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4. SARS-CoV-2 intra-host diversity, antibody response, and disease severity after reinfection by the variant of concern Gamma in Brazil

Author

Naveca, Felipe Gomes, Nascimento, Valdinete Alves, Nascimento, Fernanda, Ogrzewalska, Maria, Pauvolid-Corrêa, Alex, Araújo, Mia Ferreira, Arantes, Ighor, Batista, Érika Rocha, Magalhães, Alessandro Álvares, Vinhal, Fernando, Mattos, Tirza Peixoto, Riediger, Irina, Debur, Maria do Carmo, Grinsztejn, Beatriz, Veloso, Valdiléa G., Brasil, Patrícia, Rodrigues, Rodrigo Ribeiro, Rovaris, Darcita Buerger, Fernandes, Sandra Bianchini, Fernandes, Cristiano, Santos, João Hugo Abdalla, Abdalla, Lígia Fernandes, Costa-Filho, Rubens, Silva, Marineide, Souza, Victor, Costa, Ágatha Araújo, Mejía, Matilde, Brandão, Maria Júlia, Gonçalves, Luciana Fé, Silva, George Allan, de Jesus, Michele Silva, Pessoa, Karina, Corado, André de Lima Guerra, Duarte, Debora Camila Gomes, Machado, Ana Beatriz, Zukeram, Ketiuce de Azevedo, Valente, Natalia, Lopes, Renata Serrano, Pereira, Elisa Cavalcante, Appolinario, Luciana Reis, Rocha, Alice Sampaio, Tort, Luis Fernando Lopez, Sekizuka, Tsuyoshi, Itokawa, Kentaro, Hashino, Masanori, Kuroda, Makoto, Dezordi, Filipe Zimmer, Wallau, Gabriel Luz, Delatorre, Edson, Gräf, Tiago, Siqueira, Marilda Mendonça, Bello, Gonzalo, and Resende, Paola Cristina

Published
2023
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5. Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates

Author

Uraki, Ryuta, Iida, Shun, Halfmann, Peter J., Yamayoshi, Seiya, Hirata, Yuichiro, Iwatsuki-Horimoto, Kiyoko, Kiso, Maki, Ito, Mutsumi, Furusawa, Yuri, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Kuroda, Makoto, Maemura, Tadashi, Kim, Taksoo, Mine, Sohtaro, Iwamoto, Noriko, Li, Rong, Liu, Yanan, Larson, Deanna, Fukushi, Shuetsu, Watanabe, Shinji, Maeda, Ken, Wang, Zhongde, Ohmagari, Norio, Theiler, James, Fischer, Will, Korber, Bette, Imai, Masaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2023
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6. SARS-CoV-2 Infection in Wrestlers after International Tournaments, April 2021

Author

Kuribayashi, Sakiko Tabata, Kasamatsu, Ayu, Ikenoue, Chiaki, Fukusumi, Munehisa, Kamiya, Hajime, Shimada, Tomoe, Tanaka, Teppei, Murakami, Kuniko, McLellan, Rieko Takahashi, Sekizuka, Tsuyoshi, Kuroda, Makoto, and Sunagawa, Tomimasa

Subjects
Olympic athletes -- Health aspects, Wrestlers -- Health aspects, Health
Abstract

Two international wrestling tournaments were held in Almaty, Kazakhstan, during the worldwide COVID-19 pandemic, on April 9-18, 2021: the Wrestling Asian Olympic Games Qualifier and the Wrestling Asian Championships. Approximately [...]

Published
2023
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8. Characterization of SARS-CoV-2 Omicron BA.4 and BA.5 isolates in rodents

Author

Uraki, Ryuta, Halfmann, Peter J., Iida, Shun, Yamayoshi, Seiya, Furusawa, Yuri, Kiso, Maki, Ito, Mutsumi, Iwatsuki-Horimoto, Kiyoko, Mine, Sohtaro, Kuroda, Makoto, Maemura, Tadashi, Sakai-Tagawa, Yuko, Ueki, Hiroshi, Li, Rong, Liu, Yanan, Larson, Deanna, Fukushi, Shuetsu, Watanabe, Shinji, Maeda, Ken, Pekosz, Andrew, Kandeil, Ahmed, Webby, Richard J., Wang, Zhongde, Imai, Masaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2022
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10. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2

Author

Uraki, Ryuta, Kiso, Maki, Iida, Shun, Imai, Masaki, Takashita, Emi, Kuroda, Makoto, Halfmann, Peter J., Loeber, Samantha, Maemura, Tadashi, Yamayoshi, Seiya, Fujisaki, Seiichiro, Wang, Zhongde, Ito, Mutsumi, Ujie, Michiko, Iwatsuki-Horimoto, Kiyoko, Furusawa, Yuri, Wright, Ryan, Chong, Zhenlu, Ozono, Seiya, Yasuhara, Atsuhiro, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Li, Rong, Liu, Yanan, Larson, Deanna, Koga, Michiko, Tsutsumi, Takeya, Adachi, Eisuke, Saito, Makoto, Yamamoto, Shinya, Hagihara, Masao, Mitamura, Keiko, Sato, Tetsuro, Hojo, Masayuki, Hattori, Shin-ichiro, Maeda, Kenji, Valdez, Riccardo, Okuda, Moe, Murakami, Jurika, Duong, Calvin, Godbole, Sucheta, Douek, Daniel C., Maeda, Ken, Watanabe, Shinji, Gordon, Aubree, Ohmagari, Norio, Yotsuyanagi, Hiroshi, Diamond, Michael S., Hasegawa, Hideki, Mitsuya, Hiroaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2022
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11. Spin absorption at ferromagnetic-metal/platinum-oxide interface

Author

Asami, Akio, An, Hongyu, Musha, Akira, Kuroda, Makoto, and Ando, Kazuya

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We investigate the absorption of a spin current at a ferromagnetic-metal/Pt-oxide interface by measuring current-induced ferromagnetic resonance. The spin absorption was characterized by the magnetic damping of the heterostructure. We show that the magnetic damping of a Ni$_{81}$Fe$_{19}$ film is clearly enhanced by attaching Pt-oxide on the Ni$_{81}$Fe$_{19}$ film. The damping enhancement is disappeared by inserting an ultrathin Cu layer between the Ni$_{81}$Fe$_{19}$ and Pt-oxide layers. These results demonstrate an essential role of the direct contact between the Ni$_{81}$Fe$_{19}$ and Pt-oxide to induce sizable interface spin-orbit coupling. Furthermore, the spin-absorption parameter of the Ni$_{81}$Fe$_{19}$/Pt-oxide interface is comparable to that of intensively studied heterostructures with strong spin-orbit coupling, such as an oxide interface, topological insulators, metallic junctions with Rashba spin-orbit coupling. This result illustrates strong spin-orbit coupling at the ferromagnetic-metal/Pt-oxide interface, providing an important piece of information for quantitative understanding the spin absorption and spin-charge conversion at the ferromagnetic-metal/metallic-oxide interface.

Published
2018
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13. Characterization of a new SARS-CoV-2 variant that emerged in Brazil

Author

Imai, Masaki, Halfmann, Peter J., Yamayoshi, Seiya, Iwatsuki-Horimoto, Kiyoko, Chiba, Shiho, Watanabe, Tokiko, Nakajima, Noriko, Ito, Mutsumi, Kuroda, Makoto, Kiso, Maki, Maemura, Tadashi, Takahashi, Kenta, Loeber, Samantha, Hatta, Masato, Koga, Michiko, Nagai, Hiroyuki, Yamamoto, Shinya, Saito, Makoto, Adachi, Eisuke, Akasaka, Osamu, Nakamura, Morio, Nakachi, Ichiro, Ogura, Takayuki, Baba, Rie, Fujita, Kensuke, Ochi, Junichi, Mitamura, Keiko, Kato, Hideaki, Nakajima, Hideaki, Yagi, Kazuma, Hattori, Shin-ichiro, Maeda, Kenji, Suzuki, Tetsuya, Miyazato, Yusuke, Valdez, Riccardo, Gherasim, Carmen, Furusawa, Yuri, Okuda, Moe, Ujie, Michiko, Lopes, Tiago J. S., Yasuhara, Atsuhiro, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Eisfeld, Amie J., Baczenas, John J., Baker, David A., O’Connor, Shelby L., O’Connor, David H., Fukushi, Shuetsu, Fujimoto, Tsuguto, Kuroda, Yudai, Gordon, Aubree, Maeda, Ken, Ohmagari, Norio, Sugaya, Norio, Yotsuyanagi, Hiroshi, Mitsuya, Hiroaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2021

15. Comparison of the Gut Microbiota of Patients Who Improve with Antibiotic Combination Therapy for Ulcerative Colitis and Those Who Do Not: Investigation by Fecal Metagenomic Analyses.

Author

Ohkusa, Toshifumi, Kato, Kimitoshi, Sekizuka, Tsuyoshi, Sugiyama, Toshiro, Sato, Nobuhiro, and Kuroda, Makoto

Abstract

Background/Objectives: The cause of ulcerative colitis (UC) may be related to commensal bacteria in genetically susceptible patients. We previously demonstrated that triple antibiotic combination therapy induces remission in patients with active UC in randomized controlled trials (RCTs). Now, we investigate changes in the gut microbiota of patients who responded to the antibiotic combination therapy. Methods: Thirty-one patients with UC given ATM/AFM (amoxicillin, metronidazole, and tetracycline or fosfomycin) therapy for two weeks were enrolled in this study. The clinical conditions of these UC patients were evaluated by the partial Mayo score. The gut microbiota was compared via the metagenomic shot gun analysis of fecal samples. Results: Of the 31 patients, 16 and 8 experienced complete and partial remission, respectively, over three months in response to ATM/AFM therapy, whereas ATM/AFM showed no efficacy in 7 patients. The dysbiosis before treatment in the active stage could be associated with increased populations of Bacteroides, Parabacteroides, Rickenella, Clostridium, Flavonifractor, Pelagibacter, Bordetella, Massilia, and Piscrickettsia species. Metagenomic analysis revealed dramatic changes in the gut microbiota at an early stage, that is, just two weeks after starting ATM/AFM therapy. After treatment in the responder group, the populations of bifidobacterium and lactobacilli species were significantly increased, while the population of bacteroides decreased. Conclusions: These results suggest that metagenomic analysis demonstrated a marked change in the gut microbiota after antibiotic combination treatment. In the triple antibiotic combination therapy, remission was associated with an increase in bifidobacterium and lactobacilli species. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development

Author

Imai, Masaki, Iwatsuki-Horimoto, Kiyoko, Hatta, Masato, Loeber, Samantha, Halfmann, Peter J., Nakajima, Noriko, Watanabe, Tokiko, Ujie, Michiko, Takahashi, Kenta, Ito, Mutsumi, Yamada, Shinya, Fan, Shufang, Chiba, Shiho, Kuroda, Makoto, Guan, Lizheng, Takada, Kosuke, Armbrust, Tammy, Balogh, Aaron, Furusawa, Yuri, Okuda, Moe, Ueki, Hiroshi, Yasuhara, Atsuhiro, Sakai-Tagawa, Yuko, Lopes, Tiago J. S., Kiso, Maki, Yamayoshi, Seiya, Kinoshita, Noriko, Ohmagari, Norio, Hattori, Shin-ichiro, Takeda, Makoto, Mitsuya, Hiroaki, Krammer, Florian, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Published
2020

18. Enhanced isolation of SARS-CoV-2 by TMPRSS2- expressing cells

Author

Matsuyama, Shutoku, Nao, Naganori, Shirato, Kazuya, Kawase, Miyuki, Saito, Shinji, Takayama, Ikuyo, Nagata, Noriyo, Sekizuka, Tsuyoshi, Katoh, Hiroshi, Kato, Fumihiro, Sakata, Masafumi, Tahara, Maino, Kutsuna, Satoshi, Ohmagari, Norio, Kuroda, Makoto, Suzuki, Tadaki, Kageyama, Tsutomu, and Takeda, Makoto

Published
2020

19. Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants

Author

Changrob, Siriruk, Halfmann, Peter J., Liu, Hejun, Torres, Jonathan L., McGrath, Joshua J.C., Ozorowski, Gabriel, Li, Lei, Wilbanks, G. Dewey, Kuroda, Makoto, Maemura, Tadashi, Huang, Min, Zheng, Nai-Ying, Turner, Hannah L., Erickson, Steven A., Fu, Yanbin, Yasuhara, Atsuhiro, Singh, Gagandeep, Monahan, Brian, Mauldin, Jacob, Srivastava, Komal, Simon, Viviana, Krammer, Florian, Sather, D. Noah, Ward, Andrew B., Wilson, Ian A., Kawaoka, Yoshihiro, and Wilson, Patrick C.

Subjects
Viral antibodies -- Health aspects, Antibodies -- Health aspects, Health care industry
Abstract

The rapid evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identified S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) that was derived from an individual previously infected with WT SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrated broad cross-neutralization of all dominant variants, including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1/XBB). Furthermore, S728-1157 protected hamsters against in vivo challenges with WT, Delta, and BA.1 viruses. Structural analysis showed that this antibody targets a class 1/RBS-A epitope in the receptor binding domain via multiple hydrophobic and polar interactions with its heavy chain complementarity determining region 3 (CDR-H3), in addition to common motifs in CDR-H1/CDR-H2 of class 1/RBS-A antibodies. Importantly, this epitope was more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared with diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential and may inform target-driven vaccine designs against future SARS-CoV-2 variants., Introduction Since the start of the pandemic in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has led to over 660 million cases of coronavirus disease 2019 [...]

Published
2023
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26. Chromobacterium haemolyticum Pneumonia Associated with Near-Drowning and River Water, Japan

Author

Kanamori, Hajime, Aoyagi, Tetsuji, Kuroda, Makoto, Sekizuka, Tsuyoshi, Katsumi, Makoto, Ishikawa, Kenichiro, Hosaka, Tatsuhiko, Baba, Hiroaki, Oshima, Kengo, Tokuda, Koichi, Hasegawa, Masatsugu, Kawazoe, Yu, Kushimoto, Shigeki, and Kaku, Mitsuo

Subjects
Tetracyclines -- Health aspects, Microbial drug resistance -- Health aspects, Pneumonia -- Health aspects, Genomics -- Health aspects, Meropenem -- Health aspects, Health
Abstract

Chromobacterium is a genus of gram-negative, facultative anaerobic bacteria; application of 16S rRNA gene sequencing into bacterial taxonomy is expanding its species (1-5). Most Chromobacterium infections in humans have been [...]

Published
2020
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27. Clinicopathologic and Immunohistochemical Findings from Autopsy of Patient with COVID-19, Japan

Author

Adachi, Takuya, Chong, Ja-Mun, Nakajima, Noriko, Sano, Masahiro, Yamazaki, Jun, Miyamoto, Ippei, Nishioka, Haruka, Akita, Hidetaka, Sato, Yuko, Kataoka, Michiyo, Katano, Harutaka, Tobiume, Minoru, Sekizuka, Tsuyoshi, Itokawa, Kentaro, Kuroda, Makoto, and Suzuki, Tadaki

Subjects
Sulbactam -- Health aspects, Coronaviruses -- Health aspects, Epidemics -- Health aspects, Medical research -- Health aspects, COVID-19 -- Health aspects, Methicillin -- Health aspects, Health
Abstract

Coronavirus disease (COVID-19), which was first reported in December 2019 in Wuhan, China, has been spreading rapidly and on a global scale. The causative virus is severe acute respiratory syndrome [...]

Published
2020
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28. Candidatus Mycoplasma haemohominis in Human, Japan

Author

Hattori, Norimichi, Kuroda, Makoto, Katano, Harutaka, Takuma, Takahiro, Ito, Takayoshi, Arai, Nana, Yanai, Ryo, Sekizuka, Tsuyoshi, Ishii, Sho, Miura, Yoko, Tokunaga, Takahiro, Watanabe, Hiroyuki, Nomura, Norihiro, Eguchi, Junichi, Hasegawa, Hideki, Nakamaki, Tsuyoshi, Wakita, Takaji, and Niki, Yoshihito

Subjects
Tetracyclines -- Health aspects, Levofloxacin -- Health aspects, Gene mutation -- Health aspects, Infection -- Genetic aspects -- Health aspects, Genomes -- Health aspects, Genomics -- Health aspects, Medical schools -- Health aspects, Beef cattle, Moxifloxacin, Fluoroquinolones, Genes, Microscopy, Pathogenic microorganisms, Minocycline, Characterization, Electron microscopy, Health
Abstract

Hemotropic mycoplasmas (or hemoplasmas; size We identified and characterized Candidatus M. haemohominis infections in a patient with pyrexia of unknown origin. The patient had various life-threatening symptoms that were not [...]

Published
2020
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33. Development of a High-Throughput Analytical Method for Antimicrobials in Wastewater Using an Automated Pipetting and Solid-Phase Extraction System.

Author

Azuma, Takashi, Matsunaga, Nobuaki, Ohmagari, Norio, and Kuroda, Makoto

Subjects
SOLID phase extraction, SEWAGE, ENVIRONMENTAL health, DRUG resistance in microorganisms, ANTI-infective agents
Abstract

Antimicrobial resistance (AMR) has emerged and spread globally. Recent studies have also reported the presence of antimicrobials in a wide variety of aquatic environments. Conducting a nationwide monitoring survey of AMR in the environment to elucidate its status and to assess its impact on ecosystems and human health is of social importance. In this study, we developed a novel high-throughput analysis (HTA) system based on a 96-well plate solid-phase extraction (SPE), using automated pipetting and an SPE pre-treatment system. The effectiveness of the system as an HTA for antimicrobials in environmental water was verified by comparing it with a conventional manual analytical system in a domestic hospital over a period of two years and four months. The results of the manual analysis and HTA using a combination of automated pipetting and SPE systems were generally consistent, and no statistically significant difference was observed (p > 0.05) between the two systems. The agreement ratios between the measured concentrations based on the conventional and HTA methods were positively correlated with a correlation coefficient of r = 0.99. These results indicate that HTA, which combines automated pipetting and an SPE pre-treatment system for rapid, high-volume analysis, can be used as an effective approach for understanding the environmental contamination of antimicrobials at multiple sites. To the best of our knowledge, this is the first report to present the accuracy and agreement between concentrations based on a manual analysis and those measured using HTA in hospital wastewater. These findings contribute to a comprehensive understanding of antimicrobials in aquatic environments and assess the ecological and human health risks associated with antimicrobials and antimicrobial-resistant bacteria to maintain the safety of aquatic environments. [ABSTRACT FROM AUTHOR]

Published
2024
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36. Impact of COVID-19 and closed transmission of SARS-CoV-2 during the first wave in Toyama Prefecture, Japan, March 30 to May 18, 2020

Author

Tamura, Kosuke, primary, Inasaki, Noriko, additional, Itamochi, Masae, additional, Saga, Yumiko, additional, Shimada, Takahisa, additional, Yazawa, Shunsuke, additional, Sasajima, Hitoshi, additional, Kawashiri, Chikako, additional, Yamazaki, Emiko, additional, Ichikawa, Tomomi, additional, Kaya, Hiroyasu, additional, Yamamoto, Yoshihiro, additional, Morinaga, Yoshitomo, additional, Yamashiro, Seiji, additional, Nomura, Satoshi, additional, Takeda, Shinichi, additional, Itoh, Hiroyuki, additional, Hirota, Koujiro, additional, Horie, Yukio, additional, Hirano, Norikazu, additional, Sekizuka, Tsuyoshi, additional, Kuroda, Makoto, additional, Tani, Hideki, additional, and Oishi, Kazunori, additional

Published
2023
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37. Pet Animals Were Infected with SARS-CoV-2 from Their Owners Who Developed COVID-19: Case Series Study

Author

Kuroda, Yudai, primary, Watanabe, Kei, additional, Yamamoto, Tsukasa, additional, Suzuki, Hiroki, additional, Park, Eun-sil, additional, Ishijima, Keita, additional, Tatemoto, Kango, additional, Virhuez-Mendoza, Milagros, additional, Inoue, Yusuke, additional, Harada, Michiko, additional, Nishino, Ayano, additional, Sekizuka, Tsuyoshi, additional, Kuroda, Makoto, additional, Fujimoto, Tsuguto, additional, Ishihara, Genki, additional, Horie, Ryo, additional, Kawamoto, Kosuke, additional, and Maeda, Ken, additional

Published
2023
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38. Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants

Author

Nagasawa, Norika, primary, Kimura, Ryusuke, additional, Akagawa, Mao, additional, Shirai, Tatsuya, additional, Sada, Mitsuru, additional, Okayama, Kaori, additional, Sato-Fujimoto, Yuka, additional, Saito, Makoto, additional, Kondo, Mayumi, additional, Katayama, Kazuhiko, additional, Ryo, Akihide, additional, Kuroda, Makoto, additional, and Kimura, Hirokazu, additional

Published
2023
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39. Novel SARS-CoV-2 Variant in Travelers from Brazil to Japan

Author

Fujino, Takahisa, Nomoto, Hidetoshi, Kutsuna, Satoshi, Ujiie, Mugen, Suzuki, Tetsuya, Sato, Rubuna, Fujimoto, Tsuguto, Kuroda, Makoto, Wakita, Takaji, and Ohmagari, Norio

Subjects
Travelers -- Medical examination, Health
Abstract

Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (1), has wreaked havoc worldwide. SARS-CoV-2 causes severe respiratory failure, often rapidly in susceptible patients. Moreover, new variants [...]

Published
2021
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41. Epidemiology and Genetic Analysis of SARS-CoV-2 in Myanmar during the Community Outbreaks in 2020

Author

Wint Wint Phyu, Reiko Saito, Keita Wagatsuma, Takashi Abe, Htay Htay Tin, Eh Htoo Pe, Su Mon Kyaw Win, Nay Chi Win, Lasham Di Ja, Sekizuka Tsuyoshi, Kuroda Makoto, Yadanar Kyaw, Irina Chon, Shinji Watanabe, Hideki Hasegawa, and Hisami Watanabe

Subjects
SARS-CoV-2, COVID-19, community transmission, case fatality rate, reproductive number, molecular epidemiology, Microbiology, QR1-502
Abstract

We aimed to analyze the situation of the first two epidemic waves in Myanmar using the publicly available daily situation of COVID-19 and whole-genome sequencing data of SARS-CoV-2. From March 23 to December 31, 2020, there were 33,917 confirmed cases and 741 deaths in Myanmar (case fatality rate of 2.18%). The first wave in Myanmar from March to July was linked to overseas travel, and then a second wave started from Rakhine State, a western border state, leading to the second wave spreading countrywide in Myanmar from August to December 2020. The estimated effective reproductive number (Rt) nationwide reached 6–8 at the beginning of each wave and gradually decreased as the epidemic spread to the community. The whole-genome analysis of 10 Myanmar SARS-CoV-2 strains together with 31 previously registered strains showed that the first wave was caused by GISAID clade O or PANGOLIN lineage B.6 and the second wave was changed to clade GH or lineage B.1.36.16 with a close genetic relationship with other South Asian strains. Constant monitoring of epidemiological situations combined with SARS-CoV-2 genome analysis is important for adjusting public health measures to mitigate the community transmissions of COVID-19.

Published
2022
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42. Limitations of Ribotyping as Genotyping Method for Corynebacterium ulcerans

Author

Sekizuka, Tsuyoshi, Katsukawa, Chihiro, Kuroda, Makoto, Shibayama, Keigo, Otsuji, Ken, Saito, Mitsumasa, Yamamoto, Akihiko, and Iwaki, Masaaki

Subjects
Bacterial proteins -- Methods -- Analysis, DNA sequencing -- Methods -- Analysis, DNA -- Analysis -- Methods, Genomes -- Analysis -- Methods, Zoonoses -- Analysis -- Methods, Genomics -- Methods -- Analysis, Health
Abstract

Corynebacterium ulcerans is a zoonotic pathogen that causes an illness categorized in World Health Organization documents as diphtheria (1). Genotyping methods such as ribotyping, multilocus sequence typing (MLST), and whole-genome [...]

Published
2020
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45. A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid

Author

Yamagishi, Takuya, Matsui, Mari, Sekizuka, Tsuyoshi, Ito, Hiroaki, Fukusumi, Munehisa, Uehira, Tomoko, Tsubokura, Miyuki, Ogawa, Yoshihiko, Miyamoto, Atsushi, Nakamori, Shoji, Tawa, Akio, Yoshimura, Takahisa, Yoshida, Hideki, Hirokawa, Hidetetsu, Suzuki, Satowa, Matsui, Tamano, Shibayama, Keigo, Kuroda, Makoto, and Oishi, Kazunori

Published
2020
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46. Phylogeny and Immunoreactivity of Norovirus GII.P16-GII.2, Japan, Winter 2016-17

Author

Nagasawa, Koo, Matsushima, Yuki, Motoya, Takumi, Mizukoshi, Fuminori, Ueki, Yo, Sakon, Naomi, Murakami, Koichi, Shimizu, Tomomi, Okabe, Nobuhiko, Nagata, Noriko, Shirabe, Komei, Shinomiya, Hiroto, Suzuki, Wataru, Kuroda, Makoto, Sekizuka, Tsuyoshi, Ryo, Akihide, Fujita, Kiyotaka, Oishi, Kazunori, Katayama, Kazuhiko, and Kimura, Hirokazu

Subjects
Communicable diseases -- Reports -- Analysis, Phylogeny -- Reports -- Analysis, Gastroenteritis -- Reports -- Analysis, Health
Abstract

Norovirus is a major cause of acute gastroenteritis in humans and is genetically classified into 7 genogroups (GI-GVII). Among them, norovirus GI, GII, and GIV infect humans, and human norovirus [...]

Published
2018
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50. Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2

Author

Uraki, Ryuta, Kiso, Maki, Iida, Shun, Imai, Masaki, Takashita, Emi, Kuroda, Makoto, Halfmann, Peter J., Loeber, Samantha, Maemura, Tadashi, Yamayoshi, Seiya, Fujisaki, Seiichiro, Wang, Zhongde, Ito, Mutsumi, Ujie, Michiko, Iwatsuki-Horimoto, Kiyoko, Furusawa, Yuri, Wright, Ryan, Chong, Zhenlu, Ozono, Seiya, Yasuhara, Atsuhiro, Ueki, Hiroshi, Sakai-Tagawa, Yuko, Li, Rong, Liu, Yanan, Larson, Deanna, Koga, Michiko, Tsutsumi, Takeya, Adachi, Eisuke, Saito, Makoto, Yamamoto, Shinya, Hagihara, Masao, Mitamura, Keiko, Sato, Tetsuro, Hojo, Masayuki, Hattori, Shin-ichiro, Maeda, Kenji, Valdez, Riccardo, Okuda, Moe, Murakami, Jurika, Duong, Calvin, Godbole, Sucheta, Douek, Daniel C., Maeda, Ken, Watanabe, Shinji, Gordon, Aubree, Ohmagari, Norio, Yotsuyanagi, Hiroshi, Diamond, Michael S., Hasegawa, Hideki, Mitsuya, Hiroaki, Suzuki, Tadaki, and Kawaoka, Yoshihiro

Abstract

The recent emergence of SARS-CoV-2 Omicron (B.1.1.529 lineage) variants possessing numerous mutations has raised concerns of decreased effectiveness of current vaccines, therapeutic monoclonal antibodies and antiviral drugs for COVID-19 against these variants1,2. The original Omicron lineage, BA.1, prevailed in many countries, but more recently, BA.2 has become dominant in at least 68 countries3. Here we evaluated the replicative ability and pathogenicity of authentic infectious BA.2 isolates in immunocompetent and human ACE2-expressing mice and hamsters. In contrast to recent data with chimeric, recombinant SARS-CoV-2 strains expressing the spike proteins of BA.1 and BA.2 on an ancestral WK-521 backbone4, we observed similar infectivity and pathogenicity in mice and hamsters for BA.2 and BA.1, and less pathogenicity compared with early SARS-CoV-2 strains. We also observed a marked and significant reduction in the neutralizing activity of plasma from individuals who had recovered from COVID-19 and vaccine recipients against BA.2 compared to ancestral and Delta variant strains. In addition, we found that some therapeutic monoclonal antibodies (REGN10987 plus REGN10933, COV2-2196 plus COV2-2130, and S309) and antiviral drugs (molnupiravir, nirmatrelvir and S-217622) can restrict viral infection in the respiratory organs of BA.2-infected hamsters. These findings suggest that the replication and pathogenicity of BA.2 is similar to that of BA.1 in rodents and that several therapeutic monoclonal antibodies and antiviral compounds are effective against Omicron BA.2 variants.

Published
2024
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