{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:48:58Z","timestamp":1760147338219,"version":"build-2065373602"},"reference-count":36,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T00:00:00Z","timestamp":1674691200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not always available in diagnostic laboratories. The test presented in this study aimed to detect, using traditional real-time PCR, the presence of the main variants described for the spike protein of the SARS-CoV-2 genome. The primers and probes were designed to detect the main deletions that characterize the different variants. The amplification targets were deletions in the S gene: 25\u201327, 69\u201370, 241\u2013243, and 157\u2013158. In the ORF1a gene, the deletion 3675\u20133677 was chosen. Some of these mutations can be considered specific variants, while others can be identified by the simultaneous presence of one or more deletions. We avoided using point mutations in order to improve the speed of the test. Our test can help clinical and medical microbiologists quickly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs). The test can also be used to identify variants of the virus that could potentially be more diffusive as well as not responsive to the vaccine.<\/jats:p>","DOI":"10.3390\/v15020353","type":"journal-article","created":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T01:58:59Z","timestamp":1674784739000},"page":"353","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Rapid System to Detect Variants of SARS-CoV-2 in Nasopharyngeal Swabs"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2184-8054","authenticated-orcid":false,"given":"Marco","family":"Favaro","sequence":"first","affiliation":[{"name":"Department Experimental Medicine, University of Rome \u201cTor Vergata\u201d, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paola","family":"Zampini","sequence":"additional","affiliation":[{"name":"Via Luigi Einaudi, Guidonia Montecelio, 00012 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enrico","family":"Pistoia","sequence":"additional","affiliation":[{"name":"Department Experimental Medicine, University of Rome \u201cTor Vergata\u201d, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1970-2670","authenticated-orcid":false,"given":"Roberta","family":"Gaziano","sequence":"additional","affiliation":[{"name":"Department Experimental Medicine, University of Rome \u201cTor Vergata\u201d, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1028-3203","authenticated-orcid":false,"given":"Sandro","family":"Grelli","sequence":"additional","affiliation":[{"name":"Department Experimental Medicine, University of Rome \u201cTor Vergata\u201d, 00133 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2198-1947","authenticated-orcid":false,"given":"Carla","family":"Fontana","sequence":"additional","affiliation":[{"name":"National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41564-020-0771-4","article-title":"Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic","volume":"5","author":"Boni","year":"2020","journal-title":"Nat. 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