{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T11:09:57Z","timestamp":1769166597786,"version":"3.49.0"},"reference-count":41,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020884","name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","doi-asserted-by":"publisher","award":["11221308"],"award-info":[{"award-number":["11221308"]}],"id":[{"id":"10.13039\/501100020884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020884","name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","doi-asserted-by":"publisher","award":["1201664"],"award-info":[{"award-number":["1201664"]}],"id":[{"id":"10.13039\/501100020884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020884","name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","doi-asserted-by":"publisher","award":["1211841"],"award-info":[{"award-number":["1211841"]}],"id":[{"id":"10.13039\/501100020884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020884","name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","doi-asserted-by":"publisher","award":["COVID1038"],"award-info":[{"award-number":["COVID1038"]}],"id":[{"id":"10.13039\/501100020884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002941","name":"Departamento de Investigaciones Cient\u00edficas y Tecnol\u00f3gicas, Universidad de Santiago de Chile","doi-asserted-by":"publisher","award":["021943AC"],"award-info":[{"award-number":["021943AC"]}],"id":[{"id":"10.13039\/501100002941","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Public Health"],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>The COVID-19 pandemic is still in force, causing global public health challenges and threats. Although vaccination and herd immunity have proven to be the most efficient way to control the pandemic, massive and early testing of patients using the RT-qPCR technique is crucial for constant genomic surveillance. The appearance of variants of SARS-CoV-2 with new mutations can reduce the efficiency of diagnostic detection. In this sense, several commercial RT-qPCR kits have been the target of extensive analysis because low assay performance could lead to false-negative diagnoses.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>In this study, we evaluated the performance of three commercial RT-qPCR kits; Thermo Fisher (TaqMan 2019-nCoV Assay Kit v1), BGI and Roche (LightCycler<jats:sup>\u00ae<\/jats:sup> Multiplex RNA Virus Master) used for the diagnosis of COVID-19 throughout the pandemic in Santiago de Chile.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Under our best assay conditions, we found significant differences in Cq amplification values for control and viral probes, against the same nasopharyngeal swab samples (NPSs). In addition, in some cases, the sensitivity of the RT-qPCR kits decreased against viral variants.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our study suggests evaluating the RT-qPCR kits used to detect SARS-CoV-2 because variants such as Omicron, which has several mutations, can compromise their detection and underestimate viral circulation.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fpubh.2022.1010336","type":"journal-article","created":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T06:36:01Z","timestamp":1669617361000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Evaluation and comparison of the sensitivity of three commercial RT-qPCR kits used for the detection of SARS-CoV-2 in Santiago, Chile"],"prefix":"10.3389","volume":"10","author":[{"given":"Roberto","family":"Luraschi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00c1lvaro","family":"Santib\u00e1\u00f1ez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Barrera-Avalos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eva","family":"Vallejos-Vidal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Mateluna-Flores","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javiera","family":"Alarc\u00f3n","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javiera","family":"Cayunao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Mella-Torres","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felipe","family":"Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ailen","family":"Inostroza-Molina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Vald\u00e9s","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M\u00f3nica","family":"Imarai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudio","family":"Acu\u00f1a-Castillo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felipe E.","family":"Reyes-L\u00f3pez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana Mar\u00eda","family":"Sandino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"157","DOI":"10.23750\/abm.v91i1.9397","article-title":"WHO declares COVID-19 a pandemic","volume":"91","author":"Cucinotta","year":"2020","journal-title":"Acta Biomedica."},{"key":"B2","unstructured":"XuS\n            HuangR\n            SyLS\n            GlennSC\n            Denison\n            RyanS\n            MorrissetteK\n            ShayDK\n          COVID-19 Vaccination Mortality Risk not associated with COVID-19\u2014Seven Integrated Health Care Organizations, United States2020"},{"key":"B3","doi-asserted-by":"publisher","first-page":"6984","DOI":"10.1016\/j.vaccine.2021.10.038","article-title":"COVID-19 vaccine\u2013long term immune decline and breakthrough infections","volume":"39","author":"Khoury","year":"2021","journal-title":"Vaccine."},{"key":"B4","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1038\/s41586-022-04690-5","article-title":"Defining the risk of SARS-CoV-2 variants on immune protection","volume":"605","author":"DeGrace","year":"2022","journal-title":"Nature."},{"key":"B5","doi-asserted-by":"publisher","first-page":"278","DOI":"10.3389\/fimmu.2021.766278","article-title":"Evaluation of the immune response induced by CoronaVac 28-day schedule vaccination in a healthy population group","volume":"12","author":"Escobar","year":"2022","journal-title":"Front Immunol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1727","DOI":"10.1007\/s00109-020-01992-x","article-title":"Diagnosing the novel SARS-CoV-2 by quantitative RT-PCR: variations and opportunities","volume":"98","author":"Barreto","year":"2020","journal-title":"J Mol Med."},{"key":"B7","doi-asserted-by":"publisher","first-page":"5618","DOI":"10.1002\/jmv.27051","article-title":"Evaluation of the diagnostic performance of nine commercial RT-PCR kits for the detection of SARS-CoV-2 in Colombia","volume":"93","author":"Hern\u00e1ndez","year":"2021","journal-title":"J Med Virol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2022\/2594564","article-title":"The comparative analysis of Two RT-qPCR Kits for detecting SARS-CoV-2 reveals a higher risk of false-negative diagnosis in samples with high quantification cycles for viral and internal genes","volume":"2022","author":"Luraschi","year":"2022","journal-title":"Can J Infect Dis Med Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"552","DOI":"10.3389\/fcimb.2021.630552","article-title":"Analytical and clinical evaluation of \u201cAccuPower SARS-CoV-2 multiplex RT-PCR kit (Bioneer, South Korea)\u201d and \u201cAllplex 2019-nCoV assay (Seegene, South Korea)\u201d for SARS-CoV-2 RT-PCR Diagnosis: Korean CDC EUA as a quality control proxy for developing countries","volume":"11","author":"Freire-Paspuel","year":"2021","journal-title":"Front Cell Infect Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"306","DOI":"10.3390\/microorganisms10020306","article-title":"Comparative analysis of five multiplex RT-PCR assays in the screening of SARS-CoV-2 Variants","volume":"10","author":"de Pace","year":"2022","journal-title":"Microorganisms."},{"key":"B11","doi-asserted-by":"publisher","first-page":"411","DOI":"10.2471\/BLT.21.287398","article-title":"Equitable distribution of SARS-CoV-2 tests","volume":"100","author":"Garcia-Bereguiain","year":"2022","journal-title":"Bull World Health Organ."},{"key":"B12","doi-asserted-by":"publisher","first-page":"104510","DOI":"10.1016\/j.jcv.2020.104510","article-title":"Comparison of commercial realtime reverse transcription PCR assays for the detection of SARS-CoV-2","volume":"129","author":"Igl\u00f3i","year":"2020","journal-title":"J Clin Virol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"104412","DOI":"10.1016\/j.jcv.2020.104412","article-title":"Comparison of seven commercial RT-PCR diagnostic kits for COVID-19","volume":"128","author":"van Kasteren","year":"2020","journal-title":"J Clin Virol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"521","DOI":"10.3389\/fmed.2020.00521","article-title":"Evaluation of four commercial kits for SARS-CoV-2 real-time reverse-transcription polymerase chain reaction approved by emergency-use-authorization in Korea","volume":"7","author":"Hur","year":"2020","journal-title":"Front Med (Lausanne)."},{"key":"B15","unstructured":"IpsosGroup\n          La Crisis del Coronavirus; Encuesta a l\u00edderes de opini\u00f3n de Latinoam\u00e9rica2020"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1002\/jmv.27446","article-title":"Analysis by real-time PCR of five transport and conservation mediums of nasopharyngeal swab samples to COVID-19 diagnosis in Santiago of Chile","volume":"94","author":"Barrera-Avalos","year":"2022","journal-title":"J Med Virol."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.9.e45","article-title":"A new mathematical model for relative quantification in real-time RT-PCR","author":"Pfaffl","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"B18","doi-asserted-by":"publisher","first-page":"307","DOI":"10.3389\/fpubh.2017.00307","article-title":"Sensitivity, specificity, and predictive values: foundations, pliabilities, and pitfalls in research and practice","volume":"5","author":"Trevethan","year":"2017","journal-title":"Front Public Health"},{"key":"B19","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1016\/j.jmoldx.2021.04.009","article-title":"A comparative study of real-time RT-PCR\u2013based SARS-CoV-2 detection methods and its application to human-derived and surface swabbed material","volume":"23","author":"Tastanova","year":"2021","journal-title":"J Mol Diagnos."},{"key":"B20","first-page":"1","article-title":"Comparison of the performance of six SARS-CoV-2 nucleic acid detection kit in positive samples using RT-PCR","volume":"4","author":"Zhao","year":"2021","journal-title":"J Clin Chemi Lab Med."},{"key":"B21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jcla.23554","article-title":"Comparison of the diagnostic efficacy between two PCR test kits for SARS-CoV-2 nucleic acid detection","volume":"34","author":"Lu","year":"2020","journal-title":"J Clin Lab Anal."},{"key":"B22","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1007\/s10096-021-04159-9","article-title":"Comparison of nine different commercially available molecular assays for detection of SARS-CoV-2 RNA","volume":"40","author":"Eberle","year":"2021","journal-title":"Eur J Clin Microbiol Infect Dis."},{"key":"B23","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.3390\/v13071321","article-title":"Comparison and sensitivity evaluation of three different commercial real-time quantitative PCR kits for SARS-CoV-2 detection","volume":"13","author":"Banko","year":"2021","journal-title":"Viruses."},{"key":"B24","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/s12985-020-01445-4","article-title":"Garcia-Bereguiain MA. Poor sensitivity of \u201cAccuPower SARS-CoV-2 real time RT-PCR kit (Bioneer, South Korea)\u201d","volume":"17","author":"Freire-Paspuel","year":"2020","journal-title":"Virol J"},{"key":"B25","unstructured":"COVID-19 Target Product Profiles for Priority Diagnostics to Support Response to the COVID-19 Pandemic v.1.02020"},{"key":"B26","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1021\/acs.jcim.1c01451","article-title":"Wei G-W. Omicron Variant (B11529): infectivity, vaccine breakthrough, and antibody resistance","volume":"62","author":"Chen","year":"2022","journal-title":"J Chem Inf Model."},{"key":"B27","doi-asserted-by":"publisher","first-page":"e26486","DOI":"10.7759\/cureus.26486","article-title":"The impact of the highly virulent SARS-CoV-2 Gamma variant on young adults in the state of S\u00e3o Paulo: was it inevitable?","volume":"14","author":"Spira","year":"2022","journal-title":"Cureus."},{"key":"B28","doi-asserted-by":"publisher","first-page":"2009","DOI":"10.1007\/s00216-020-02490-2","article-title":"PCR inhibition in qPCR, dPCR and MPS\u2014mechanisms and solutions","volume":"412","author":"Sidstedt","year":"2020","journal-title":"Anal Bioanal Chem."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1111\/j.1365-2672.2012.05384.x","article-title":"Inhibitors\u2013occurrence, properties and removal","volume":"113","author":"Schrader","year":"2012","journal-title":"J Appl Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.bdq.2015.01.005","article-title":"How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments","volume":"3","author":"Svec","year":"2015","journal-title":"Biomol Detect Quantif."},{"key":"B31","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments","volume":"55","author":"Bustin","year":"2009","journal-title":"Clin Chem."},{"key":"B32","doi-asserted-by":"publisher","first-page":"496","DOI":"10.3390\/life11060496","article-title":"Use and Misuse of Cq in qPCR Data Analysis and Reporting","volume":"11","author":"Ruiz-Villalba","year":"2021","journal-title":"Life."},{"key":"B33","doi-asserted-by":"publisher","first-page":"e0246302","DOI":"10.1371\/journal.pone.0246302","article-title":"Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection","volume":"16","author":"L\u00e1zaro-Perona","year":"2021","journal-title":"PLoS ONE."},{"key":"B34","doi-asserted-by":"publisher","first-page":"113969","DOI":"10.1016\/j.jviromet.2020.113969","article-title":"Accuracy of a RT-qPCR SARS-CoV-2 detection assay without prior RNA extraction","volume":"287","author":"Beltr\u00e1n-Pavez","year":"2021","journal-title":"J Virol Methods."},{"key":"B35","doi-asserted-by":"publisher","first-page":"e243","DOI":"10.1515\/cclm-2020-1375","article-title":"Pooling for SARS-CoV-2-testing: comparison of three commercially available RT-qPCR kits in an experimental approach","volume":"59","author":"Cibali","year":"2021","journal-title":"(CCLM)."},{"key":"B36","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1093\/clinchem\/hvab052","article-title":"Efficiency correction is required for accurate quantitative PCR analysis and reporting","volume":"67","author":"Ruijter","year":"2021","journal-title":"Clin Chem."},{"key":"B37","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1186\/s12967-020-02344-6","article-title":"Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant","volume":"18","author":"Pachetti","year":"2020","journal-title":"J Transl Med."},{"key":"B38","unstructured":"Genetic Variants of SARS-CoV-2 May Lead to False Negative Results with Molecular Tests for Detection of SARS-CoV-2-Letter to Clinical Laboratory Staff and Health Care Providers.2021"},{"key":"B39","doi-asserted-by":"publisher","first-page":"298","DOI":"10.35248\/2168-9784.2020.9.298","article-title":"Medical diagnostic methods effectiveness of different gene-target strategies for SARS-CoV-2 screening by RT-PCR and Other modalities: a scoping review","volume":"9","author":"Kalita","year":"2020","journal-title":"J Med Diagn Meth."},{"key":"B40","unstructured":"COVID-19 At-Home Test Shows Good Results in Detecting Omicron2022"},{"key":"B41","unstructured":"Tracking SARS-CoV-2 Variants2022"}],"container-title":["Frontiers in Public Health"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2022.1010336\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T06:36:11Z","timestamp":1669617371000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2022.1010336\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,28]]},"references-count":41,"alternative-id":["10.3389\/fpubh.2022.1010336"],"URL":"https:\/\/doi.org\/10.3389\/fpubh.2022.1010336","relation":{},"ISSN":["2296-2565"],"issn-type":[{"value":"2296-2565","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,28]]},"article-number":"1010336"}}