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5 results on '"The Genotype to Phenotype Japan (G2P-Japan)"'

1. 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

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

Author

80728270, 50632098, 10759509, Saito, Akatsuki, Tamura, Tomokazu, Zahradnik, Jiri, Deguchi, Sayaka, Tabata, Koshiro, Anraku, Yuki, Kimura, Izumi, Ito, Jumpei, Yamasoba, Daichi, Nasser, Hesham, Toyoda, Mako, Nagata, Kayoko, Uriu, Keiya, Kosugi, Yusuke, Fujita, Shigeru, Shofa, Maya, Monira Begum, M.S.T., Shimizu, Ryo, Oda, Yoshitaka, Suzuki, Rigel, Ito, Hayato, Nao, Naganori, Wang, Lei, Tsuda, Masumi, Yoshimatsu, Kumiko, Kuramochi, Jin, Kita, Shunsuke, Sasaki-Tabata, Kaori, Fukuhara, Hideo, Maenaka, Katsumi, Yamamoto, Yuki, Nagamoto, Tetsuharu, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Ueno, Takamasa, Schreiber, Gideon, Takaori-Kondo, Akifumi, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Shirakawa, Kotaro, Sawa, Hirofumi, Irie, Takashi, Hashiguchi, Takao, Takayama, Kazuo, Matsuno, Keita, Tanaka, Shinya, Ikeda, Terumasa, Fukuhara, Takasuke, Sato, Kei, 80728270, 50632098, 10759509, Saito, Akatsuki, Tamura, Tomokazu, Zahradnik, Jiri, Deguchi, Sayaka, Tabata, Koshiro, Anraku, Yuki, Kimura, Izumi, Ito, Jumpei, Yamasoba, Daichi, Nasser, Hesham, Toyoda, Mako, Nagata, Kayoko, Uriu, Keiya, Kosugi, Yusuke, Fujita, Shigeru, Shofa, Maya, Monira Begum, M.S.T., Shimizu, Ryo, Oda, Yoshitaka, Suzuki, Rigel, Ito, Hayato, Nao, Naganori, Wang, Lei, Tsuda, Masumi, Yoshimatsu, Kumiko, Kuramochi, Jin, Kita, Shunsuke, Sasaki-Tabata, Kaori, Fukuhara, Hideo, Maenaka, Katsumi, Yamamoto, Yuki, Nagamoto, Tetsuharu, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Ueno, Takamasa, Schreiber, Gideon, Takaori-Kondo, Akifumi, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Shirakawa, Kotaro, Sawa, Hirofumi, Irie, Takashi, Hashiguchi, Takao, Takayama, Kazuo, Matsuno, Keita, Tanaka, Shinya, Ikeda, Terumasa, Fukuhara, Takasuke, and Sato, Kei

Abstract

The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.

Published
2022

3. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance

Author

80728270, Kimura, Izumi, Kosugi, Yusuke, Wu, Jiaqi, Zahradnik, Jiri, Yamasoba, Daichi, Butlertanaka, Erika P., Tanaka, Yuri L., Uriu, Keiya, Liu, Yafei, Morizako, Nanami, Shirakawa, Kotaro, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Tokunaga, Kenzo, Ueno, Takamasa, Takaori-Kondo, Akifumi, Schreiber, Gideon, Arase, Hisashi, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Motozono, Chihiro, Saito, Akatsuki, Nakagawa, So, Sato, Kei, 80728270, Kimura, Izumi, Kosugi, Yusuke, Wu, Jiaqi, Zahradnik, Jiri, Yamasoba, Daichi, Butlertanaka, Erika P., Tanaka, Yuri L., Uriu, Keiya, Liu, Yafei, Morizako, Nanami, Shirakawa, Kotaro, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Tokunaga, Kenzo, Ueno, Takamasa, Takaori-Kondo, Akifumi, Schreiber, Gideon, Arase, Hisashi, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Motozono, Chihiro, Saito, Akatsuki, Nakagawa, So, and Sato, Kei

Abstract

SARS-CoV-2 Lambda, a variant of interest, has spread in some South American countries; however, its virological features and evolutionary traits remain unknown. In this study, we use pseudoviruses and reveal that the spike protein of the Lambda variant is more infectious than that of other variants due to the T76I and L452Q mutations. The RSYLTPGD246-253N mutation, a unique 7-amino-acid deletion in the N-terminal domain of the Lambda spike protein, is responsible for evasion from neutralizing antibodies and further augments antibody-mediated enhancement of infection. Although this mutation generates a nascent N-linked glycosylation site, the additional N-linked glycan is dispensable for the virological property conferred by this mutation. Since the Lambda variant has dominantly spread according to the increasing frequency of the isolates harboring the RSYLTPGD246-253N mutation, our data suggest that the RSYLTPGD246-253N mutation is closely associated with the substantial spread of the Lambda variant in South America.

Published
2022

4. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance

Author

Kimura, Izumi, Kosugi, Yusuke, Wu, Jiaqi, Zahradnik, Jiri, Yamasoba, Daichi, Butlertanaka, Erika P., Tanaka, Yuri L., Uriu, Keiya, Liu, Yafei, Morizako, Nanami, Shirakawa, Kotaro, Kazuma, Yasuhiro, Nomura, Ryosuke, Horisawa, Yoshihito, Tokunaga, Kenzo, Ueno, Takamasa, Takaori-Kondo, Akifumi, Schreiber, Gideon, Arase, Hisashi, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Motozono, Chihiro, Saito, Akatsuki, Nakagawa, So, and Sato, Kei

Subjects
Adult, Male, Lambda, Glycosylation, SARS-CoV-2, Immunity, COVID-19, C.37, Middle Aged, Antibodies, Viral, spike protein, Antibodies, Neutralizing, General Biochemistry, Genetics and Molecular Biology, Cell Line, HEK293 Cells, Report, Mutation, Spike Glycoprotein, Coronavirus, Humans, Female, Aged
Abstract

SARS-CoV-2 Lambda, a variant of interest, has spread in some South American countries; however, its virological features and evolutionary traits remain unknown. In this study, we use pseudoviruses and reveal that the spike protein of the Lambda variant is more infectious than that of other variants due to the T76I and L452Q mutations. The RSYLTPGD246-253N mutation, a unique 7-amino-acid deletion in the N-terminal domain of the Lambda spike protein, is responsible for evasion from neutralizing antibodies and further augments antibody-mediated enhancement of infection. Although this mutation generates a nascent N-linked glycosylation site, the additional N-linked glycan is dispensable for the virological property conferred by this mutation. Since the Lambda variant has dominantly spread according to the increasing frequency of the isolates harboring the RSYLTPGD246-253N mutation, our data suggest that the RSYLTPGD246-253N mutation is closely associated with the substantial spread of the Lambda variant in South America., Graphical Abstract, Kimura et al. reveal the characteristics of SARS-CoV-2 Lambda variant of interest. Lambda spike is more infectious than that of other variants due to the T76I and L452Q mutations. The RSYLTPGD246-253N mutation is responsible for evasion from neutralizing antibodies and further augments antibody-mediated enhancement of infection.

Published
2022

5. Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant

Author

Saito, Akatsuki, Tamura, Tomokazu, Zahradnik, Jiri, Deguchi, Sayaka, Tabata, Koshiro, Anraku, Yuki, Kimura, Izumi, Ito, Jumpei, Yamasoba, Daichi, Nasser, Hesham, Toyoda, Mako, Nagata, Kayoko, Uriu, Keiya, Kosugi, Yusuke, Fujita, Shigeru, Shofa, Maya, Monira Begum, M.S.T., Shimizu, Ryo, Oda, Yoshitaka, Suzuki, Rigel, Ito, Hayato, Nao, Naganori, Wang, Lei, Tsuda, Masumi, Yoshimatsu, Kumiko, Kuramochi, Jin, Kita, Shunsuke, Sasaki-Tabata, Kaori, Fukuhara, Hideo, Maenaka, Katsumi, Yamamoto, Yuki, Nagamoto, Tetsuharu, Asakura, Hiroyuki, Nagashima, Mami, Sadamasu, Kenji, Yoshimura, Kazuhisa, Ueno, Takamasa, Schreiber, Gideon, Takaori-Kondo, Akifumi, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Shirakawa, Kotaro, Sawa, Hirofumi, Irie, Takashi, Hashiguchi, Takao, Takayama, Kazuo, Matsuno, Keita, Tanaka, Shinya, Ikeda, Terumasa, Fukuhara, Takasuke, and Sato, Kei

Subjects
SARS-CoV-2, Omicron, antiviral drug resistance, COVID-19, Antibodies, Viral, Antibodies, Neutralizing, Antiviral Agents, Microbiology, Virology, Spike Glycoprotein, Coronavirus, Humans, BA.2.75, transmissibility, pathogenicity, Parasitology, immune resistance, COVID-19 Serotherapy
Abstract

The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5., SARS-CoV-2オミクロンBA.2.75株（通称ケンタウロス）のウイルス学的性状の解明. 京都大学プレスリリース. 2022-10-12.

Published
2022
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