{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:08:08Z","timestamp":1787242088076,"version":"build-2736575974"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T00:00:00Z","timestamp":1678665600000},"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":"\n Background<\/jats:title>\n Nasopharyngeal swab (NPS) remains the recommended sample type for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) diagnosis. However, the collection procedure causes discomfort and irritation to the patients, lowering the quality of the sample and exposing healthcare workers to risk. Furthermore, there is also a shortage of flocked swabs and personnel protective equipment in low-income settings. Therefore, this necessitates an alternative diagnostic specimen. The purpose of this study was to evaluate the performance of saliva against NPS for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n Comparative cross-sectional study was conducted from June 28 to July 30, 2022. A total of 227 paired saliva and NPS samples were collected from 227 COVID-19 suspected patients. Saliva and NPS samples were collected and transported to the Somali Regional Molecular Laboratory. Extraction was conducted using DaAn kit (DaAn Gene Co., Ltd China). Veri-Q RT-qPCR was used for amplification and detection (Mico BioMed Co, Ltd, Republic of Korea). The data were entered into Epi-data version 4.6 and analyzed using SPSS 25. McNemar\u2019s test was used to compare the detection rate. Agreement between NPS and saliva was performed using Cohen\u2019s Kappa. The mean and median of cycle threshold values were compared using paired t-tests and the correlation between cycle threshold values was measured using Pearson correlation coefficient. P value < 0.05 was considered statistically significant.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n The overall positivity rate of SARS-CoV-2 RNA was 22.5% (95% CI 17\u201328%). Saliva showed higher sensitivity (83.8%, 95% CI, 73\u201394.5%) than NPS (68.9%, 95% CI 60.8\u201376.8%). The specificity of saliva was 92.6% (95% CI, 80.6% - 100%) compared to NPS (96.7%, 95% CI, 87% - 100%). The positive, negative, and overall percent agreement between NPS and saliva was 83.8%, 92.6%, and 91.2% respectively (\u03ba = 0.703, 95% CI 0.58\u20130.825,\n P<\/jats:italic>\n = 0.00). The concordance rate between the two samples was 60.8%. NPS showed a higher viral load than saliva. There was low positive correlation between the cycle threshold values of the two samples (r = 0.41, 95% CI -1.69 to -0.98,\n P<\/jats:italic>\n >0.05).\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n Saliva showed a higher detection rate for SARS-CoV-2 molecular diagnosis than NPS and there was significant agreement between the two specimens. Therefore, saliva could be suitable and easily obtainable alternative diagnostic specimen for SARS-CoV-2 molecular diagnosis.<\/jats:p>\n <\/jats:sec>","DOI":"10.1371\/journal.pone.0282976","type":"journal-article","created":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T13:32:12Z","timestamp":1678714332000},"page":"e0282976","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["Comparative evaluation of saliva and nasopharyngeal swab for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia"],"prefix":"10.1371","volume":"18","author":[{"given":"Bawlah","family":"Tahir","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7867-1483","authenticated-orcid":true,"given":"Fitsum","family":"Weldegebreal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3372-3227","authenticated-orcid":true,"given":"Firayad","family":"Ayele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1544-7492","authenticated-orcid":true,"given":"Desalegn Admassu","family":"Ayana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,3,13]]},"reference":[{"issue":"4","key":"pone.0282976.ref001","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/s41591-020-0820-9","article-title":"The proximal origin of SARS-CoV-2","volume":"26","author":"K.G. 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HCP","year":"2020"},{"issue":"22","key":"pone.0282976.ref009","doi-asserted-by":"crossref","first-page":"e76","DOI":"10.1056\/NEJMvcm2010260","article-title":"How to obtain a nasopharyngeal swab specimen","volume":"382","author":"F.M. Marty","year":"2020","journal-title":"The New England journal of medicine"},{"key":"pone.0282976.ref010","article-title":"SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance.","author":"C.B. 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Lisa","year":"2020","journal-title":"First Saliva Test for COVID-19 Approved for Emergency Use by FDA|The Scientist Magazine\u00ae."},{"issue":"8","key":"pone.0282976.ref028","doi-asserted-by":"crossref","first-page":"e01109","DOI":"10.1128\/JCM.01109-20","article-title":"Saliva as an alternate specimen source for detection of SARS-CoV-2 in symptomatic patients using Cepheid Xpert Xpress SARS-CoV-2","volume":"58","author":"C. McCormick-Baw","year":"2020","journal-title":"Journal of clinical microbiology"},{"issue":"3","key":"pone.0282976.ref029","doi-asserted-by":"crossref","first-page":"642","DOI":"10.3390\/microorganisms9030642","article-title":"High efficacy of saliva in detecting SARS-CoV-2 by RT-PCR in adults and children.","volume":"9","author":"M. 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Landry","year":"2020","journal-title":"Journal of Clinical Virology"},{"issue":"8","key":"pone.0282976.ref032","doi-asserted-by":"crossref","first-page":"e300","DOI":"10.1097\/INF.0000000000003198","article-title":"Performance of RT-PCR on saliva specimens compared with nasopharyngeal swabs for the detection of SARS-CoV-2 in children: A prospective comparative clinical trial","volume":"40","author":"Y. Foug\u00e8re","year":"2021","journal-title":"The Pediatric infectious disease journal"},{"issue":"1","key":"pone.0282976.ref033","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-021-02097-2","article-title":"Saliva is superior over nasopharyngeal swab for detecting SARS-CoV2 in COVID-19 patients.","volume":"11","author":"G.T. Beyene","year":"2021","journal-title":"Scientific Reports"},{"issue":"1","key":"pone.0282976.ref034","first-page":"1","article-title":"Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection.","volume":"11","author":"A.K.J. Teo","year":"2021","journal-title":"Scientific reports"},{"issue":"11","key":"pone.0282976.ref035","doi-asserted-by":"crossref","first-page":"2939","DOI":"10.1093\/cid\/ciaa797","article-title":"Posterior oropharyngeal saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).","volume":"71","author":"S.C.Y. Wong","year":"2020","journal-title":"Clinical Infectious Diseases"},{"issue":"5","key":"pone.0282976.ref036","doi-asserted-by":"crossref","first-page":"3268","DOI":"10.1002\/jmv.26839","article-title":"Self\u2010collected saliva for SARS\u2010CoV\u20102 detection: A prospective study in the emergency room","volume":"93","author":"M. Echavarria","year":"2021","journal-title":"Journal of medical virology"},{"key":"pone.0282976.ref037","doi-asserted-by":"crossref","first-page":"465","DOI":"10.3389\/fmed.2020.00465","article-title":"Saliva as a candidate for COVID-19 diagnostic testing: a meta-analysis.","volume":"7","author":"L.M. Czumbel","year":"2020","journal-title":"Frontiers in medicine"},{"issue":"5","key":"pone.0282976.ref038","first-page":"e02881","article-title":"Performance of saliva, oropharyngeal swabs, and nasal swabs for SARS-CoV-2 molecular detection: a systematic review and meta-analysis","volume":"59","author":"R.A. Lee","year":"2021","journal-title":"Journal of clinical microbiology"},{"key":"pone.0282976.ref039","article-title":"Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs.","author":"A.L. 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Sakanashi","year":"2021","journal-title":"Journal of Infection and Chemotherapy"},{"key":"pone.0282976.ref042","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.bjid.2020.08.001","article-title":"Saliva is a reliable, non-invasive specimen for SARS-CoV-2 detection","author":"S.N. Vaz","year":"2020","journal-title":"Brazilian Journal of Infectious Diseases"},{"issue":"2","key":"pone.0282976.ref043","doi-asserted-by":"crossref","first-page":"38","DOI":"10.3390\/diseases9020038","article-title":"Saliva exhibits high sensitivity and specificity for the detection of SARS-COV-2.","volume":"9","author":"I. Warsi","year":"2021","journal-title":"Diseases"},{"issue":"4","key":"pone.0282976.ref044","doi-asserted-by":"crossref","first-page":"e03033","DOI":"10.1128\/JCM.03033-20","article-title":"Performance of Saliva Specimens for the Molecular Detection of SARS-CoV-2 in the Community Setting: Does Sample Collection Method Matter?","volume":"59","author":"M. Fern\u00e1ndez-Gonz\u00e1lez","year":"2021","journal-title":"Journal of clinical microbiology"},{"issue":"6","key":"pone.0282976.ref045","doi-asserted-by":"crossref","first-page":"e0252964","DOI":"10.1371\/journal.pone.0252964","article-title":"Detection of SARS-CoV-2 using qRT-PCR in saliva obtained from asymptomatic or mild COVID-19 patients, comparative analysis with matched nasopharyngeal samples.","volume":"16","author":"K. Ota","year":"2021","journal-title":"PLoS One,"},{"issue":"8","key":"pone.0282976.ref046","doi-asserted-by":"crossref","first-page":"e00776","DOI":"10.1128\/JCM.00776-20","article-title":"Saliva as a noninvasive specimen for detection of SARS-CoV-2","volume":"58","author":"E. Williams","year":"2020","journal-title":"Journal of clinical microbiology"},{"issue":"20","key":"pone.0282976.ref047","article-title":"Clinical significance of a high SARS-CoV-2 viral load in the saliva","volume":"35","author":"J.G. Yoon","year":"2020","journal-title":"Journal of Korean medical science"},{"issue":"2","key":"pone.0282976.ref048","doi-asserted-by":"crossref","first-page":"285. e1","DOI":"10.1016\/j.cmi.2020.05.001","article-title":"Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study","volume":"27","author":"E. Pasomsub","year":"2021","journal-title":"Clinical Microbiology and Infection"},{"key":"pone.0282976.ref049","doi-asserted-by":"crossref","first-page":"854567","DOI":"10.3389\/fmicb.2022.854567","article-title":"Understanding the role of SARS-CoV-2 ORF3a in viral pathogenesis and COVID-19","author":"J. Zhang","year":"2022","journal-title":"Frontiers in microbiology"},{"key":"pone.0282976.ref050","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1016\/j.ijbiomac.2020.12.142","article-title":"SARS-CoV-2 ORF3a: mutability and function","volume":"170","author":"M. 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Tsai","year":"2020","journal-title":"Journal of the Chinese Medical Association"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0282976","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T13:33:11Z","timestamp":1678714391000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0282976"}},"subtitle":[],"editor":[{"given":"Ruslan","family":"Kalendar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,3,13]]},"references-count":51,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2023,3,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0282976","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,13]]}}}