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Article ; Online: Genomic evidence for reinfection with different Omicron subvariants.

Hirotsu, Yosuke / Omata, Masao

2023 Volume 86, Issue 3, Page(s) e61–e63

MeSH term(s)	Humans ; Reinfection ; Genomics
Language	English
Publishing date	2023-01-12
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2023.01.010
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Article ; Online: Detection of the Omicron BA.2.75 subvariant in Japan.

Hirotsu, Yosuke / Omata, Masao

The Journal of infection

2022 Volume 86, Issue 1, Page(s) e5–e7

MeSH term(s)	Humans ; Japan ; COVID-19/diagnosis
Language	English
Publishing date	2022-09-07
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2022.08.038
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Article ; Online: Effectiveness of the severe acute respiratory syndrome coronavirus 2 Omicron BA.5 bivalent vaccine on symptoms in healthcare workers with BA.5 infection.

Hirotsu, Yosuke / Takatori, Mika / Mochizuki, Hitoshi / Omata, Masao

Vaccine: X

2024 Volume 17, Page(s) 100433

Abstract: Background: The infection status of healthcare workers (HCWs) with coronavirus disease 2019 has become a major concern worldwide. In this study, we investigated the efficacy of the number of vaccine doses on symptoms after BA.5-adapted bivalent ... ...

Abstract	Background: The infection status of healthcare workers (HCWs) with coronavirus disease 2019 has become a major concern worldwide. In this study, we investigated the efficacy of the number of vaccine doses on symptoms after BA.5-adapted bivalent vaccination in HCWs. Methods: We analyzed the occupation, route of infection, symptoms, and vaccination history of all HCWs who tested positive for severe acute respiratory syndrome coronavirus 2 and worked in our hospital from November 2020 to March 2023. A logistic regression analysis was performed to examine the association between the presence of BA.5-adapted bivalent vaccination and symptoms. Results: During the observation period, 531 HCWs became infected. Of these, 72 % were women, with a median age of 30 years. Nurses accounted for 57 % of the infected cases, and many of the infection routes were from family members. We examined the relationship between symptoms in 352 HCWs infected with the Omicron BA.5* variant and the number of vaccine doses. As the number of vaccine doses increased, the rate of fever decreased, while symptoms such as a runny nose and sore throat tended to increase. The logistic regression analysis showed that the rate of fever tended to decrease (odds ratio = 0.52, 95 % confidence interval: 0.26-1.01, p = 0.056) and that of a runny nose increased (odds ratio = 3.68, 95 % confidence interval: 1.17-10.6, p = 0.018) after BA.5-adapted bivalent vaccination. Conclusion: This study shows that fever is reduced and mild symptoms are increased after BA.5-adapted bivalent vaccination in BA.5-infected HCWs. This result highlights the potential effectiveness of tailored vaccination strategies in the management of emerging COVID-19 variants.
Language	English
Publishing date	2024-01-06
Publishing country	England
Document type	Journal Article
ISSN	2590-1362
ISSN (online)	2590-1362
DOI	10.1016/j.jvacx.2024.100433
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Article ; Online: Simulation analysis of EGFR mutation detection: Oncomine Dx target test and AmoyDx panel impact on lung cancer treatment decisions.

Hirotsu, Yosuke / Nakagomi, Takahiro / Nagakubo, Yuki / Goto, Taichiro / Omata, Masao

Scientific reports

2024 Volume 14, Issue 1, Page(s) 1594

Abstract: Lung cancer is a leading cause of cancer-related deaths worldwide. Epidermal growth factor receptor (EGFR) driver mutations are crucial for treatment decisions for patients with non-small cell lung cancer (NSCLC). This study aimed to assess the ... ...

Abstract	Lung cancer is a leading cause of cancer-related deaths worldwide. Epidermal growth factor receptor (EGFR) driver mutations are crucial for treatment decisions for patients with non-small cell lung cancer (NSCLC). This study aimed to assess the differences in EGFR mutation detection between two companion diagnostic (CDx) tests-the Oncomine Dx Target Test (ODxTT) and the AmoyDx Pan Lung Cancer PCR Panel-and their impact on treatment applicability. To this end, we used an in-house targeted sequencing dataset of 282 samples from 127 EGFR-mutated NSCLC patients to simulate the concordance between the EGFR variants targeted by the ODxTT and AmoyDx panel, the oncogenicity of the variants, and their therapeutic potential. Of the 216 EGFR mutations identified by the in-house panel, 51% were detectable by both CDx tests, 3% were specific to ODxTT, and 46% were not targeted by either test. Most non-targeted mutations did not have oncogenicity and were located outside exons 18-21. Notably, 95% of the mutations detectable by both tests had potential oncogenicity. Furthermore, among the 96 patients harboring actionable EGFR mutations, 97% had mutations detectable by both CDx tests and 1% by ODxTT, while 2% had mutations not covered by either test. These findings suggest that while both CDx tests are effective in detecting almost all actionable EGFR mutations, ODxTT provides slightly broader coverage. These results emphasize the importance of selecting appropriate CDx tests to inform treatment decisions for EGFR-positive NSCLC patients.
MeSH term(s)	Humans ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/diagnosis ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Mutation ; Exons ; ErbB Receptors/genetics ; ErbB Receptors/therapeutic use
Chemical Substances	ErbB Receptors (EC 2.7.10.1) ; EGFR protein, human (EC 2.7.10.1)
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-52006-6
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Article ; Online: In Response to p53 Immunohistochemical Staining and TP53 Gene Mutations in Endometrial Cancer: Does Null Pattern Correlate With Prognosis?

Sakamoto, Ikuko / Kagami, Keiko / Nozaki, Takahiro / Hirotsu, Yosuke / Amemiya, Kenji / Oyama, Toshio / Omata, Masao

The American journal of surgical pathology

2024 Volume 48, Issue 3, Page(s) 374–375

MeSH term(s)	Female ; Humans ; Tumor Suppressor Protein p53/genetics ; Genes, p53 ; Mutation ; Prognosis ; Endometrial Neoplasms/genetics
Chemical Substances	Tumor Suppressor Protein p53 ; TP53 protein, human
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	752964-8
ISSN	1532-0979 ; 0147-5185
ISSN (online)	1532-0979
ISSN	0147-5185
DOI	10.1097/PAS.0000000000002181
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Article ; Online: Discovery of a SARS-CoV-2 variant from the P.1 lineage harboring K417T/E484K/N501Y mutations in Kofu, Japan.

Hirotsu, Yosuke / Omata, Masao

The Journal of infection

2021 Volume 82, Issue 6, Page(s) 276–316

MeSH term(s)	COVID-19 ; Humans ; Japan ; Mutation ; SARS-CoV-2 ; United Kingdom
Language	English
Publishing date	2021-03-23
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2021.03.013
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Article ; Online: Clinical and molecular biomarkers predicting response to PARP inhibitors in ovarian cancer.

Nozaki, Takahiro / Sakamoto, Ikuko / Kagami, Keiko / Amemiya, Kenji / Hirotsu, Yosuke / Mochizuki, Hitoshi / Omata, Masao

Journal of gynecologic oncology

2024

Abstract: Objective: To determine the useful biomarker for predicting the effects of poly-(ADP ribose)-polymerase (PARP) inhibitors in Japanese patients with ovarian cancer.: Methods: We collected clinical information and performed molecular biological ... ...

Abstract	Objective: To determine the useful biomarker for predicting the effects of poly-(ADP ribose)-polymerase (PARP) inhibitors in Japanese patients with ovarian cancer. Methods: We collected clinical information and performed molecular biological analysis on 42 patients with ovarian, fallopian tube, and primary peritoneal carcinomas who received PARP inhibitors. Results: Among the analyzed patients with ovarian cancer, 23.8% had germline Conclusion: We found that HRRm can be a useful biomarker for predicting the effects of PARP inhibitors in treating ovarian cancer and that the PFI can also be useful in recurrent ovarian cancer.
Language	English
Publishing date	2024-01-24
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2478405-9
ISSN	2005-0399 ; 2005-0380
ISSN (online)	2005-0399
ISSN	2005-0380
DOI	10.3802/jgo.2024.35.e55
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Article ; Online: Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan.

Hirotsu, Yosuke / Omata, Masao

PLoS pathogens

2021 Volume 17, Issue 6, Page(s) e1009619

Abstract: We aimed to investigate novel emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients ... ...

Abstract	We aimed to investigate novel emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients with coronavirus disease 2019 (COVID-19) were subjected to whole genome sequencing. The SARS-CoV-2 genome sequences from these patients were examined for variants in spike protein RBD. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. These three patients were living in Japan and had no history of traveling abroad. After identifying these cases, we developed a TaqMan assay to screen for the above hallmark mutations and identified an additional 14 patients with the same mutations. The associated virus strain was classified into the GR clade (Global Initiative on Sharing Avian Influenza Data [GISAID]), 20B clade (Nextstrain), and R.1 lineage (Phylogenetic Assignment of Named Global Outbreak [PANGO] Lineages). As of April 22, 2021, R.1 lineage SARS-CoV-2 has been identified in 2,388 SARS-CoV-2 entries in the GISAID database, many of which were from Japan (38.2%; 913/2,388) and the United States (47.1%; 1,125/2,388). Compared with that in the United States, the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly over the period from October 24, 2020 to April 18, 2021. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world.
MeSH term(s)	Adult ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Child ; Humans ; Japan ; Mutation ; Phylogeny ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-06-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1009619
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Article ; Online: SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community.

Hirotsu, Yosuke / Omata, Masao

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2021 Volume 95, Page(s) 105088

Abstract: Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of ... ...

Abstract	Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan. Methods: We performed the whole genome sequencing using SARS-CoV-2 positive samples collected from February 2020 to the end of June 2021. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages. Results: We successfully obtained 325 viral genome sequences and the number of analyzed samples accounted for 15.4% of the total 2109 COVID-19 patients identified in our district. We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta). These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April 2021. Conclusion: We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Epidemiological Monitoring ; Genome, Viral ; Humans ; Japan/epidemiology ; Phylogeny ; Prevalence ; RNA, Viral/genetics ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/growth & development ; SARS-CoV-2/pathogenicity ; Whole Genome Sequencing
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-09-21
Publishing country	Netherlands
Document type	Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2021.105088
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Zs.A 5645: Show issues

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Article ; Online: Antibody Response to the BA.5 Bivalent Vaccine Shot: a Two-Year Follow-Up Study following Initial COVID-19 mRNA Vaccination.

Hirotsu, Yosuke / Sugiura, Hiroki / Takatori, Mika / Mochizuki, Hitoshi / Omata, Masao

Microbiology spectrum

2023 Volume 11, Issue 3, Page(s) e0131623

Abstract: Although many studies have been conducted on the increase in spike antibody levels after vaccination, there is insufficient prospective and longitudinal information on the BA.5-adapted bivalent vaccine up to the fifth vaccination. In this study, we ... ...

Abstract	Although many studies have been conducted on the increase in spike antibody levels after vaccination, there is insufficient prospective and longitudinal information on the BA.5-adapted bivalent vaccine up to the fifth vaccination. In this study, we conducted a follow-up study of spike antibody levels and infection history in 46 health care workers who received up to 5 vaccinations. Monovalent vaccines were administered for the first to fourth vaccinations, and a bivalent vaccine was administered for the fifth vaccination. 11 serum samples were collected from each participant, and antibody levels were measured in a total of 506 serum samples. During the observation period, 43 of the 46 health care workers had no infection history, and 3 had a history of infection. Spike antibody levels peaked at 1 week after the second booster vaccination and gradually declined until the 27th week after the second vaccination. After 2 weeks following the fifth BA.5-adapted bivalent vaccine, the spike antibody levels significantly increased (median: 23,756 [IQR: 16,450 to 37,326]), compared to those measured before vaccination (median: 9,354 [IQR: 5,904 to 15,784]) (paired Wilcoxon signed-rank test,
MeSH term(s)	Humans ; Antibody Formation ; Vaccines, Combined ; Follow-Up Studies ; COVID-19 Vaccines ; Prospective Studies ; COVID-19/prevention & control ; Vaccination ; RNA, Messenger ; Antibodies, Viral
Chemical Substances	Vaccines, Combined ; COVID-19 Vaccines ; RNA, Messenger ; Antibodies, Viral
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01316-23
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