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Review

Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

1
Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
2
Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal
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Evidence-Based Hub, CiiEM, Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal
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Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
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UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal
*
Author to whom correspondence should be addressed.
Academic Editor: Renzo Boldorini
Diagnostics 2021, 11(2), 363; https://doi.org/10.3390/diagnostics11020363
Received: 28 January 2021 / Revised: 16 February 2021 / Accepted: 19 February 2021 / Published: 21 February 2021
(This article belongs to the Collection Diagnostic Virology)
The 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). View Full-Text
Keywords: COVID-19; SARS-CoV-2; diagnostic; specimens; swab; saliva; deep-throat saliva; sputum; urine; feces; tears COVID-19; SARS-CoV-2; diagnostic; specimens; swab; saliva; deep-throat saliva; sputum; urine; feces; tears
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MDPI and ACS Style

Moreira, V.M.; Mascarenhas, P.; Machado, V.; Botelho, J.; Mendes, J.J.; Taveira, N.; Almeida, M.G. Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis. Diagnostics 2021, 11, 363. https://doi.org/10.3390/diagnostics11020363

AMA Style

Moreira VM, Mascarenhas P, Machado V, Botelho J, Mendes JJ, Taveira N, Almeida MG. Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis. Diagnostics. 2021; 11(2):363. https://doi.org/10.3390/diagnostics11020363

Chicago/Turabian Style

Moreira, Vânia M., Paulo Mascarenhas, Vanessa Machado, João Botelho, José J. Mendes, Nuno Taveira, and M. G. Almeida. 2021. "Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis" Diagnostics 11, no. 2: 363. https://doi.org/10.3390/diagnostics11020363

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