{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T13:27:14Z","timestamp":1788787634000,"version":"build-2803163510"},"reference-count":45,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T00:00:00Z","timestamp":1755475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"PUTI Grant from Universitas Indonesia","award":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"],"award-info":[{"award-number":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"]}]},{"name":"PUTI Grant from Universitas Indonesia","award":["JP253fa627004"],"award-info":[{"award-number":["JP253fa627004"]}]},{"name":"PUTI Grant from Universitas Indonesia","award":["24jm0210114h0001"],"award-info":[{"award-number":["24jm0210114h0001"]}]},{"name":"PUTI Grant from Universitas Indonesia","award":["24K10246"],"award-info":[{"award-number":["24K10246"]}]},{"name":"Japan Agency of Medical Research and Development (AMED)","award":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"],"award-info":[{"award-number":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"]}]},{"name":"Japan Agency of Medical Research and Development (AMED)","award":["JP253fa627004"],"award-info":[{"award-number":["JP253fa627004"]}]},{"name":"Japan Agency of Medical Research and Development (AMED)","award":["24jm0210114h0001"],"award-info":[{"award-number":["24jm0210114h0001"]}]},{"name":"Japan Agency of Medical Research and Development (AMED)","award":["24K10246"],"award-info":[{"award-number":["24K10246"]}]},{"name":"Japanese Society of Promotion and Science (JSPS) KAKENHI","award":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"],"award-info":[{"award-number":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"]}]},{"name":"Japanese Society of Promotion and Science (JSPS) KAKENHI","award":["JP253fa627004"],"award-info":[{"award-number":["JP253fa627004"]}]},{"name":"Japanese Society of Promotion and Science (JSPS) KAKENHI","award":["24jm0210114h0001"],"award-info":[{"award-number":["24jm0210114h0001"]}]},{"name":"Japanese Society of Promotion and Science (JSPS) KAKENHI","award":["24K10246"],"award-info":[{"award-number":["24K10246"]}]},{"name":"SDGs Research Project of Shimane University","award":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"],"award-info":[{"award-number":["NKB-1373\/UN2.RST\/KHP.05.00\/2022"]}]},{"name":"SDGs Research Project of Shimane University","award":["JP253fa627004"],"award-info":[{"award-number":["JP253fa627004"]}]},{"name":"SDGs Research Project of Shimane University","award":["24jm0210114h0001"],"award-info":[{"award-number":["24jm0210114h0001"]}]},{"name":"SDGs Research Project of Shimane University","award":["24K10246"],"award-info":[{"award-number":["24K10246"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>During the COVID-19 pandemic, the standard diagnostic assay for SARS-CoV-2 detection was RT-qPCR using TaqMan probes, with samples primarily taken through nasal and oropharyngeal swabs. The TaqMan-based method is costly, highlighting the need for a more affordable alternative for SARS-CoV-2 diagnosis. As an alternative strategy, we developed and evaluated a SYBR Green-based RT-qPCR method targeting the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2. Under optimized RT-qPCR conditions, the sensitivity and linearity of the SYBR assays were assessed by using in vitro-transcribed RNA and RNA extracted from cultured SARS-CoV-2 isolates of the Wuhan reference strain and various circulating variants. Our results demonstrated that the SYBR Green-based RT-qPCR method was successfully developed with sufficient performance. The assay could detect up to 25 copies of in vitro-transcript RNA per reaction. Meanwhile, using the RNA extracted from cultured virus, the SYBR green assay was able to detect virus concentrations at least as low as 1 PFU\/mL per reaction for all the variants tested. When tested on clinically relevant samples (88 naso-oropharyngeal swabs and 47 saliva samples), comparable results with the TaqMan assay were demonstrated. The Ct values of both methods for the positively detected samples were similar, with a difference in Ct of 0.72 \u00b1 0.83 (p = 0.392) and \u22120.7765 \u00b1 0.6107 (p = 0.209) for naso-oropharyngeal swab and saliva samples, respectively. These findings suggest that the SYBR method is reliable and thus offers an alternative assay for the detection of SARS-CoV-2. In particular, using saliva specimens could allow this assay to serve as a simple approach for SARS-CoV-2 detection.<\/jats:p>","DOI":"10.3390\/v17081130","type":"journal-article","created":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T13:28:22Z","timestamp":1755523702000},"page":"1130","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["High Concordance Between SYBR Green and TaqMan PCR for SARS-CoV-2 Detection in Nasopharyngeal and Saliva Samples"],"prefix":"10.3390","volume":"17","author":[{"given":"Muhareva","family":"Raekiansyah","sequence":"first","affiliation":[{"name":"Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ratika","family":"Rahmasari","sequence":"additional","affiliation":[{"name":"Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fathan","family":"Baihaqy","sequence":"additional","affiliation":[{"name":"Helix Laboratory, Depok 16431, West Java, Indonesia"},{"name":"Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung 40132, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhamad","family":"Irhamsyah","sequence":"additional","affiliation":[{"name":"Helix Laboratory, Depok 16431, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3917-1020","authenticated-orcid":false,"given":"Nurul Izza","family":"Fajriani","sequence":"additional","affiliation":[{"name":"Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung 40132, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1492-9459","authenticated-orcid":false,"given":"Mila Meilani","family":"Putri","sequence":"additional","affiliation":[{"name":"Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Botefilia","family":"Maharani","sequence":"additional","affiliation":[{"name":"Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rani","family":"Sauriasari","sequence":"additional","affiliation":[{"name":"Clinical Pharmacy and Social Pharmacy Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok 16424, West Java, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takeshi","family":"Urano","sequence":"additional","affiliation":[{"name":"Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 693-8501, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8986-6307","authenticated-orcid":false,"given":"Mya Myat","family":"Ngwe Tun","sequence":"additional","affiliation":[{"name":"Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 693-8501, Japan"},{"name":"Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8391-1157","authenticated-orcid":false,"given":"Kouichi","family":"Morita","sequence":"additional","affiliation":[{"name":"Department of Tropical Viral Vaccine Development, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 693-8501, Japan"},{"name":"Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan"},{"name":"DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Cornish, N.E., Bachmann, L.H., Diekema, D.J., McDonald, L.C., McNult, P., Stevens-Garcia, J., Raphael, B.H., and Miller, M.B. 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