{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T21:57:39Z","timestamp":1747173459971,"version":"3.40.5"},"reference-count":20,"publisher":"Cambridge University Press (CUP)","license":[{"start":{"date-parts":[[2023,11,24]],"date-time":"2023-11-24T00:00:00Z","timestamp":1700784000000},"content-version":"unspecified","delay-in-days":327,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Epidemiol. Infect."],"published-print":{"date-parts":[[2023]]},"abstract":"<jats:title>Abstract<\/jats:title>\n\t  <jats:p>This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69\/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.<\/jats:p>","DOI":"10.1017\/s095026882300184x","type":"journal-article","created":{"date-parts":[[2023,11,24]],"date-time":"2023-11-24T09:06:08Z","timestamp":1700816768000},"update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":2,"title":["Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice"],"prefix":"10.1017","volume":"151","author":[{"given":"Luc\u00eda","family":"Chaves-Blanco","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adolfo","family":"de Salazar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Fuentes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Vi\u00f1uela","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Perez-Florido","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joaqu\u00edn","family":"Dopazo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7611-781X","authenticated-orcid":false,"given":"Federico","family":"Garc\u00eda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"56","published-online":{"date-parts":[[2023,11,24]]},"reference":[{"key":"S095026882300184X_r16","unstructured":"[16] SARS-CoV-2 Whole Genome Sequencing Circuit in Andalusia. Available at https:\/\/www.clinbioinfosspa.es\/COVID_circuit\/ (accessed 22 February 2023)."},{"key":"S095026882300184X_r12","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41579-022-00809-7","article-title":"SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies","volume":"21","author":"Cox","year":"2023","journal-title":"Nature Reviews Microbiology"},{"key":"S095026882300184X_r8","unstructured":"[8] Tracking SARS-CoV-2 Variants. Available at https:\/\/www.who.int\/activities\/tracking-SARS-CoV-2-variants (accessed 9 March 2023)."},{"key":"S095026882300184X_r9","unstructured":"[9] Centers for Disease Control and Prevention (2020). Coronavirus Disease 2019 (COVID-19). Available at https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/variants\/index.html (accessed 9 March 2023)."},{"key":"S095026882300184X_r17","doi-asserted-by":"crossref","first-page":"7003","DOI":"10.1038\/s41467-022-33713-y","article-title":"Global disparities in SARS-CoV-2 genomic surveillance","volume":"13","author":"Brito","year":"2022","journal-title":"Nature Communications"},{"key":"S095026882300184X_r14","doi-asserted-by":"crossref","first-page":"e0092621","DOI":"10.1128\/JCM.00926-21","article-title":"Mutation-specific SARS-CoV-2 PCR screen: Rapid and accurate detection of variants of concern and the identification of a newly emerging variant with spike L452R mutation","volume":"59","author":"Wang","year":"2021","journal-title":"Journal of Clinical Microbiology"},{"key":"S095026882300184X_r20","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1016\/S1473-3099(22)00365-6","article-title":"Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies","volume":"22","author":"Yamasoba","year":"2022","journal-title":"The Lancet Infectious Diseases"},{"key":"S095026882300184X_r2","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/S1473-3099(20)30120-1","article-title":"An interactive web-based dashboard to track COVID-19 in real time","volume":"20","author":"Dong","year":"2020","journal-title":"The Lancet Infectious Diseases"},{"key":"S095026882300184X_r15","doi-asserted-by":"crossref","first-page":"e0359122","DOI":"10.1128\/spectrum.03591-22","article-title":"Rapid and flexible RT-qPCR surveillance platforms to detect SARS-CoV-2 mutations","volume":"11","author":"Spiess","year":"2023","journal-title":"Microbiology Spectrum"},{"key":"S095026882300184X_r11","doi-asserted-by":"crossref","first-page":"949","DOI":"10.3390\/genes11080949","article-title":"Whole genome sequencing of SARS-CoV-2: Adapting illumina protocols for quick and accurate outbreak investigation during a pandemic","volume":"11","author":"Pillay","year":"2020","journal-title":"Genes"},{"key":"S095026882300184X_r3","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1056\/NEJMsb2104756","article-title":"SARS-CoV-2 variants in patients with immunosuppression","volume":"385","author":"Corey","year":"2021","journal-title":"New England Journal of Medicine"},{"key":"S095026882300184X_r1","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in China, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"New England Journal of Medicine"},{"key":"S095026882300184X_r7","doi-asserted-by":"crossref","first-page":"veab059","DOI":"10.1093\/ve\/veab059","article-title":"Recombinant SARS-CoV-2 genomes circulated at low levels over the first year of the pandemic","volume":"7","author":"VanInsberghe","year":"2021","journal-title":"Virus Evolution"},{"key":"S095026882300184X_r6","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1016\/j.cell.2021.08.014","article-title":"Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic","volume":"184","author":"Jackson","year":"2021","journal-title":"Cell"},{"key":"S095026882300184X_r13","doi-asserted-by":"crossref","first-page":"114512","DOI":"10.1016\/j.jviromet.2022.114512","article-title":"Fast detection of SARS-CoV-2 variants including Omicron using one-step RT-PCR and Sanger sequencing","volume":"304","author":"Bloemen","year":"2022","journal-title":"Journal of Virological Methods"},{"key":"S095026882300184X_r5","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.3390\/ijms24032419","article-title":"Detection of high level of co-infection and the emergence of novel SARS CoV-2 delta-omicron and omicron-omicron recombinants in the epidemiological surveillance of Andalusia","volume":"24","author":"Perez-Florido","year":"2023","journal-title":"International Journal of Molecular Sciences"},{"key":"S095026882300184X_r18","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41588-022-01033-y","article-title":"Global landscape of SARS-CoV-2 genomic surveillance and data sharing","volume":"54","author":"Chen","year":"2022","journal-title":"Nature Genetics"},{"key":"S095026882300184X_r19","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.03177-22","article-title":"Rapid assessment of SARS-CoV-2 variant-associated mutations in wastewater using real-time RT-PCR","volume":"11","author":"Farkas","year":"2023","journal-title":"Microbiology Spectrum"},{"key":"S095026882300184X_r4","unstructured":"[4] SARS-CoV-2 Variants of Concern as of 23 February 2023. Available at https:\/\/www.ecdc.europa.eu\/en\/covid-19\/variants-concern (accessed 9 March 2023)."},{"key":"S095026882300184X_r10","unstructured":"[10] Guidance for Surveillance of SARS-CoV-2 Variants: Interim Guidance, 9 August 2021. Available at https:\/\/www.who.int\/publications-detail-redirect\/WHO_2019-nCoV_surveillance_variants (accessed 9 March 2023)."}],"container-title":["Epidemiology and Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S095026882300184X","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,21]],"date-time":"2023-12-21T08:12:43Z","timestamp":1703146363000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S095026882300184X\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"references-count":20,"alternative-id":["S095026882300184X"],"URL":"https:\/\/doi.org\/10.1017\/s095026882300184x","relation":{},"ISSN":["0950-2688","1469-4409"],"issn-type":[{"type":"print","value":"0950-2688"},{"type":"electronic","value":"1469-4409"}],"subject":[],"published":{"date-parts":[[2023]]},"assertion":[{"value":"\u00a9 The Author(s), 2023. Published by Cambridge University Press","name":"copyright","label":"Copyright","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http:\/\/creativecommons.org\/licenses\/by\/4.0), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.","name":"license","label":"License","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}],"article-number":"e201"}}