Article
Public, Environmental & Occupational Health
Lais Albuquerque de Oliveira, Izabela Mauricio de Rezende, Vinicius Joao Navarini, Silvana Beutinger Marchioro, Alex Jose Leite Torres, Julio Croda, Mariana Garcia Croda, Crhistinne Cavalheiro Maymone Goncalves, Joilson Xavier, Emerson de Castro, Mauricio Lima, Felipe Iani, Talita Adelino, Flavia Aburjaile, Luiz Henrique Ferraz Demarchi, Deborah Ledesma Taira, Marina Castilhos Souza Umaki Zardin, Vagner Fonseca, Marta Giovanetti, Jason Andrews, Luiz Carlos Junior Alcantara, Simone Simionatto
Summary: This study found multiple introductions of different SARS-CoV-2 lineages in the indigenous population of a particular area in Brazil over time. Due to their proximity to urban areas and socioeconomic and cultural disparities, these indigenous populations need to be isolated and protected. Genomic surveillance is crucial for monitoring viral dynamics and directing specific actions to prevent the spread of new emerging viruses.
FRONTIERS IN PUBLIC HEALTH
(2023)
Review
Health Care Sciences & Services
Miguel A. Ortega, Cielo Garcia-Montero, Oscar Fraile-Martinez, Paolo Colet, Ardak Baizhaxynova, Kymbat Mukhtarova, Melchor Alvarez-Mon, Kaznagul Kanatova, Angel Asunsolo, Antonio Sarria-Santamera
Summary: This article reviews the latest variants of SARS-CoV-2 and their impact on the global situation. Understanding the mechanisms behind the emergence of these variants is crucial for better management of this pandemic.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Review
Geriatrics & Gerontology
Zhen Yang, Shuo Zhang, Yu-Ping Tang, Sai Zhang, Ding-Qiao Xu, Shi-Jun Yue, Qi-Ling Liu
Summary: This article reviews the global emergence of new variants of the SARS-CoV-2 virus and provides detailed information on several variants of concern and their characteristics. The article emphasizes the clinical characteristics of these variants and provides up-to-date information on the recent variants. The summarized information can help researchers formulate reasonable strategies to combat the ongoing COVID-19 pandemic.
Article
Infectious Diseases
Marco Cacciabue, Pablo Aguilera, Maria Ines Gismondi, Oscar Taboga
Summary: Covidex is an open-source machine learning tool for subtyping SARS-CoV-2 genome sequences, providing fast and accurate classification based on different naming systems and variant definitions.
INFECTION GENETICS AND EVOLUTION
(2022)
Article
Genetics & Heredity
Solat Eslami, Mark C. Glassy, Soudeh Ghafouri-Fard
Summary: The study analyzed 176 complete and high-quality Iranian SARS-COV-2 S glycoprotein sequences from April 2020 to May 2021, and discussed the impact of different variants on infectivity and neutralizing antibody response. It was found that the Delta variant is widely circulating in different regions of Iran, with some variants carrying an additional mutation that may enhance viral/cell membrane fusion. This research provides important insights for predicting disease spread and developing vaccines and drugs.
Review
Virology
Chiranjib Chakraborty, Manojit Bhattacharya, Ashish Ranjan Sharma
Summary: The study discusses the emergence of alarming SARS-CoV-2 variants globally, highlighting key properties, mutations, and clinical characteristics of both variant of concern (VOC) and variant of interest (VOI) variants. The comprehensive review offers updated information on these newly appearing variants to aid researchers in formulating strategies to control the COVID-19 pandemic.
REVIEWS IN MEDICAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ahmad F. Eweas, Hosam-Eldin H. Osman, Ibrahim A. Naguib, Mohammed A. S. Abourehab, Ahmed S. Abdel-Moneim
Summary: This study aimed to assess the binding ability of different variants of SARS-CoV-2 to repurposed drugs. The results showed that all tested drugs had moderate to high binding energies to the receptor-binding domain of different variants, with cefoperazone having the highest binding energy.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Infectious Diseases
Nicla Giovacchini, Marco Coppi, Noemi Aiezza, Ilaria Baccani, Francesca Malentacchi, Simona Pollini, Alberto Antonelli, Gian Maria Rossolini
Summary: This study identified a specific testing method for VOC-Alpha, which allows for simultaneous screening and detection of the virus, providing a convenient tool for rapid screening of variants.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Microbiology
Abdelmajeed Nasereddin, Hadar Golan Berman, Dana G. Wolf, Esther Oiknine-Djian, Sheera Adar
Summary: This study presents a method called VOC-NGS for genotyping SARS-CoV-2, which offers a balance of accuracy, rapidity, and cost effectiveness in detecting and tracking VOCs and some VOI globally. It allows testing of a large number of clinical samples simultaneously. Efficient detection and identification of strains with rapid introduction of new mutations in the spike protein site are essential for treatment selection, vaccination strategies, and public health planning.
MICROBIOLOGY SPECTRUM
(2022)
Article
Genetics & Heredity
Etile A. Anoh, Oby Wayoro, Pacome Monemo, Essia Belarbi, Andreas Sachse, Eduan Wilkinson, James E. San, Fabian H. Leendertz, Bamourou Diane, Sebastien Calvignac-Spencer, Chantal Akoua-Koffi, Grit Schubert
Summary: In this study, the epidemiology of SARS-CoV-2 variants in Cote d'Ivoire, Western sub-Saharan Africa, was investigated. It was found that the second wave in 2021 was driven by the spread of the Alpha (B.1.1.7) and Eta (B.1.525) variant. The results suggest that subregional travel had a greater impact on local pandemic waves in Cote d'Ivoire than direct intercontinental travel.
Article
Immunology
Rana Abdelnabi, Caroline S. Foo, Steven De Jonghe, Piet Maes, Birgit Weynand, Johan Neyts
Summary: The emergence of SARS-CoV-2 variants of concern has worsened the COVID-19 pandemic, with current monoclonal antibodies and vaccines showing reduced efficacy against some of these variants. However, antivirals targeting conserved proteins of SARS-CoV-2 are likely to remain effective. Research on molnupiravir has shown effectiveness against different variants, highlighting its potential in combating current and future variants.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Cell Biology
Hsing-Yi Chung, Ming- Jian, Chih-Kai Chang, Jung-Chung Lin, Kuo-Ming Yeh, Ya-Sung Yang, Chien-Wen Chen, Shan-Shan Hsieh, Sheng-Hui Tang, Cherng-Lih Perng, Feng-Yee Chang, Kuo-Sheng Hung, En-Sung Chen, Mei-Hsiu Yang, Hung-Sheng Shang
Summary: This study aimed to evaluate the performance and analytical sensitivity of the LabTurbo AIO 48 system for SARS-CoV-2, influenza A/B, and RSV using 652 nasopharyngeal swab clinical samples. The system demonstrated consistent performance and high sensitivity in detecting these viruses, suggesting its potential for streamlined testing in the future. The multiplex RT-PCR on the LabTurbo AIO 48 open platform provided highly sensitive, robust, and accurate results for detecting B.1.1.7, influenza A/B, and RSV efficiently.
Article
Infectious Diseases
Yosuke Hirotsu, Makoto Maejima, Masahiro Shibusawa, Yume Natori, Yuki Nagakubo, Kazuhiro Hosaka, Hitomi Sueki, Hitoshi Mochizuki, Toshiharu Tsutsui, Yumiko Kakizaki, Yoshihiro Miyashita, Masao Omata
Summary: A TaqMan assay was developed to identify Omicron sublineage variants, showing high accuracy in distinguishing between different variants. The study analyzed 171 samples and found a concordance rate of 100% between whole genome sequencing results and the TaqMan assay, indicating the effectiveness of this method in variant identification.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Infectious Diseases
Paul Wollschlaeger, Daniel Todt, Nadja Gerlitz, Stephanie Pfaender, Thomas Bollinger, Andreas Sing, Alexandra Dangel, Nickolaus Ackermann, Klaus Korn, Armin Ensser, Eike Steinmann, Michael Buhl, Joerg Steinmann
Summary: The study evaluated a commercially available qRT-PCR assay for identifying SARS-CoV-2 B.1.1.7 lineage samples, showing a significant N gene dropout or Ct value shift compared to the S or RdRp gene. The assay reliably discriminated between B.1.1.7 and non-B.1.1.7 positive samples, making it a rapid tool for high-throughput diagnostics.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Virology
Melissa Caza, Catherine A. Hogan, Agatha Jassem, Natalie Prystajecky, Amir Hadzic, Amanda Wilmer
Summary: The Seegene AllplexTM SARS-CoV-2 Variants I assay shows 100% sensitivity and specificity for detecting the HV69/70 deletion, N501Y, and E484K mutations of the S gene of SARS-CoV-2. The assay is found to be stable, reproducible, and has a high limit of detection, making it acceptable for clinical use in detecting variants of concern and interest.
JOURNAL OF CLINICAL VIROLOGY
(2021)
Article
Pathology
Hiroshi Ohyama, Yosuke Hirotsu, Kenji Amemiya, Hiroyuki Amano, Sumio Hirose, Kenji Hosoda, Toshio Oyama, Yuji Iimuro, Yuichiro Kojima, Rintaro Mikata, Hitoshi Mochizuki, Naoya Kato, Masao Omata
Summary: This study demonstrates the usefulness of genomic analysis of archived cytological specimens (ACSs) in identifying oncogenic mutations in pancreatic cancer, with comparable sensitivity and detection rate to formalin-fixed paraffin-embedded (FFPE) tissues.
ANNALS OF DIAGNOSTIC PATHOLOGY
(2022)
Article
Oncology
Hideki Watanabe, Hiroshi Nakagomi, Yosuke Hirotsu, Kenji Amemiya, Hitoshi Mochizuki, Masayuki Inoue, Ayako Kimura, Masao Omata
Summary: The study found that drug-tolerant persister (DTP) in HER2-positive breast cancer often had TP53 gene mutations, which may be the most important clinical challenge leading to relapse.
BREAST CANCER RESEARCH AND TREATMENT
(2022)
Article
Oncology
Kenji Amemiya, Yosuke Hirotsu, Hitoshi Mochizuki, Rumi Higuchi, Takahiro Nakagomi, Taichiro Goto, Toshio Oyama, Tetsuo Kondo, Masao Omata
Summary: Whole genome amplification of cytological specimens can serve as a feasible alternative method for detecting oncogenic and drug-matched variants, with higher DNA quality and quantity.
CANCER CYTOPATHOLOGY
(2023)
Letter
Infectious Diseases
Yosuke Hirotsu, Masao Omata
JOURNAL OF INFECTION
(2023)
Article
Oncology
Ikuko Sakamoto, Yosuke Hirotsu, Kenji Amemiya, Takahiro Nozaki, Hitoshi Mochizuki, Masao Omata
Summary: This study investigated the clonal origin of synchronous endometrial and ovarian cancers (SEOs) through gene sequencing, mismatch microsatellite instability analysis, and immunohistochemistry. The results suggest that most SEOs are likely to be a single tumor with metastasis from the endometrium, and have a high frequency of MMR gene abnormalities.
JOURNAL OF GYNECOLOGIC ONCOLOGY
(2023)
Letter
Infectious Diseases
Yosuke Hirotsu, Masao Omata
JOURNAL OF INFECTION
(2023)
Article
Oncology
Kenichiro Okimoto, Yosuke Hirotsu, Makoto Arai, Kenji Amemiya, Naoki Akizue, Yuki Ohta, Takashi Taida, Keiko Saito, Hiroshi Ohyama, Tomoaki Matsumura, Motoi Nishimura, Kazuyuki Matsushita, Keisuke Matsusaka, Toshio Oyama, Hitoshi Mochizuki, Tetsuhiro Chiba, Jun Kato, Jun-ichiro Ikeda, Osamu Yokosuka, Naoya Kato, Masao Omata
Summary: This study aimed to validate the pathological diagnosis of early CRC (E-CRC) by comparing genetic background data of E-CRC with colorectal adenoma (CRA) and advanced CRC (AD-CRC). The results showed that E-CRC had a similar genetic profile to AD-CRC, but significantly different from CRA, especially in the Wnt signaling pathway.
Article
Oncology
Hiroshi Ohyama, Yosuke Hirotsu, Kenji Amemiya, Yoshifumi Miura, Sumio Hirose, Toshio Oyama, Yuji Iimuro, Yuichiro Kojima, Rintaro Mikata, Hitoshi Mochizuki, Naoya Kato, Masao Omata
Summary: This study found that liquid biopsies using bile were more effective than plasma in identifying oncogenic and drug-matched mutations in patients with pancreaticobiliary cancer. Bile had a significantly higher amount of DNA compared to plasma, and was more sensitive in detecting druggable mutations. Therefore, using bile for liquid biopsies may help in the search for therapeutic agents and improve the prognosis of patients with pancreaticobiliary cancer.
Article
Genetics & Heredity
Yuki Nagakubo, Yosuke Hirotsu, Kenji Amemiya, Hitoshi Mochizuki, Toshiharu Tsutsui, Yumiko Kakizaki, Yoshihiro Miyashita, Rumi Higuchi, Takahiro Nakagomi, Taichiro Goto, Toshio Oyama, Masao Omata
Summary: This study evaluated the relationship between the amount of nucleic acid, degree of RNA degradation, and the success of ODxTT. Out of 223 samples, 219 were successfully analyzed, with DNA analysis failing in 2 samples due to low concentrations and RNA analysis failing in 2 samples due to high degradation. The results showed that DNA concentration and RNA degradation are key factors for the success of ODxTT.
MOLECULAR DIAGNOSIS & THERAPY
(2023)
Article
Microbiology
Yosuke Hirotsu, Hiroki Sugiura, Mika Takatori, Hitoshi Mochizuki, Masao Omata
Summary: A study found that COVID-19 vaccines can increase antibody levels and showed a significant increase after the fifth vaccination based on tracking observations of 46 healthcare workers who received up to five doses.
MICROBIOLOGY SPECTRUM
(2023)
Article
Medicine, General & Internal
Mai Okamoto, Makoto Maejima, Taichiro Goto, Takahiro Mikawa, Kazuhiro Hosaka, Yuki Nagakubo, Yosuke Hirotsu, Kenji Amemiya, Hitomi Sueki, Masao Omata
Summary: Bacteremia is a serious disease with high mortality. The introduction of the FilmArray multiplex PCR panel for blood culture identification has greatly improved the prompt identification and treatment of the disease. The use of FA significantly reduced the duration of antibiotic use and improved overall survival in patients with bacteremia.
Article
Oncology
Kei Kunimasa, Yosuke Hirotsu, Kenji Amemiya, Keiichiro Honma, Harumi Nakamura, Kazumi Nishino, Masao Omata
Summary: In this study, the association between PD-L1 expression in tumor cells and underlying genetic mutations was investigated using laser microdissection and next-generation sequencing analysis. The analysis showed no association between PD-L1 expression heterogeneity and genetic variants, but revealed a correlation between PD-L1 expression and the number of tumor infiltrating lymphocytes.
Article
Medicine, Research & Experimental
Yosuke Hirotsu, Hiroaki Kobayashi, Yumiko Kakizaki, Akitoshi Saito, Toshiharu Tsutsui, Makoto Kawaguchi, Sou Shimamura, Kouki Hata, Syunya Hanawa, Jun Toyama, Yoshihiro Miyashita, Masao Omata
Summary: This study reports a case of an immunocompromised patient with SARS-CoV-2 infection who failed to control viral replication despite receiving multiple antiviral and antibody therapies. Genome analysis revealed the occurrence of drug-resistant mutations in the virus within the host, indicating their survival fitness.
Article
Medicine, Research & Experimental
Yosuke Hirotsu, Yumiko Kakizaki, Akitoshi Saito, Toshiharu Tsutsui, Syunya Hanawa, Haruna Yamaki, Syuichiro Ide, Makoto Kawaguchi, Hiroaki Kobayashi, Yoshihiro Miyashita, Masao Omata
Summary: The presence of pneumonia and pathogenesis varies depending on the SARS-CoV-2 variant. Infection with different variants results in different prevalence of pneumonia and severity of lung damage, with BA.2 variant showing the lowest prevalence and mild lung pathogenesis.
COMMUNICATIONS MEDICINE
(2023)
Article
Pathology
Kenji Amemiya, Yosuke Hirotsu, Yuki Nagakubo, Hitoshi Mochizuki, Toshio Oyama, Masao Omata
Summary: Analyzing RNA samples from formalin-fixed paraffin-embedded (FFPE) tissues is crucial for precision medicine. This study found that longer fixation times resulted in decreased RNA quantity and quality, as well as reduced sequencing reads. FFPE blocks stored for a longer duration also showed lower RNA yield and quality. It is important to avoid short and over-fixation during the fixation process for cancer patients, and adhere to recommended guidelines.
PATHOLOGY INTERNATIONAL
(2023)