zahradnik, Jiri, additional, Andrikopoulos, Prokopios, additional, Padilla-Blanco, Miguel, additional, Konar, Aditi, additional, Ito, Jumpei, additional, Ikeda, Terumasa, additional, Tanaka, Shinya, additional, Matsuno, Keita, additional, Fukuhara, Takasuke, additional, Takayama, Kazuo, additional, and Sato, Kei, additional

Published
2024
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17. Corrigendum: Direct evidence of abortive lytic infection-mediated establishment of Epstein-Barr virus latency during B-cell infection

Author

Inagaki, Tomoki, primary, Sato, Yoshitaka, additional, Ito, Jumpei, additional, Takaki, Mitsuaki, additional, Okuno, Yusuke, additional, Yaguchi, Masahiro, additional, Masud, H. M. Abdullah Al, additional, Watanabe, Takahiro, additional, Sato, Kei, additional, Iwami, Shingo, additional, Murata, Takayuki, additional, and Kimura, Hiroshi, additional

Published
2024
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21. Virological characteristics of the SARS-CoV-2 BA.2.86 variant

Author

10759509, Tamura, Tomokazu, Mizuma, Keita, Nasser, Hesham, Deguchi, Sayaka, Padilla-Blanco, Miguel, Oda, Yoshitaka, Uriu, Keiya, Tolentino, Jarel E.M., Tsujino, Shuhei, Suzuki, Rigel, Kojima, Isshu, Nao, Naganori, Shimizu, Ryo, Wang, Lei, Tsuda, Masumi, Jonathan, Michael, Kosugi, Yusuke, Guo, Ziyi, Hinay, Alfredo A., Putri, Olivia, Kim, Yoonjin, Tanaka, Yuri L., Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito, Akatsuki, Ito, Jumpei, Irie, Takashi, Tanaka, Shinya, Zahradnik, Jiri, Ikeda, Terumasa, Takayama, Kazuo, Matsuno, Keita, Fukuhara, Takasuke, Sato, Kei, 10759509, Tamura, Tomokazu, Mizuma, Keita, Nasser, Hesham, Deguchi, Sayaka, Padilla-Blanco, Miguel, Oda, Yoshitaka, Uriu, Keiya, Tolentino, Jarel E.M., Tsujino, Shuhei, Suzuki, Rigel, Kojima, Isshu, Nao, Naganori, Shimizu, Ryo, Wang, Lei, Tsuda, Masumi, Jonathan, Michael, Kosugi, Yusuke, Guo, Ziyi, Hinay, Alfredo A., Putri, Olivia, Kim, Yoonjin, Tanaka, Yuri L., Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito, Akatsuki, Ito, Jumpei, Irie, Takashi, Tanaka, Shinya, Zahradnik, Jiri, Ikeda, Terumasa, Takayama, Kazuo, Matsuno, Keita, Fukuhara, Takasuke, and Sato, Kei

Abstract

In late 2023, several SARS-CoV-2 XBB descendants, notably EG.5.1, were predominant worldwide. However, a distinct SARS-CoV-2 lineage, the BA.2.86 variant, also emerged. BA.2.86 is phylogenetically distinct from other Omicron sublineages, accumulating over 30 amino acid mutations in its spike protein. Here, we examined the virological characteristics of the BA.2.86 variant. Our epidemic dynamics modeling suggested that the relative reproduction number of BA.2.86 is significantly higher than that of EG.5.1. Additionally, four clinically available antivirals were effective against BA.2.86. Although the fusogenicity of BA.2.86 spike is similar to that of the parental BA.2 spike, the intrinsic pathogenicity of BA.2.86 in hamsters was significantly lower than that of BA.2. Since the growth kinetics of BA.2.86 are significantly lower than those of BA.2 both in vitro and in vivo, the attenuated pathogenicity of BA.2.86 is likely due to its decreased replication capacity. These findings uncover the features of BA.2.86, providing insights for control and treatment.

Published
2024

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

Author

50632098, 10759509, Tamura, Tomokazu, Irie, Takashi, Deguchi, Sayaka, Yajima, Hisano, Tsuda, Masumi, Nasser, Hesham, Mizuma, Keita, Plianchaisuk, Arnon, Suzuki, Saori, Uriu, Keiya, Begum, Mst Monira, Shimizu, Ryo, Jonathan, Michael, Suzuki, Rigel, Kondo, Takashi, Ito, Hayato, Kamiyama, Akifumi, Yoshimatsu, Kumiko, Shofa, Maya, Hashimoto, Rina, Anraku, Yuki, Kimura, Kanako Terakado, Kita, Shunsuke, Sasaki, Jiei, Sasaki-Tabata, Kaori, Maenaka, Katsumi, Nao, Naganori, Wang, Lei, Oda, Yoshitaka, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda, Terumasa, Saito, Akatsuki, Matsuno, Keita, Ito, Jumpei, Tanaka, Shinya, Sato, Kei, Hashiguchi, Takao, Takayama, Kazuo, Fukuhara, Takasuke, 50632098, 10759509, Tamura, Tomokazu, Irie, Takashi, Deguchi, Sayaka, Yajima, Hisano, Tsuda, Masumi, Nasser, Hesham, Mizuma, Keita, Plianchaisuk, Arnon, Suzuki, Saori, Uriu, Keiya, Begum, Mst Monira, Shimizu, Ryo, Jonathan, Michael, Suzuki, Rigel, Kondo, Takashi, Ito, Hayato, Kamiyama, Akifumi, Yoshimatsu, Kumiko, Shofa, Maya, Hashimoto, Rina, Anraku, Yuki, Kimura, Kanako Terakado, Kita, Shunsuke, Sasaki, Jiei, Sasaki-Tabata, Kaori, Maenaka, Katsumi, Nao, Naganori, Wang, Lei, Oda, Yoshitaka, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ikeda, Terumasa, Saito, Akatsuki, Matsuno, Keita, Ito, Jumpei, Tanaka, Shinya, Sato, Kei, Hashiguchi, Takao, Takayama, Kazuo, and Fukuhara, Takasuke

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.

Published
2024

24. Virological characteristics of the SARS-CoV-2 BA.2.86 variant

Author

Tamura, Tomokazu, primary, Mizuma, Keita, additional, Nasser, Hesham, additional, Deguchi, Sayaka, additional, Padilla-Blanco, Miguel, additional, Oda, Yoshitaka, additional, Uriu, Keiya, additional, Tolentino, Jarel E.M., additional, Tsujino, Shuhei, additional, Suzuki, Rigel, additional, Kojima, Isshu, additional, Nao, Naganori, additional, Shimizu, Ryo, additional, Wang, Lei, additional, Tsuda, Masumi, additional, Jonathan, Michael, additional, Kosugi, Yusuke, additional, Guo, Ziyi, additional, Hinay, Alfredo A., additional, Putri, Olivia, additional, Kim, Yoonjin, additional, Tanaka, Yuri L., additional, Asakura, Hiroyuki, additional, Nagashima, Mami, additional, Sadamasu, Kenji, additional, Yoshimura, Kazuhisa, additional, Saito, Akatsuki, additional, Ito, Jumpei, additional, Irie, Takashi, additional, Tanaka, Shinya, additional, Zahradnik, Jiri, additional, Ikeda, Terumasa, additional, Takayama, Kazuo, additional, Matsuno, Keita, additional, Fukuhara, Takasuke, additional, and Sato, Kei, additional

Published
2024
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25. Virological characteristics of the SARS-CoV-2 JN.1 variant

Author

Kaku, Yu, primary, Okumura, Kaho, additional, Padilla-Blanco, Miguel, additional, Kosugi, Yusuke, additional, Uriu, Keiya, additional, Hinay, Alfredo A, additional, Chen, Luo, additional, Plianchaisuk, Arnon, additional, Kobiyama, Kouji, additional, Ishii, Ken J, additional, Zahradnik, Jiri, additional, Ito, Jumpei, additional, and Sato, Kei, additional

Published
2024
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30. Transmissibility, infectivity, and immune evasion of the SARS-CoV-2 BA.2.86 variant

Author

Uriu, Keiya, primary, Ito, Jumpei, additional, Kosugi, Yusuke, additional, Tanaka, Yuri L, additional, Mugita, Yuka, additional, Guo, Ziyi, additional, Hinay, Alfredo A, additional, Putri, Olivia, additional, Kim, Yoonjin, additional, Shimizu, Ryo, additional, Begum, MST Monira, additional, Jonathan, Michael, additional, Saito, Akatsuki, additional, Ikeda, Terumasa, additional, and Sato, Kei, additional

Published
2023
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34. SARS-CoV-2 ORF7a Mutation Found in BF.5 and BF.7 Sublineages Impacts Its Functions.

Author

Timilsina, Uddhav, Ivey, Emily B., Duffy, Sean, Plianchaisuk, Arnon, Ito, Jumpei, Sato, Kei, and Stavrou, Spyridon

Subjects
TYPE I interferons, SARS-CoV-2, MAJOR histocompatibility complex
Abstract

A feature of the SARS-CoV-2 Omicron subvariants BF.5 and BF.7 that recently circulated mainly in China and Japan was the high prevalence of the ORF7a: H47Y mutation, in which the 47th residue of ORF7a has been mutated from a histidine (H) to a tyrosine (Y). Here, we evaluated the effect of this mutation on the three main functions ascribed to the SARS-CoV-2 ORF7a protein. Our findings show that H47Y mutation impairs the ability of SARS-CoV-2 ORF7a to antagonize the type I interferon (IFN-I) response and to downregulate major histocompatibility complex I (MHC-I) cell surface levels, but had no effect in its anti-SERINC5 function. Overall, our results suggest that the H47Y mutation of ORF7a affects important functions of this protein, resulting in changes in virus pathogenesis. [ABSTRACT FROM AUTHOR]

Published
2024
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38. Multicolor and multi-spot observations of Starlink’s Visorsat

Author

Horiuchi, Takashi, primary, Hanayama, Hidekazu, additional, Ohishi, Masatoshi, additional, Nakaoka, Tatsuya, additional, Imazawa, Ryo, additional, Kawabata, Koji S, additional, Takahashi, Jun, additional, Onozato, Hiroki, additional, Saito, Tomoki, additional, Yamanaka, Masayuki, additional, Nogami, Daisaku, additional, Tampo, Yusuke, additional, Kojiguchi, Naoto, additional, Ito, Jumpei, additional, Shibata, Masaaki, additional, Schramm, Malte, additional, Oasa, Yumiko, additional, Kanai, Takahiro, additional, Oide, Kohei, additional, Murata, Katsuhiro L, additional, Hosokawa, Ryohei, additional, Takamatsu, Yutaka, additional, Imai, Yuri, additional, Ito, Naohiro, additional, Niwano, Masafumi, additional, Takagi, Seiko, additional, Ono, Tatsuharu, additional, and Kouprianov, Vladimir V, additional

Published
2023
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39. Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5

Author

10759509, 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, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Yokota, Isao, Matsuno, Keita, Takayama, Kazuo, Tanaka, Shinya, Sato, Kei, Fukuhara, Takasuke, 10759509, 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, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Yokota, Isao, Matsuno, Keita, Takayama, Kazuo, Tanaka, Shinya, Sato, Kei, and Fukuhara, Takasuke

Abstract

The unremitting emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants necessitates ongoing control measures. Given its rapid spread, the new Omicron subvariant BA.5 requires urgent characterization. Here, we comprehensively analyzed BA.5 with the other Omicron variants BA.1, BA.2, and ancestral B.1.1. Although in vitro growth kinetics of BA.5 was comparable among the Omicron subvariants, BA.5 was much more fusogenic than BA.1 and BA.2. Airway-on-a-chip analysis showed that, among Omicron subvariants, BA.5 had enhanced ability to disrupt the respiratory epithelial and endothelial barriers. Furthermore, in our hamster model, in vivo pathogenicity of BA.5 was slightly higher than that of the other Omicron variants and less than that of ancestral B.1.1. Notably, BA.5 gains efficient virus spread compared with BA.1 and BA.2, leading to prompt immune responses. Our findings suggest that BA.5 has low pathogenicity compared with the ancestral strain but enhanced virus spread /inflammation compared with earlier Omicron subvariants.

Published
2023

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

Author

80833334, 10759509, 50632098, 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, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito, Akatsuki, Matsuno, Keita, Takayama, Kazuo, Hashiguchi, Takao, Tanaka, Shinya, Fukuhara, Takasuke, Ikeda, Terumasa, Sato, Kei, 80833334, 10759509, 50632098, 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, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Saito, Akatsuki, Matsuno, Keita, Takayama, Kazuo, Hashiguchi, Takao, Tanaka, Shinya, Fukuhara, Takasuke, Ikeda, Terumasa, and Sato, Kei

Abstract

In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.

Published
2023

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

Author

50632098, 10759509, 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, The Genotype to Phenotype Japan (G2P-Japan), Hashiguchi, Takao, Ikeda, Terumasa, Fukuhara, Takasuke, Saito, Akatsuki, Tanaka, Shinya, Matsuno, Keita, Takayama, Kazuo, Sato, Kei, 50632098, 10759509, 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, The Genotype to Phenotype Japan (G2P-Japan), Hashiguchi, Takao, Ikeda, Terumasa, Fukuhara, Takasuke, Saito, Akatsuki, Tanaka, Shinya, Matsuno, Keita, Takayama, Kazuo, and Sato, Kei

Abstract

In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.

Published
2023

45. ORF3c is expressed in SARS‐CoV‐2‐infected cells and inhibits innate sensing by targeting MAVS.

Author

Müller, Martin, Herrmann, Alexandra, Fujita, Shigeru, Uriu, Keiya, Kruth, Carolin, Strange, Adam, Kolberg, Jan E, Schneider, Markus, Ito, Jumpei, Müller, Marcel A, Drosten, Christian, Ensser, Armin, Sato, Kei, and Sauter, Daniel

Abstract

Most SARS‐CoV‐2 proteins are translated from subgenomic RNAs (sgRNAs). While the majority of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. One example is the ORF3a sgRNA that also encodes ORF3c, an enigmatic 41‐amino‐acid peptide. Here, we show that ORF3c is expressed in SARS‐CoV‐2‐infected cells and suppresses RIG‐I‐ and MDA5‐mediated IFN‐β induction. ORF3c interacts with the signaling adaptor MAVS, induces its C‐terminal cleavage, and inhibits the interaction of RIG‐I with MAVS. The immunosuppressive activity of ORF3c is conserved among members of the subgenus sarbecovirus, including SARS‐CoV and coronaviruses isolated from bats. Notably, however, the SARS‐CoV‐2 delta and kappa variants harbor premature stop codons in ORF3c, demonstrating that this reading frame is not essential for efficient viral replication in vivo and is likely compensated by other viral proteins. In agreement with this, disruption of ORF3c does not significantly affect SARS‐CoV‐2 replication in CaCo‐2, CaLu‐3, or Rhinolophus alcyone cells. In summary, we here identify ORF3c as an immune evasion factor of SARS‐CoV‐2 that suppresses innate sensing in infected cells. Synopsis: SARS‐CoV‐2‐encoded ORF3c is expressed in infected cells. This small viral protein is conserved among sarbecoviruses and suppresses the induction of IFN‐β by targeting the signaling adaptor protein MAVS.SARS‐CoV‐2 ORF3c is expressed in infected cells and suppresses IFN‐β induction.SARS‐CoV‐2 ORF3c interacts with the signaling adaptor MAVS.SARS‐CoV‐2 ORF3c induces C‐terminal cleavage of MAVS and inhibits its interaction with RIG‐I.The immunosuppressive activity of ORF3c is conserved among sarbecoviruses. [ABSTRACT FROM AUTHOR]

Published
2023
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46. Impact of Imprinted Immunity Induced by mRNA Vaccination in an Experimental Animal Model.

Author

Fujita, Shigeru, Uriu, Keiya, Pan, Lin, Nao, Naganori, Tabata, Koshiro, Kishimoto, Mai, Itakura, Yukari, Sawa, Hirofumi, Kida, Izumi, Tamura, Tomokazu, Consortium, The Genotype to Phenotype Japan (G2P-Japan), Fukuhara, Takasuke, Ito, Jumpei, Matsuno, Keita, and Sato, Kei

Subjects
SARS-CoV-2, HUMORAL immunity, HERD immunity, ANIMAL vaccination, SARS-CoV-2 Omicron variant, LABORATORY animals
Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has led to concerns that ancestral SARS-CoV-2-based vaccines may not be effective against newly emerging Omicron subvariants. The concept of "imprinted immunity" suggests that individuals vaccinated with ancestral virus-based vaccines may not develop effective immunity against newly emerging Omicron subvariants, such as BQ.1.1 and XBB.1. In this study, we investigated this possibility using hamsters. Although natural infection induced effective antiviral immunity, breakthrough infections in hamsters with BQ.1.1 and XBB.1 Omicron subvariants after receiving the 3-dose mRNA-lipid nanoparticle vaccine resulted in only faintly induced humoral immunity, supporting the possibility of imprinted immunity. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Monitoring fusion kinetics of viral and target cell membranes in living cells using a SARS-CoV-2 spike-protein-mediated membrane fusion assay

Author

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

Published
2022
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