{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T15:19:39Z","timestamp":1787239179177,"version":"build-2736575974"},"reference-count":25,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2023,3,2]],"date-time":"2023-03-02T00:00:00Z","timestamp":1677715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministry of Health","award":["101003544"],"award-info":[{"award-number":["101003544"]}]},{"name":"Italian Ministry of Health","award":["101005075"],"award-info":[{"award-number":["101005075"]}]},{"name":"Italian Ministry of Health","award":["848096"],"award-info":[{"award-number":["848096"]}]},{"name":"European Commission\u2014Horizon 2020","award":["101003544"],"award-info":[{"award-number":["101003544"]}]},{"name":"European Commission\u2014Horizon 2020","award":["101005075"],"award-info":[{"award-number":["101005075"]}]},{"name":"European Commission\u2014Horizon 2020","award":["848096"],"award-info":[{"award-number":["848096"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>To compare the detection of the SARS-CoV-2 Omicron variant in nasopharyngeal-swab (NPS) and oral saliva samples. 255 samples were obtained from 85 Omicron-infected patients. SARS-CoV-2 load was measured in the NPS and saliva samples by using Simplexa\u2122 COVID-19 direct and Alinity m SARS-CoV-2 AMP assays. Results obtained with the two diagnostic platforms showed very good inter-assay concordance (91.4 and 82.4% for saliva and NPS samples, respectively) and a significant correlation among cycle threshold (Ct) values. Both platforms revealed a highly significant correlation among Ct obtained in the two matrices. Although the median Ct value was lower in NPS than in saliva samples, the Ct drop was comparable in size for both types of samples after 7 days of antiviral treatment of the Omicron-infected patients. Our result demonstrates that the detection of the SARS-CoV-2 Omicron variant is not influenced by the type of sample used for PCR analysis, and that saliva can be used as an alternative specimen for detection and follow-up of Omicron-infected patients.<\/jats:p>","DOI":"10.3390\/ijms24054847","type":"journal-article","created":{"date-parts":[[2023,3,2]],"date-time":"2023-03-02T04:57:38Z","timestamp":1677733058000},"page":"4847","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Comparison of SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples from Patients Infected with Omicron Variant"],"prefix":"10.3390","volume":"24","author":[{"given":"Licia","family":"Bordi","sequence":"first","affiliation":[{"name":"Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0955-2074","authenticated-orcid":false,"given":"Giuseppe","family":"Sberna","sequence":"additional","affiliation":[{"name":"Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleonora","family":"Lalle","sequence":"additional","affiliation":[{"name":"Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lavinia","family":"Fabeni","sequence":"additional","affiliation":[{"name":"Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0240-7504","authenticated-orcid":false,"given":"Valentina","family":"Mazzotta","sequence":"additional","affiliation":[{"name":"Clinical and Research Department, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6743-4001","authenticated-orcid":false,"given":"Simone","family":"Lanini","sequence":"additional","affiliation":[{"name":"Clinical and Research Department, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6235-3934","authenticated-orcid":false,"given":"Angela","family":"Corpolongo","sequence":"additional","affiliation":[{"name":"Clinical and Research Department, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna Rosa","family":"Garbuglia","sequence":"additional","affiliation":[{"name":"Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5606-8712","authenticated-orcid":false,"given":"Emanuele","family":"Nicastri","sequence":"additional","affiliation":[{"name":"Clinical and Research Department, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8182-5896","authenticated-orcid":false,"given":"Enrico","family":"Girardi","sequence":"additional","affiliation":[{"name":"Scientific Direction, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Vaia","sequence":"additional","affiliation":[{"name":"General and Health Management Direction, National Institute for Infectious Diseases \u201cL. Spallanzani\u201d IRCCS, 00149 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2121-4684","authenticated-orcid":false,"given":"Andrea","family":"Antinori","sequence":"additional","affiliation":[{"name":"Clinical and Research Department, National Institute for Infectious Diseases \u201cL. 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