{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T04:22:44Z","timestamp":1747196564201,"version":"3.40.5"},"reference-count":25,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T00:00:00Z","timestamp":1722902400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>The SARS-CoV-2 Omicron variant, with the main subtypes BA.5.2 and BF.7 in China, led to off-target effects on the S and N genes from December 1, 2022, to January 31, 2023. The kits used for studying and developing these agents were not adequately and independently evaluated. It is important to verify the performance of commercial Real-Time quantitative PCR (RT-qPCR) tests.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Objective<\/jats:title>\n<jats:p>We conducted a clinical evaluation of two Real Time SARS-CoV-2 Omicron assays to verify their performance using various detection reagents and clinical specimens.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Methods<\/jats:title>\n<jats:p>We performed clinical evaluations of two existing Chinese SARS-CoV-2 Omicron RT-qPCR kits 2019-nCoV nucleic acid diagnostic kits (Fosun Biotechnology, National instrument registration 20203400299, Shanghai, China) and COVID-19 nucleic acid detection kits (eDiagnosis Biomedicine, National instrument registration 20203400212, Wuhan, China) and using BSD (Bondson) (Guangzhou Bondson Biotechnology Co. Ltd, batch number 2022101), quality controls provided by the inspection center and a large number of clinically confirmed specimens.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Results<\/jats:title>\n<jats:p>The concordance rates for the Fosun and eDiagnosis kits were 95% and 100%, respectively. The detection limit for the Fosun and eDiagnosis kits was verified to be 300 copies\/mL and 500 copies\/mL. The Fosun assay exhibited the largest coefficient of variation (CV) for ORF1ab and N gene at the detection limit concentration (4.80%, 3.49%), whereas eDiagnosis showed a smaller CV (0.93%, 1.10%). In the reference product from the Hangzhou Clinical Laboratory Center test, it was found that Fosun had the lowest sensitivity of 93.47% and a specificity of 100%, while eDiagnosis exhibited 100% for both sensitivity and specificity. The lowest single target gene detection rate of Fosun reagents was 68.7% for the ORF1ab gene and 87.5% for the N gene, while eDiagnosis detection rate was 100%. Among the clinical group S specimens, the missed detection rate of the Fosun reagent was 10.9%, which was higher than the 3.9% of eDiagnosis. However, there was no significant difference in the clinical diagnostic efficiency of the two reagents.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec005\">\n<jats:title>Conclusions<\/jats:title>\n<jats:p>The ORF1ab and N assays of SARS-CoV-2 Omicron on the eDiagnosis platform yielded higher values compared to those on the Fosun platform. Consequently, the eDiagnosis kit has also been used as standard detection reagents. Considering that the Fosun reagent has a relatively low detection limit and targets three single genes, it is more advantageous as a confirmatory reagent for the new museum.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0305289","type":"journal-article","created":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T17:55:04Z","timestamp":1722966904000},"page":"e0305289","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diagnosis with Metagenomic Next-Generation Sequencing (mNGS) technology and real-time PCR for SARS-CoV-2 Omicron detection using various nasopharyngeal swabs in SARS-CoV-2 Omicron"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6587-8661","authenticated-orcid":true,"given":"Sujuan","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanhang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengcheng","family":"Tong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,8,6]]},"reference":[{"issue":"10317","key":"pone.0305289.ref001","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1016\/S0140-6736(21)02758-6","article-title":"Omicron SARS-CoV-2 Omicron variant: a new chapter in the COVID-19 pandemic","volume":"398","author":"S.S.A. Karim","year":"2021","journal-title":"Lancet (London, England)"},{"key":"pone.0305289.ref002","doi-asserted-by":"crossref","first-page":"153171","DOI":"10.1016\/j.scitotenv.2022.153171","article-title":"Detection of the Omicron (B.1.1.529) variant of SARS-CoV-2 Omicron in aircraft wastewater","volume":"820","author":"W. Ahmed","year":"2022","journal-title":"Science of The Total Environment"},{"issue":"5","key":"pone.0305289.ref003","doi-asserted-by":"crossref","DOI":"10.4269\/ajtmh.20-1439","article-title":"Analytical and Clinical Evaluation of Two RT-qPCR SARS-CoV-2 Omicron Diagnostic Tests with Emergency Use Authorization in Ecuador","author":"B. Freire-Paspuel","year":"2021","journal-title":"The American journal of tropical medicine and hygiene"},{"journal-title":"Scientific Reports","article-title":"Infections with the SARS-CoV-2 Omicron Delta variant exhibit fourfold increased viral loads in the upper airways compared to Alpha or non-variants of concern","author":"C.J.H.V. Wintersdorff","key":"pone.0305289.ref004"},{"issue":"4","key":"pone.0305289.ref005","doi-asserted-by":"crossref","DOI":"10.4269\/ajtmh.20-1484","article-title":"Clinical Performance and Analytical Sensitivity of Three SARS-CoV-2 Omicron Nucleic Acid Diagnostic Tests","volume":"104","author":"B. Freire-Paspuel","year":"2021","journal-title":"The American journal of tropical medicine and hygiene"},{"issue":"12","key":"pone.0305289.ref006","first-page":"2492","article-title":"SARS-CoV-2 Omicron and Variant Diagnostic Testing Approaches in the United States","volume":"13","author":"D.M. Andrews","journal-title":"Viruses"},{"journal-title":"Nature Microbiology","article-title":"Analytical sensitivity and efficiency comparisons of SARS-COV-2 OMICRON qRT-PCR assays","author":"C.B. Vogels","key":"pone.0305289.ref007"},{"key":"pone.0305289.ref008","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.cca.2021.12.004","article-title":"Performance verification of five commercial RT-qPCR diagnostic kits for SARS-CoV-2 Omicron","author":"M. Yang","year":"2022","journal-title":"Clinica Chimica Acta"},{"issue":"1","key":"pone.0305289.ref009","doi-asserted-by":"crossref","first-page":"53","DOI":"10.4038\/jccp.v51i1.7888","article-title":"Comparison of the analytical sensitivity of three real time PCR kits used in the detection of the SARS-CoV-2 Omicron","volume":"51","author":"S. Dayarathna","year":"2020","journal-title":"Journal of the Ceylon College of Physicians"},{"key":"pone.0305289.ref010","article-title":"Mutational escape from the polyclonal antibody response to SARS-CoV-2 Omicron infection is largely shaped by a single class of antibodies","author":"A.J. Greaney","year":"2021","journal-title":"bioRxiv: the preprint server for biology"},{"key":"pone.0305289.ref011","article-title":"Comparison of Automated SARS-CoV-2 Omicron Antigen Test for COVID-19 Infection with Quantitative RT-PCR using 313 Nasopharyngeal Swabs Including from 7 Serially Followed Patients","author":"Y. Hirotsu","year":"2020","journal-title":"International Journal of Infectious Diseases"},{"journal-title":"Acta Genetica Sinica: English Edition","article-title":"Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence - ScienceDirect","year":"2020","key":"pone.0305289.ref012"},{"journal-title":"Trimmomatic: A flexible read trimming tool for Illumina NGS data","year":"2014","author":"Bolger","key":"pone.0305289.ref013"},{"key":"pone.0305289.ref014","first-page":"2011","article-title":"Faster and More Accurate Sequence Alignment with SNAP","author":"M. Zaharia","year":"2011","journal-title":"Corr"},{"journal-title":"Bioinformatics","article-title":"Fast and accurate long-read alignment with Burrows\u2013Wheeler transform","year":"2010","key":"pone.0305289.ref015"},{"key":"pone.0305289.ref016","article-title":"SARS-CoV-2 Omicron variants and ending the COVID-19 pandemic","author":"A. Fontanet","year":"2021","journal-title":"The Lancet"},{"issue":"15","key":"pone.0305289.ref017","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.3390\/jcm10153276","article-title":"A Possible Role of Remdesivir and Plasma Therapy in the Selective Sweep and Emergence of New SARS-CoV-2 Omicron Variants","volume":"10","author":"P. Colson","journal-title":"Journal of clinical medicine"},{"key":"pone.0305289.ref018","doi-asserted-by":"crossref","first-page":"104476","DOI":"10.1016\/j.jcv.2020.104476","article-title":"Evaluation of the commercially available LightMix Modular E-gene kit using clinical and proficiency testing specimens for SARS-CoV-2 Omicron detection","volume":"129","author":"C.Y. Yip","year":"2020","journal-title":"Journal of Clinical Virology"},{"issue":"9","key":"pone.0305289.ref019","first-page":"e01535","article-title":"Direct Comparison of SARS-CoV-2 Omicron Analytical Limits of Detection across Seven Molecular Assays","volume":"58","author":"B. Fung","journal-title":"Journal of clinical microbiology"},{"issue":"8","key":"pone.0305289.ref020","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00783-20","article-title":"Clinical Evaluation of Three Sample-To-Answer Platforms for the Detection of SARS-CoV-2 Omicron","volume":"58","author":"W. Zhen","year":"2020","journal-title":"Journal of Clinical Microbiology"},{"journal-title":"SARS-CoV-2 Omicron transmission and control in a hospital setting: an individual-based modelling study","year":"2020","author":"Q. Huang","key":"pone.0305289.ref021"},{"issue":"4","key":"pone.0305289.ref022","doi-asserted-by":"crossref","first-page":"e0237421","DOI":"10.1128\/jcm.02374-21","article-title":"Impact of SARS-CoV-2 Omicron Variants on the Analytical Sensitivity of rRT-PCR Assays","volume":"60","author":"Y. Chen","year":"2022","journal-title":"Journal of clinical microbiology"},{"issue":"2","key":"pone.0305289.ref023","doi-asserted-by":"crossref","DOI":"10.3855\/jidc.14972","article-title":"A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 Omicron VOC202012\/01 B.1.1.7 variant","author":"G. Ibba","year":"2021","journal-title":"Journal of Infection in Developing Countries"},{"issue":"13","key":"pone.0305289.ref024","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00647-20","article-title":"The Nucleocapsid Protein of SARS\u2013CoV-2: a Target for Vaccine Development","volume":"94","author":"N.K. Dutta","year":"2020","journal-title":"Journal of Virology"},{"journal-title":"Science of The Total Environment","article-title":"Analytical performance comparison of four SARS-CoV-2 Omicron RT-qPCR primer-probe sets for wastewater samples","year":"2021","key":"pone.0305289.ref025"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0305289","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T17:55:19Z","timestamp":1722966919000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0305289"}},"subtitle":[],"editor":[{"given":"Chika Kingsley","family":"Onwuamah","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,8,6]]},"references-count":25,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2024,8,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0305289","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2024,8,6]]}}}