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Article ; Online: Global spread of a Japan-originated Delta lineage of SARS-CoV-2 after the Tokyo Olympics is most likely unrelated to the Olympics.

Shimura, Takako / Kosaki, Kenjiro

2022

Abstract: Participants of the 2021 Summer Olympics in Tokyo were required to adhere to strict health protocols, and there were no major local outbreaks within the separation bubbles. However, based on viral genomic data, we report that the Japan-specific Delta ... ...

Abstract	Participants of the 2021 Summer Olympics in Tokyo were required to adhere to strict health protocols, and there were no major local outbreaks within the separation bubbles. However, based on viral genomic data, we report that the Japan-specific Delta variants did spread out globally during or after the Olympics.
Language	English
Publishing date	2022-02-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1212504-0
ISSN	1708-8305 ; 1195-1982
ISSN (online)	1708-8305
ISSN	1195-1982
DOI	10.1093/jtm/taac017
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Article ; Online: The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals.

Uwamino, Yoshifumi / Yokoyama, Takashi / Shimura, Takako / Nishimura, Tomoyasu / Sato, Yasunori / Wakui, Masatoshi / Kosaki, Kenjiro / Hasegawa, Naoki / Murata, Mitsuru

Vaccine

2022 Volume 40, Issue 13, Page(s) 1928–1931

Abstract: The reduced vaccine efficacy against the SARS-CoV-2 variant lineage B. 1.351 (beta variant) containing the E484K and N501Y mutations is well known. The E484K mutation in SARS-CoV-2 is thought to be responsible for weakened humoral immunity. Vaccine ... ...

Abstract	The reduced vaccine efficacy against the SARS-CoV-2 variant lineage B. 1.351 (beta variant) containing the E484K and N501Y mutations is well known. The E484K mutation in SARS-CoV-2 is thought to be responsible for weakened humoral immunity. Vaccine efficacy against the R.1 lineage, which contains the E484K mutation but not the N501Y mutation, is uncertain. Serum samples were collected from 100 healthy Japanese participants three weeks after receiving the second dose of the BNT162b2 vaccine, and serum neutralization antibody titers were measured against five SARS-CoV-2 variants. The geometric mean neutralization titers measured for the original and R.1 lineages were equivalent (91.90 ± 2.40 and 102.67 ± 2.28, respectively), whereas a low titer was measured for the beta variant (18.03 ± 1.92). Although further investigations with other variant strains and serum samples are essential, our results imply that the weakened humoral response is not caused solely by the E484K mutation. (UMIN000043340).
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral ; BNT162 Vaccine ; COVID-19/prevention & control ; Humans ; Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2022-02-14
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2022.02.047
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Article: The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals

Uwamino, Yoshifumi / Yokoyama, Takashi / Shimura, Takako / Nishimura, Tomoyasu / Sato, Yasunori / Wakui, Masatoshi / Kosaki, Kenjiro / Hasegawa, Naoki / Murata, Mitsuru

Vaccine. 2022 Mar. 18, v. 40, no. 13

2022

Abstract	The reduced vaccine efficacy against the SARS-CoV-2 variant lineage B. 1.351 (beta variant) containing the E484K and N501Y mutations is well known. The E484K mutation in SARS-CoV-2 is thought to be responsible for weakened humoral immunity. Vaccine efficacy against the R.1 lineage, which contains the E484K mutation but not the N501Y mutation, is uncertain. Serum samples were collected from 100 healthy Japanese participants three weeks after receiving the second dose of the BNT162b2 vaccine, and serum neutralization antibody titers were measured against five SARS-CoV-2 variants. The geometric mean neutralization titers measured for the original and R.1 lineages were equivalent (91.90 ± 2.40 and 102.67 ± 2.28, respectively), whereas a low titer was measured for the beta variant (18.03 ± 1.92). Although further investigations with other variant strains and serum samples are essential, our results imply that the weakened humoral response is not caused solely by the E484K mutation. (UMIN000043340).
Keywords	Severe acute respiratory syndrome coronavirus 2 ; antibodies ; blood serum ; humoral immunity ; mutation ; neutralization ; vaccines
Language	English
Dates of publication	2022-0318
Size	p. 1928-1931.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2022.02.047
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Article ; Online: Multiple introductions of SARS-CoV-2 B.1.1.214 lineages from mainland Japan preceded the third wave of the COVID-19 epidemic in Hokkaido.

Shimura, Takako / Abe, Kodai / Takenouchi, Toshiki / Yamada, Mamiko / Suzuki, Hisato / Suematsu, Makoto / Nakakubo, Sho / Kamada, Keisuke / Konno, Satoshi / Teshima, Takanori / Kosaki, Kenjiro

Travel medicine and infectious disease

2021 Volume 44, Page(s) 102210

Abstract: Background: The third wave of the COVID-19 epidemic in the island of Hokkaido, the second largest island in Japan, began abruptly in October 2020.: Methods: We conducted a phylodynamic analysis of the SARS-CoV-2 genome sequences obtained from ... ...

Abstract	Background: The third wave of the COVID-19 epidemic in the island of Hokkaido, the second largest island in Japan, began abruptly in October 2020. Methods: We conducted a phylodynamic analysis of the SARS-CoV-2 genome sequences obtained from tertiary medical centers in the Greater Tokyo Area and Sapporo, the largest city in the island of Hokkaido, and genome sequences published by GISAID, an international SARS-CoV-2 genome database. We also analyzed the statistics on the person-nights of travelers in the island of Hokkaido from the Greater Tokyo Area in 2019 versus 2020. Results: At least eight sub-lineages belonging to the B.1.1.214 lineage were introduced to the island of Hokkaido from the island of Honshu, the mainland of Japan from late July to November 2020, during the governmental travel promotion program. Five of the eight sub-lineages originated from the Greater Tokyo Area. Comparison of the monthly ratios of the person-nights of travelers in the island of Hokkaido from the Greater Tokyo Area in 2019 and 2020 revealed that the highest value occurred in October 2020. Conclusion: We contend that the Japanese governmental travel promotion program contributed to the introduction of the B.1.1.214 sub-lineages from the main island of Honshu to the island of Hokkaido, and drove the third wave in Hokkaido, even if we are unable to establish the causality.
MeSH term(s)	COVID-19 ; Epidemics ; Humans ; Japan/epidemiology ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2021-11-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2170891-5
ISSN	1873-0442 ; 1477-8939
ISSN (online)	1873-0442
ISSN	1477-8939
DOI	10.1016/j.tmaid.2021.102210
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Article ; Online: Correction to: Effect of early tumor response on the health-related quality of life among patients on second-line chemotherapy for advanced gastric cancer in the ABSOLUTE trial.

Fujitani, Kazumasa / Shitara, Kohei / Takashima, Atsuo / Koeda, Keisuke / Hara, Hiroki / Nakayama, Norisuke / Hironaka, Shuichi / Nishikawa, Kazuhiro / Kimura, Yutaka / Amagai, Kenji / Hosaka, Hisashi / Komatsu, Yoshito / Shimada, Ken / Kawabata, Ryohei / Ohdan, Hideki / Kodera, Yasuhiro / Nakamura, Masato / Nakajima, Takako Eguchi / Miyata, Yoshinori /

Moriwaki, Toshikazu / Kusumoto, Tetsuya / Nishikawa, Kazuo / Ogata, Kazuhiro / Shimura, Masashi / Morita, Satoshi / Koizumi, Wasaburo

Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association

2020 Volume 24, Issue 2, Page(s) 477–478

Language	English
Publishing date	2020-12-09
Publishing country	Japan
Document type	Published Erratum
ZDB-ID	1463526-4
ISSN	1436-3305 ; 1436-3291
ISSN (online)	1436-3305
ISSN	1436-3291
DOI	10.1007/s10120-020-01144-7
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Article ; Online: Identification of B.1.346 Lineage of SARS-CoV-2 in Japan: Genomic Evidence of Re-entry of Clade 20C.

Abe, Kodai / Shimura, Takako / Takenouchi, Toshiki / Iwasaki, Yuka W / Ishizu, Hirotsugu / Uwamino, Yoshifumi / Uno, Shunsuke / Gotoh, Jun / Tachikawa, Natsuo / Takeuchi, Yuriko / Katayama, Junpei / Nozaki, Hiroyuki / Fujii, Susumu / Seki, Shikou / Nakamura, Morio / Uda, Kazuhiro / Misumi, Takahiko / Ishihara, Jun / Yamada, Kenichiro /

Kanai, Toshio / Murai, Shinji / Araki, Kazuhiro / Ebihara, Tamotsu / Siomi, Haruhiko / Hasegawa, Naoki / Kitagawa, Yuko / Amagai, Masayuki / Suematsu, Makoto / Kosaki, Kenjiro

The Keio journal of medicine

2021 Volume 70, Issue 2, Page(s) 44–50

Abstract: SARS-CoV-2 whole-genome sequencing of samples from COVID-19 patients is useful for informing infection control. Datasets of these genomes assembled from multiple hospitals can give critical clues to regional or national trends in infection. Herein, we ... ...

Abstract	SARS-CoV-2 whole-genome sequencing of samples from COVID-19 patients is useful for informing infection control. Datasets of these genomes assembled from multiple hospitals can give critical clues to regional or national trends in infection. Herein, we report a lineage summary based on data collected from hospitals located in the Tokyo metropolitan area. We performed SARS-CoV-2 whole-genome sequencing of specimens from 198 patients with COVID-19 at 13 collaborating hospitals located in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions were performed to differentiate and classify the viral lineages. More than 90% of the identified strains belonged to Clade 20B, which has been prevalent in European countries since March 2020. Only two lineages (B.1.1.284 and B.1.1.214) were found to be predominant in Japan. However, one sample from a COVID-19 patient admitted to a hospital in the Kanto region in November 2020 belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in the western United States since November 2020. The patient had no history of overseas travel or any known contact with anyone who had travelled abroad. Consequently, the Clade 20C strain belonging to the B.1.346 lineage appeared likely to have been imported from the western United States to Japan across the strict quarantine barrier. B.1.1.284 and B.1.1.214 lineages were found to be predominant in the Kanto region, but a single case of the B.1.346 lineage of clade 20C, probably imported from the western United States, was also identified. These results illustrate that a decentralized network of hospitals offers significant advantages as a highly responsive system for monitoring regional molecular epidemiologic trends.
MeSH term(s)	COVID-19/virology ; Genome, Viral ; Humans ; Phylogeny ; SARS-CoV-2/genetics ; Whole Genome Sequencing/methods
Language	English
Publishing date	2021-04-14
Publishing country	Japan
Document type	Journal Article
ZDB-ID	390981-5
ISSN	1880-1293 ; 0022-9717
ISSN (online)	1880-1293
ISSN	0022-9717
DOI	10.2302/kjm.2021-0005-OA
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Article ; Online: Effect of early tumor response on the health-related quality of life among patients on second-line chemotherapy for advanced gastric cancer in the ABSOLUTE trial.

Moriwaki, Toshikazu / Kusumoto, Tetsuya / Nishikawa, Kazuo / Ogata, Kazuhiro / Shimura, Masashi / Morita, Satoshi / Koizumi, Wasaburo

Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association

2020 Volume 24, Issue 2, Page(s) 467–476

Abstract: Background: This study evaluated the association between early tumor response at 8 weeks, previously reported as a positive outcome prognosticator, and health-related quality of life (HRQOL) in advanced gastric cancer (AGC) patients enrolled in the ... ...

Abstract	Background: This study evaluated the association between early tumor response at 8 weeks, previously reported as a positive outcome prognosticator, and health-related quality of life (HRQOL) in advanced gastric cancer (AGC) patients enrolled in the ABSOLUTE trial. Methods: HRQOL was assessed using the EuroQol-5 Dimension (EQ-5D) utility index score in patients with complete response (CR) + partial response (PR) and progressive disease (PD) at 8 weeks, and time-to-deterioration (TtD) of the EQ-5D score, with the preset minimally important difference (MID) of 0.05, was compared between these populations. Among the enrolled patients, 143 and 160 patients were assessable in weekly solvent-based paclitaxel (Sb-PTX) arm and weekly nanoparticle albumin-bound paclitaxel (nab-PTX) arm, respectively. Results: Changes of the EQ-5D score from baseline to 8 weeks in the nab-PTX arm were 0.0009 and - 0.1229 in CR + PR and PD patients, respectively; the corresponding values for the Sb-PTX arm were - 0.0019 and - 0.1549. For both treatments, changes of the EQ-5D score from baseline at 8 weeks were significantly larger in patients with PD than in those with CR + PR. The median TtD was 3.9 and 2.2 months in patients with CR + PR and PD, respectively, for nab-PTX [hazard ratio (HR) = 0.595, 95% confidence interval (CI) 0.358-0.989]. For Sb-PTX, the corresponding values were 4.7 and 2.0 months (HR = 0.494, 95% CI 0.291-0.841). Conclusions: Early tumor shrinkage was associated with maintained HRQOL in AGC patients on the second-line chemotherapy with taxanes.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Albumins/administration & dosage ; Antineoplastic Agents, Phytogenic/administration & dosage ; Female ; Humans ; Japan ; Male ; Middle Aged ; Nanoparticle Drug Delivery System ; Paclitaxel/administration & dosage ; Quality of Life ; Solvents/administration & dosage ; Stomach Neoplasms/drug therapy ; Stomach Neoplasms/psychology ; Treatment Outcome
Chemical Substances	130-nm albumin-bound paclitaxel ; Albumins ; Antineoplastic Agents, Phytogenic ; Nanoparticle Drug Delivery System ; Solvents ; Paclitaxel (P88XT4IS4D)
Keywords	covid19
Language	English
Publishing date	2020-11-02
Publishing country	Japan
Document type	Clinical Trial, Phase III ; Equivalence Trial ; Journal Article ; Multicenter Study ; Randomized Controlled Trial
ZDB-ID	1463526-4
ISSN	1436-3305 ; 1436-3291
ISSN (online)	1436-3305
ISSN	1436-3291
DOI	10.1007/s10120-020-01131-y
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Article ; Online: Identification of B.1.346 lineage of SARS-CoV-2 in Japan: Genomic evidence of re-entry of Clade 20C

Kodai, Abe / Takako, Shimura / Toshiki, Takenouchi / Yuka, Iwasaki / Hirotsugu, Ishizu / Yoshifumi, Uwamino / Shunsuke, Uno / Jun, Gotoh / Natsuo, Tachikawa / Yuriko, Takeuchi / Junpei, Katayama / Hiroyuki, Nozaki / Susumu, Fujii / Shikou, Seki / Morio, Nakamura / Kazuhiro, Uda / Takahiko, Misumi / Jun, Ishihara / Kenichiro, Yamada /

Toshio, Kanai / Shinji, Murai / Kazuhiro, Araki / Tamotsu, Ebihara / Haruhiko, Shiomi / Naoki, Hasegawa / Masayuki, Amagai / Yuko, Kitagawa / Makoto, Suematsu / Kenjiro, Kosaki

medRxiv

Abstract: Objectives Whole SARS-CoV-2 genome sequencing from COVID-19 patients is useful for infection control and regional trends evaluation. We report a lineage data collected from hospitals in the Kanto region of Japan. Methods We performed whole genome ... ...

Abstract	Objectives Whole SARS-CoV-2 genome sequencing from COVID-19 patients is useful for infection control and regional trends evaluation. We report a lineage data collected from hospitals in the Kanto region of Japan. Methods We performed whole genome sequencing in specimens of 198 COVID-19 patients at 13 collaborating hospitals in the Kanto region. Phylogenetic analysis and fingerprinting of the nucleotide substitutions underwent to differentiate and classify the viral lineages. Results More than 90% of the strains belonged to Clade 20B and two lineages (B.1.1.284 and B.1.1.214) have been detected predominantly in the Kanto region. However, one sample from a COVID-19 patient in November 2020, belonged to the B.1.346 lineage of Clade 20C, which has been prevalent in western United States. The patient had no history of overseas travel and no contact with anyone who had travelled abroad, suggesting that this strain appeared likely to have been imported from western United States, across the strict quarantine barrier. Conclusion B.1.1.284 and B.1.1.214 have been identified predominantly in the Kanto region and B.1.346 of clade 20C in one patient was probably imported from western United States. These results illustrate that a decentralized network of hospitals can be significantly advantageous for monitoring regional molecular epidemiologic trends.
Keywords	covid19
Language	English
Publishing date	2021-02-01
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.01.29.21250798
Database	COVID19

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Article: A strategy for screening an inhibitor of viral silencing suppressors, which attenuates symptom development of plant viruses.

Shimura, Hanako / Fukagawa, Takako / Meguro, Ayano / Yamada, Hirokazu / Oh-Hira, Mahito / Sano, Shinsuke / Masuta, Chikara

FEBS letters

2008 Volume 582, Issue 29, Page(s) 4047–4052

Abstract: To find out whether we can control plant virus diseases by blocking viral RNA silencing suppressors (RSSs), we developed a strategy to screen inhibitors that block the association of RSSs with siRNAs using a surface plasmon resonance assay. The screened ... ...

Abstract	To find out whether we can control plant virus diseases by blocking viral RNA silencing suppressors (RSSs), we developed a strategy to screen inhibitors that block the association of RSSs with siRNAs using a surface plasmon resonance assay. The screened chemicals were tested in competition with RSSs for binding to siRNAs using a mobility shift assay. We then confirmed that tested chemicals actually inhibited the RSS activity in vivo using a protoplast assay which was developed for this purpose. This entire system can be adapted to screening inhibitors of not only plant viruses but also some animal viruses possessing RSSs.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/isolation & purification ; Antiviral Agents/pharmacology ; Drug Discovery ; Plant Diseases/virology ; Plant Viruses/drug effects ; Plant Viruses/genetics ; RNA Interference/drug effects ; RNA, Small Interfering/drug effects ; RNA, Viral/drug effects
Chemical Substances	Antiviral Agents ; RNA, Small Interfering ; RNA, Viral
Language	English
Publishing date	2008-12-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2008.10.046
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Article ; Online: aCGH Analysis of Predictive Biomarkers for Response to Bevacizumab plus Oxaliplatin- or Irinotecan-Based Chemotherapy in Patients with Metastatic Colorectal Cancer.

Fujita, Yoshihiko / Taguri, Masataka / Yamazaki, Kentaro / Tsurutani, Junji / Sakai, Kazuko / Tsushima, Takahiro / Nagase, Michitaka / Tamagawa, Hiroshi / Ueda, Shinya / Tamura, Takao / Tsuji, Yasushi / Murata, Kohei / Taira, Koichi / Denda, Tadamichi / Moriwaki, Toshikazu / Funai, Sadao / Nakajima, Takako Eguchi / Muro, Kei / Tsuji, Akihito /

Yoshida, Motoki / Suyama, Koichi / Kurimoto, Takuya / Sugimoto, Naotoshi / Baba, Eishi / Seki, Nobuhiko / Sato, Mikio / Shimura, Takaya / Boku, Narikazu / Hyodo, Ichinosuke / Yamanaka, Takeharu / Nishio, Kazuto

The oncologist

2018 Volume 24, Issue 3, Page(s) 327–337

Abstract: Background: The randomized phase III study (WJOG4407G) showed equivalent efficacy between FOLFOX and FOLFIRI in combination with bevacizumab as the first-line treatment for metastatic colorectal cancer (mCRC). We studied whole genome copy number ... ...

Abstract	Background: The randomized phase III study (WJOG4407G) showed equivalent efficacy between FOLFOX and FOLFIRI in combination with bevacizumab as the first-line treatment for metastatic colorectal cancer (mCRC). We studied whole genome copy number profiles using array-based comparative genomic hybridization (aCGH) analysis of tumor tissue samples obtained in this study. The aim of this study was to identify gene copy number alterations that could aid in selecting either FOLFOX or FOLFIRI in combination with bevacizumab for patients with mCRC. Materials and methods: DNA was purified from 154 pretreatment formalin-fixed paraffin-embedded tissue samples (75 from the FOLFOX arm and 79 from the FOLFIRI arm) of 395 patients enrolled in the WJOG4407G trial and analyzed by aCGH. Genomic regions greater than 1.2-fold were regarded as copy number gain (CNG). Results: Patient characteristics between the treatment arms were well balanced except for tumor laterality (left side; 64% in FOLFOX arm and 80% in FOLFIRI arm, Conclusion: Chromosome 8q24.1-q24.2 may contain genes that could potentially serve as predictive markers for selecting either FOLFOX or FOLFIRI in combination with bevacizumab for treatment of patients with mCRC. Implications for practice: Bevacizumab has been used as a standard first-line treatment for patients with metastatic colorectal cancer (mCRC) in combination with either oxaliplatin-based or irinotecan-based chemotherapy. Until now, there has been no predictive marker to choose between the two combination chemotherapies. This array-based comparative genomic hybridization analysis revealed that the difference in therapeutic effect between the two combination chemotherapies is prominent in patients with mCRC with gene copy number gain in chromosome 8p24.1-p24.2. Such patients showed more favorable response and survival when treated with irinotecan-based combination chemotherapy. Overlapping genes commonly found in this region may be predictive biomarkers of the efficacy of the combination chemotherapy with bevacizumab.
MeSH term(s)	Antineoplastic Combined Chemotherapy Protocols/pharmacology ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Bevacizumab/pharmacology ; Bevacizumab/therapeutic use ; Biomarkers/metabolism ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/mortality ; Colorectal Neoplasms/pathology ; Comparative Genomic Hybridization/methods ; Female ; Humans ; Irinotecan/pharmacology ; Irinotecan/therapeutic use ; Male ; Middle Aged ; Neoplasm Metastasis ; Oxaliplatin/pharmacology ; Oxaliplatin/therapeutic use ; Prognosis ; Survival Analysis
Chemical Substances	Biomarkers ; Oxaliplatin (04ZR38536J) ; Bevacizumab (2S9ZZM9Q9V) ; Irinotecan (7673326042)
Language	English
Publishing date	2018-11-13
Publishing country	United States
Document type	Clinical Trial, Phase III ; Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	1409038-7
ISSN	1549-490X ; 1083-7159
ISSN (online)	1549-490X
ISSN	1083-7159
DOI	10.1634/theoncologist.2018-0119
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