Rapid Detection of SARS-CoV-2 RNA Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA) with Lateral Flow for N-Protein Gene and Variant-Specific Deletion–Insertion Mutation in S-Protein Gene

Malaga, Jose L.; Pajuelo, Mónica; Okamoto, Michiko; Tsinda, Emmanuel Kagning; Otani, Kanako; Tsukayama, Pablo; Mascaro, Lucero; Cuicapuza, Diego; Katsumi, Masaharu; Kawamura, Kazuhisa; Nishimura, Hidekazu; Sakagami, Akie; Ueki, Yo; Omiya, Suguru; Okamoto, Satoshi; Nakayama, Asami; Fujimaki, Shin; Yu, Chuyao; Azam, Sikander; Kodama, Eiichi; Dapat, Clyde; Oshitani, Hitoshi; Saito, Mayuko

doi:10.3390/v15061254

Cited by 8 publications

(4 citation statements)

References 53 publications

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“…In the past four years, isothermal amplification market has gained huge recognition, and it is expected to grow at a compound annual growth rate of 12.2% during the next forecast decade. Popular isothermal amplification tests include RT-RPA (Recombinase Polymerase Amplification) [27], LAMP (Loop-Mediated Isothermal Amplification) [28], and NEAA (Nicking enzyme-assisted amplification) [29].…”

Section: Nucleic Acid-based Detectionmentioning

confidence: 99%

Pathogen Discovery in the Post-COVID Era

Guo,

2024

Pathogens

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Pathogen discovery plays a crucial role in the fields of infectious diseases, clinical microbiology, and public health. During the past four years, the global response to the COVID-19 pandemic highlighted the importance of early and accurate identification of novel pathogens for effective management and prevention of outbreaks. The post-COVID era has ushered in a new phase of infectious disease research, marked by accelerated advancements in pathogen discovery. This review encapsulates the recent innovations and paradigm shifts that have reshaped the landscape of pathogen discovery in response to the COVID-19 pandemic. Primarily, we summarize the latest technology innovations, applications, and causation proving strategies that enable rapid and accurate pathogen discovery for both acute and historical infections. We also explored the significance and the latest trends and approaches being employed for effective implementation of pathogen discovery from various clinical and environmental samples. Furthermore, we emphasize the collaborative nature of the pandemic response, which has led to the establishment of global networks for pathogen discovery.

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Section: Nucleic Acid-based Detectionmentioning

confidence: 99%

Pathogen Discovery in the Post-COVID Era

Guo,

2024

Pathogens

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“…In their study, Almeida et al utilized RT-LAMP targeting the N and E genes to detect a broad spectrum of Omicron variants (Almeida et al, 2022). Jose L et al devised two RT-RPA assays tailored for detecting deletion-insertion mutations unique to the Omicron BA.1 variant within the partial N and S genes of SARS-CoV-2 (Malaga et al, 2023). The N protein is abundantly expressed in the host following viral infection.…”

Section: Diagnostics and Drug Development Targeting N Proteinmentioning

confidence: 99%

“…Jose L et al. devised two RT-RPA assays tailored for detecting deletion-insertion mutations unique to the Omicron BA.1 variant within the partial N and S genes of SARS-CoV-2 ( Malaga et al., 2023 ). The N protein is abundantly expressed in the host following viral infection.…”

Section: Diagnostics and Drug Development Targeting N Proteinmentioning

confidence: 99%

Molecular characterization of SARS-CoV-2 nucleocapsid protein

Huang,

Chen,

Chen

et al. 2024

Front. Cell. Infect. Microbiol.

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Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world is still endeavoring to develop new ways to diagnose and treat COVID-19. At present, the clinical prevention and treatment of COVID-19 mainly targets the spike protein on the surface of SRAS-CoV-2. However, with the continuous emergence of SARS-CoV-2 Variants of concern (VOC), targeting the spike protein therapy shows a high degree of limitation. The Nucleocapsid Protein (N protein) of SARS-CoV-2 is highly conserved in virus evolution and is involved in the key process of viral infection and assembly. It is the most expressed viral structural protein after SARS-CoV-2 infection in humans and has high immunogenicity. Therefore, N protein as the key factor of virus infection and replication in basic research and clinical application has great potential research value. This article reviews the research progress on the structure and biological function of SARS-CoV-2 N protein, the diagnosis and drug research of targeting N protein, in order to promote researchers’ further understanding of SARS-CoV-2 N protein, and lay a theoretical foundation for the possible outbreak of new and sudden coronavirus infectious diseases in the future.

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“…RPA is a highly sensitive and specific technique with a detection limit of 1-10 copies of DNA template. Several studies have evaluated RT-RPA performance in the detection of the SARS-CoV-2 virus and demonstrated specificities ranging from 77% to 100% and sensitivities ranging from 65% to 100% (Malaga et al, 2023).…”

Section: Sensitivity and Specificitymentioning

confidence: 99%

Molecular Point‐of‐Care Assay Development: Design and Considerations

Hassman,

Rouchka,

Sunino

et al. 2024

Current Protocols

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Molecular diagnostic point‐of‐care (MDx POC) testing is gaining momentum and is increasingly important for infectious disease detection and monitoring, as well as other diagnostic areas such as oncology. Molecular testing has traditionally required high‐complexity laboratories. Laboratory testing complexity is determined by utilizing the Clinical Laboratory Improvement Amendments of 1988 (CLIA) Categorization Criteria scorecard, utilizing seven criteria that are scored on a scale of one to three. Previously, most commercially available point‐of‐care (POC) tests use other analytes and technologies that were not found to be highly complex by the CLIA scoring system. However, during the COVID‐19 pandemic, MDx POC testing became much more prominent. Utilization during the COVID‐19 pandemic has demonstrated that MDx POC testing applications can have outstanding advantages compared to available non‐molecular POC diagnostic tests. This article introduces MDx POC testing to students, technologists, researchers, and others, providing a general algorithm for MDx POC test development. This algorithm is an introductory, step‐by‐step decision tree for defining a molecular POC diagnostic device meeting the functional requirements for a desired application. The technical considerations driving the decision‐making include nucleic acid selection method (DNA, RNA), extraction methods, sample preparation, number of targets, amplification technology, and detection method. The scope of this article includes neither higher‐order multiplexing, nor quantitative molecular analysis. This article covers key application considerations, such as sensitivity, specificity, turnaround time, and shipping/storage requirements. This article provides an overall understanding of the best resources and practices to use when developing a MDx POC assay that may be a helpful resource for readers without extensive molecular testing experience as well as for those who are already familiar with molecular testing who want to increase MDx availability at the POC. © 2024 Wiley Periodicals LLC.

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Rapid Detection of SARS-CoV-2 RNA Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA) with Lateral Flow for N-Protein Gene and Variant-Specific Deletion–Insertion Mutation in S-Protein Gene

Cited by 8 publications

References 53 publications

Pathogen Discovery in the Post-COVID Era

Pathogen Discovery in the Post-COVID Era

Molecular characterization of SARS-CoV-2 nucleocapsid protein

Molecular Point‐of‐Care Assay Development: Design and Considerations

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