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Diagnosis of SARS-CoV-2 infection by RT-PCR using specimens other than naso- and oropharyngeal swabs: a systematic review and meta-analysis

2021-02-21Journal article Open access
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dc.contributor.authorMoreira, Vânia M.
dc.contributor.authorMascarenhas, Paulo
dc.contributor.authorMachado, Vanessa
dc.contributor.authorBotelho, João
dc.contributor.authorMendes, José João
dc.contributor.authorTaveira, Nuno
dc.contributor.authorAlmeida, M. Gabriela
dc.date.accessioned2021-04-29T13:31:30Z
dc.date.available2021-04-29T13:31:30Z
dc.date.issued2021-02-21
dc.description.abstractThe rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0-98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4-88.8) and specificity of 96.4% (95% CI: 89.5-98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3-95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3-96.9) and specificity of 63.1% (95% CI: 36.8-89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMOREIRA, Vânia M.; [et al] – Diagnosis of SARS-Cov-2 infection by RT-PCR using specimens other than Naso- and Oropharyngeal Swabs: a systematic review and meta-analysis. Diagnostics. eISSN 2075-4418. Vol. 11, N.º 2 (2021), pp. 1-24pt_PT
dc.identifier.doi10.3390/diagnostics11020363pt_PT
dc.identifier.eissn2075-4418
dc.identifier.urihttp://hdl.handle.net/10400.21/13249
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMDPIpt_PT
dc.relationIDB/04585/2020 - FCT through the Centro de Investigação Interdisciplinar Egas Monizpt_PT
dc.relationPOCI-01-0145FEDER-007728 - European Regional Development Fund under the PT2020 Partnership Agreementpt_PT
dc.relation662 - European Regional Development Fund under program Research4COVID 19pt_PT
dc.subjectCOVID-19pt_PT
dc.subjectSARS-CoV-2pt_PT
dc.subjectDiagnosticpt_PT
dc.subjectSpecimenspt_PT
dc.subjectSwabpt_PT
dc.subjectSalivapt_PT
dc.subjectDeep-throat salivapt_PT
dc.subjectSputumpt_PT
dc.subjectUrinept_PT
dc.subjectFecespt_PT
dc.subjectTearspt_PT
dc.titleDiagnosis of SARS-CoV-2 infection by RT-PCR using specimens other than naso- and oropharyngeal swabs: a systematic review and meta-analysispt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FMulti%2F04378%2F2013/PT
oaire.citation.endPage24pt_PT
oaire.citation.issue2pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleDiagnosticspt_PT
oaire.citation.volume11pt_PT
oaire.fundingStream5876
person.familyNameMascarenhas
person.familyNameMachado
person.familyNameBotelho
person.familyNameTaveira
person.familyNameAlmeida
person.givenNamePaulo
person.givenNameVanessa
person.givenNameJoão
person.givenNameNuno
person.givenNameGabriela
person.identifier.ciencia-id671B-BE80-50F2
person.identifier.ciencia-id7318-90D4-B716
person.identifier.ciencia-id461D-04AF-2777
person.identifier.ciencia-id7111-3383-A926
person.identifier.ciencia-idDF16-FBB4-3564
person.identifier.orcid0000-0002-6584-1199
person.identifier.orcid0000-0003-2503-260X
person.identifier.orcid0000-0002-1019-8263
person.identifier.orcid0000-0003-0176-5585
person.identifier.orcid0000-0002-4508-7379
person.identifier.ridD-8265-2013
person.identifier.scopus-author-id15768609100
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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