Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis
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 compl...
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| Format: | Article |
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MDPI AG
2021-02-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/11/2/363 |
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| author | Vânia M. Moreira Paulo Mascarenhas Vanessa Machado João Botelho José João Mendes Nuno Taveira M. Gabriela Almeida |
| author_facet | Vânia M. Moreira Paulo Mascarenhas Vanessa Machado João Botelho José João Mendes Nuno Taveira M. Gabriela Almeida |
| author_sort | Vânia M. Moreira |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-03-09T00:39:28Z |
| format | Article |
| id | doaj.art-6183c8078dfd4a468866d1f900489c97 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-09T00:39:28Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-6183c8078dfd4a468866d1f900489c972023-12-11T17:53:53ZengMDPI AGDiagnostics2075-44182021-02-0111236310.3390/diagnostics11020363Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-AnalysisVânia M. Moreira0Paulo Mascarenhas1Vanessa Machado2João Botelho3José João Mendes4Nuno Taveira5M. Gabriela Almeida6Área Departamental de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, PortugalCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, PortugalCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, PortugalCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, PortugalCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, PortugalCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, PortugalCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz–Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, PortugalThe 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).https://www.mdpi.com/2075-4418/11/2/363COVID-19SARS-CoV-2diagnosticspecimensswabsaliva |
| spellingShingle | Vânia M. Moreira Paulo Mascarenhas Vanessa Machado João Botelho José João Mendes Nuno Taveira M. Gabriela Almeida Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis Diagnostics COVID-19 SARS-CoV-2 diagnostic specimens swab saliva |
| title | Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis |
| title_full | Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis |
| title_fullStr | Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis |
| title_full_unstemmed | Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis |
| title_short | Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis |
| title_sort | diagnosis of sars cov 2 infection by rt pcr using specimens other than naso and oropharyngeal swabs a systematic review and meta analysis |
| topic | COVID-19 SARS-CoV-2 diagnostic specimens swab saliva |
| url | https://www.mdpi.com/2075-4418/11/2/363 |
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