{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T23:17:37Z","timestamp":1780528657452,"version":"3.54.1"},"reference-count":55,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2023,5,26]],"date-time":"2023-05-26T00:00:00Z","timestamp":1685059200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science Fund, KAKENHI","doi-asserted-by":"publisher","award":["JP19K24679"],"award-info":[{"award-number":["JP19K24679"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science Fund, KAKENHI","doi-asserted-by":"publisher","award":["JP20wm0125001"],"award-info":[{"award-number":["JP20wm0125001"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science Fund, KAKENHI","doi-asserted-by":"publisher","award":["045-2020"],"award-info":[{"award-number":["045-2020"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Japan Agency for Medical Research and Development (AMED)","award":["JP19K24679"],"award-info":[{"award-number":["JP19K24679"]}]},{"name":"Japan Agency for Medical Research and Development (AMED)","award":["JP20wm0125001"],"award-info":[{"award-number":["JP20wm0125001"]}]},{"name":"Japan Agency for Medical Research and Development (AMED)","award":["045-2020"],"award-info":[{"award-number":["045-2020"]}]},{"name":"National Fund for Scientific, Technological Development, and Innovation (FONDECYT)","award":["JP19K24679"],"award-info":[{"award-number":["JP19K24679"]}]},{"name":"National Fund for Scientific, Technological Development, and Innovation (FONDECYT)","award":["JP20wm0125001"],"award-info":[{"award-number":["JP20wm0125001"]}]},{"name":"National Fund for Scientific, Technological Development, and Innovation (FONDECYT)","award":["045-2020"],"award-info":[{"award-number":["045-2020"]}]},{"name":"Ministry of Education, Culture, Sports, Science, and Technology Scholarship","award":["JP19K24679"],"award-info":[{"award-number":["JP19K24679"]}]},{"name":"Ministry of Education, Culture, Sports, Science, and Technology Scholarship","award":["JP20wm0125001"],"award-info":[{"award-number":["JP20wm0125001"]}]},{"name":"Ministry of Education, Culture, Sports, Science, and Technology Scholarship","award":["045-2020"],"award-info":[{"award-number":["045-2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion\u2013insertion mutations (del211\/ins214). Both tests had a detection limit of 10 copies\/\u00b5L in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (&gt;9015.7 copies\/\u00b5L, cycle quantification (Cq): &lt; 25) and moderate (385.5\u20139015.7 copies\/\u00b5L, Cq: 25\u201329.9) viral load, 83.3% for low (16.5\u2013385.5 copies\/\u00b5L, Cq: 30\u201334.9), and 14.3% for very low (&lt;16.5 copies\/\u00b5L, Cq: 35\u201340). The sensitivities of the Omicron BA.1 (S) RT-RPA-LF were 94.9%, 78%, 23.8%, and 0%, respectively, and the specificity against non-BA.1 SARS-CoV-2-positive samples was 96%. The assays seemed more sensitive than rapid antigen detection in moderate viral load samples. Although implementation in resource-limited settings requires additional improvements, deletion\u2013insertion mutations were successfully detected by the RT-RPA-LF technique.<\/jats:p>","DOI":"10.3390\/v15061254","type":"journal-article","created":{"date-parts":[[2023,5,27]],"date-time":"2023-05-27T16:10:53Z","timestamp":1685203853000},"page":"1254","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["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\u2013Insertion Mutation in S-Protein Gene"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6946-6621","authenticated-orcid":false,"given":"Jose L.","family":"Malaga","sequence":"first","affiliation":[{"name":"Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3662-2250","authenticated-orcid":false,"given":"Monica J.","family":"Pajuelo","sequence":"additional","affiliation":[{"name":"Laboratorio Microbiolog\u00eda Molecular, Laboratorios de Investigaci\u00f3n y Desarrollo, Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima 15102, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3505-5939","authenticated-orcid":false,"given":"Michiko","family":"Okamoto","sequence":"additional","affiliation":[{"name":"Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1186-7657","authenticated-orcid":false,"given":"Emmanuel Kagning","family":"Tsinda","sequence":"additional","affiliation":[{"name":"Department of Virology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan"},{"name":"Center for Biomedical Innovation, Sinskey Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9964-8146","authenticated-orcid":false,"given":"Kanako","family":"Otani","sequence":"additional","affiliation":[{"name":"National Institute of Infectious Diseases, Tokyo 162-8640, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Tsukayama","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00f3mica Microbiana, Universidad Peruana Cayetano Heredia, Lima 15102, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucero","family":"Mascaro","sequence":"additional","affiliation":[{"name":"Laboratorio Microbiolog\u00eda Molecular, Laboratorios de Investigaci\u00f3n y Desarrollo, Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima 15102, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5735-4614","authenticated-orcid":false,"given":"Diego","family":"Cuicapuza","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00f3mica Microbiana, Universidad Peruana Cayetano Heredia, Lima 15102, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masamichi","family":"Katsumi","sequence":"additional","affiliation":[{"name":"Sendai City Institute of Health, Sendai 984-0002, Japan"},{"name":"Sendai Shirayuri Women\u2019s College, Sendai 981-3107, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhisa","family":"Kawamura","sequence":"additional","affiliation":[{"name":"Kawamura Children\u2019s Clinic, Sendai 981-0907, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hidekazu","family":"Nishimura","sequence":"additional","affiliation":[{"name":"Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9651-2681","authenticated-orcid":false,"given":"Akie","family":"Sakagami","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai 983-0836, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yo","family":"Ueki","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, Sendai 983-0836, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suguru","family":"Omiya","sequence":"additional","affiliation":[{"name":"Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, 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