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Janostiakova N, Gnip A, Kodada D, Saade R, Blandova G, Mikova E, Tibenska E, Repiska V, Minarik G. SARS-CoV-2 testing in the Slovak Republic from March 2020 to September 2022 - summary of the pandemic trends. Front Med (Lausanne) 2023; 10:1225596. [PMID: 38020161 PMCID: PMC10658709 DOI: 10.3389/fmed.2023.1225596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
The COVID-19 pandemic has been part of Slovakia since March 2020. Intensive laboratory testing ended in October 2022, when the number of tests dropped significantly, but the state of the pandemic continues to this day. For the management of COVID-19, it is important to find an indicator that can predict pandemic changes in the community. The average daily/weekly Ct value with a certain time delay can predict changes in the number of cases of SARS-CoV-2 infection, which can be a useful indicator for the healthcare system. The study analyzed the results of 1,420,572 RT-qPCR tests provided by one accredited laboratory during the ongoing pandemic in Slovakia from March 2020 to September 2022. The total positivity of the analyzed tests was 24.64%. The average Ct values found were the highest in the age group of 3-5 years, equal to the number 30.75; the lowest were in the age group >65 years, equal to the number 27. The average weekly Ct values ranged from 22.33 (pandemic wave week) to 30.12 (summer week). We have summarized the results of SARS-CoV-2 diagnostic testing in Slovakia with the scope defined by the rate and positivity of tests carried out at Medirex a.s. laboratories.
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Affiliation(s)
- Nikola Janostiakova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | | | - Dominik Kodada
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Rami Saade
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Gabriela Blandova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | | | - Elena Tibenska
- Medirex, a.s., Pezinok, Slovakia
- 5th Department of Internal Medicine, Faculty of Medicine, University Hospital, Comenius University, Bratislava, Slovakia
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
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2
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Al-Shaibari KSA, Mousa HAL, Alqumber MAA, Alqfail KA, Mohammed A, Bzeizi K. The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies. Diagnostics (Basel) 2023; 13:3057. [PMID: 37835801 PMCID: PMC10572802 DOI: 10.3390/diagnostics13193057] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process. METHODOLOGY A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes. RESULTS A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively. CONCLUSIONS NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.
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Affiliation(s)
| | | | | | | | | | - Khalid Bzeizi
- Department of Liver Transplantation, King Faisal Specialist Hospital and Research Center, Riyadh 13541, Saudi Arabia
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3
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Ting M, Dahlkemper A, Schwartz JJ, Woodfork M, Suzuki JB. Preprocedural Viral Load Effects of Oral Antiseptics on SARS-CoV-2 in Patients with COVID-19: A Systematic Review. Biomedicines 2023; 11:1694. [PMID: 37371789 DOI: 10.3390/biomedicines11061694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
(1) There are limited clinical trials to support the effectiveness of mouth rinses when used as a preprocedural rinse against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This systematic review aims to evaluate the efficacy of antiseptic mouth rinses as a preprocedural rinse in reducing SARS-CoV-2 oral viral load in-vivo. (2) Methods: A literature search was conducted through November 2022 for the following databases: PubMed, Web of Science, Cochrane Library, and Google Scholar. The evaluated outcomes were quantitative changes in viral load and the statistical significance of that change after using antiseptic mouth rinses. (3) Results: 14 randomized controlled trials (RCT) were selected for risk of bias assessment and data extraction. (4) Conclusion: Within the limits of this systematic review, preprocedural mouth rinses may significantly reduce SARS-CoV-2 in the mouth, thus, reducing the viral particles available for airborne dispersion. Preprocedural mouth rinses may be an effective strategy for reducing airborne SARS-CoV-2 dispersion in the environment. Their use may be a preventive strategy to reduce the spread of COVID-19 in selected medical and healthcare facilities, including dental clinics. Potential preprocedural mouth rinses are identified for use as an integral part of safe practice for healthcare protocols. This systematic review was registered with the National Institute for Health Research, international prospective register of systematic reviews (PROSPERO): CRD42022315177.
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Affiliation(s)
- Miriam Ting
- Department of Periodontics, University of Pennsylvania, Philadelphia, PA 19104, USA
- General Practice Residency, Albert Einstein Medical Center, Philadelphia, PA 19141, USA
- Think Dental Learning Institute, Paoli, PA 19301, USA
| | - Alex Dahlkemper
- General Practice Residency, Albert Einstein Medical Center, Philadelphia, PA 19141, USA
| | - Jeremy J Schwartz
- General Practice Residency, Albert Einstein Medical Center, Philadelphia, PA 19141, USA
| | - Manzel Woodfork
- General Practice Residency, Albert Einstein Medical Center, Philadelphia, PA 19141, USA
| | - Jon B Suzuki
- Department of Graduate Periodontics, University of Maryland, Baltimore, MD 21201, USA
- Department of Graduate Prosthodontics, University of Washington, Seattle, WA 98015, USA
- Department of Graduate Periodontics, Nova Southeastern University, Ft. Lauderdale, FL 33314, USA
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4
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Alemany A, Perez-Zsolt D, Raïch-Regué D, Muñoz-Basagoiti J, Ouchi D, Laporte-Villar C, Baro B, Henríquez N, Prat N, Gianinetto MO, Gutiérrez MV, Sánchez-Paniagua MG, Henríquez NL, Vicente JM, Ara J, Rodriguez-Arias MA, Puig J, Blanco I, Lopez CC, Hernández Á, Bordoy AE, Redondo CE, Soler VG, Giménez M, Blanc V, León R, Gispert J, Clotet B, Izquierdo-Useros N, Mitjà O. Cetylpyridinium Chloride Mouthwash to Reduce Shedding of Infectious SARS-CoV-2: A Double-Blind Randomized Clinical Trial. J Dent Res 2022; 101:1450-1456. [PMID: 35727681 DOI: 10.1177/00220345221102310] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via respiratory fluids and droplets suggests that mouthwashes containing substances with virucidal activity can help reduce viral spread. We conducted a multicenter, double-blind, placebo-controlled, randomized trial to assess the virucidal activity of cetylpyridinium chloride (CPC) mouthwashes. Outpatients who tested positive for SARS-CoV-2 infection with or without symptoms were randomized to perform washes and gargles for 1 min with 15 mL of either colored distilled water or 0.07% CPC (Vitis CPC Protect) mouthwash. The study outcomes were the SARS-CoV-2 log10 viral RNA load and the nucleocapsid protein levels, both in saliva at 1 and 3 h after the intervention. In total, 118 patients were enrolled and randomized (mean [SD], age 46 [14] y). Thirteen of 118 participants (11%) did not complete follow-up or had insufficient sample volume for testing and were excluded from the analysis. The assessment of the viral load showed no significant differences between groups at any of the investigated points. However, the levels of SARS-CoV-2 nucleocapsid protein of lysed viruses were significantly higher in the CPC group compared with the control group at 1 h (adjusted difference 269.3 pg/mL; 95% confidence interval [CI], 97.1-441.5) and at 3 h postintervention (561.1 pg/mL; 95% CI, 380.0-742.2). In nonhospitalized patients with asymptomatic or mild symptomatic SARS-CoV-2 infection, a 0.07% CPC mouthwash, compared to placebo, was associated with a significant increase of nucleocapsid protein levels in saliva, indicating enhanced disruption of viral particles.
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Affiliation(s)
- A Alemany
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain.,Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Facultat de Medicina-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | - D Ouchi
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - B Baro
- ISGlobal, Hospital Clinic Universitat de Barcelona, Barcelona, Spain
| | - N Henríquez
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - N Prat
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - M Ochoa Gianinetto
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - M Viaplana Gutiérrez
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | | | - N Larrosa Henríquez
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - J Moreno Vicente
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - J Ara
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - M A Rodriguez-Arias
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain.,Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - J Puig
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | - I Blanco
- Metropolitana Nord Laboratory, Institut Català de la Salut, Badalona, Spain
| | - C Casañ Lopez
- Microbiology Department, Clinical Laboratory Metropolitana Nord, Badalona, Barcelona, Spain
| | - Á Hernández
- Universitat Autònoma de Barcelona, Barcelona, Spain.,Microbiology Department, Clinical Laboratory Metropolitana Nord, Badalona, Barcelona, Spain
| | - A E Bordoy
- Microbiology Department, Clinical Laboratory Metropolitana Nord, Badalona, Barcelona, Spain
| | - C Esteban Redondo
- Microbiology Department, Clinical Laboratory Metropolitana Nord, Badalona, Barcelona, Spain
| | - V González Soler
- Microbiology Department, Clinical Laboratory Metropolitana Nord, Badalona, Barcelona, Spain.,Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain.,CIBER Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain
| | - M Giménez
- Microbiology Department, Clinical Laboratory Metropolitana Nord, Badalona, Barcelona, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - V Blanc
- DENTAID Research Center, Cerdanyola del Vallès, Spain
| | - R León
- DENTAID Research Center, Cerdanyola del Vallès, Spain
| | - J Gispert
- DENTAID Research Center, Cerdanyola del Vallès, Spain
| | | | - B Clotet
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain.,Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,IrsiCaixa AIDS Research Institute, Badalona, Spain.,Universitat de Vic-Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
| | - N Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Germans Trias i Pujol Research Institute, Badalona, Spain
| | - O Mitjà
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain.,Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Universitat de Vic-Universitat Central de Catalunya (UVIC-UCC), Vic, Spain.,Lihir Medical Centre, International SOS, Lihir Island, Papua New Guinea
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5
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Ahmadieh A, Dincer S, Navazesh M. Is saliva collected passively without forceful coughing sensitive to detect SARS-CoV-2 in ambulatory cases? A systematic review. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 133:530-538. [PMID: 35227640 PMCID: PMC8743389 DOI: 10.1016/j.oooo.2022.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 01/09/2023]
Abstract
OBJECTIVE This systematic review was conducted to assess the sensitivity rate of SARS-CoV-2 detection in the saliva of ambulatory asymptomatic and mildly symptomatic patients, with saliva being collected passively without any forceful coughing. STUDY DESIGN A literature search was performed from January 2020 to July 2021. Prospective studies excluding letters to editors were included in our review only if saliva and nasopharyngeal samples were collected simultaneously and sensitivity was reported using reverse transcription polymerase chain reaction (RT-PCR) in asymptomatic or mildly symptomatic ambulatory cases. RESULTS A total of 436 studies were assessed; 10 (4 cohorts and 6 cross-sectional) studies met our inclusion criteria. The sensitivity rate of saliva to detect SARS-CoV-2 varied from 85.7% to 98.6% in all except for 3 studies. Lower sensitivity levels were attributed to low viral load (51.9% and 63.8%) or lack of supervision while collecting saliva (66.7%). CONCLUSIONS Passively collected saliva in the absence of coughing has a high sensitivity rate to detect SARS-CoV-2 in asymptomatic and mildly symptomatic patients compared with nasopharyngeal swabs. Limitations of previous studies, such as lack of attention to the method of saliva collection, stages, and severity of the disease at the time of sample collection, can be researched in future investigations.
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Affiliation(s)
- Azadeh Ahmadieh
- Clinical Assistant Professor of Dentistry, Division of Biomedical Sciences, Herman Ostrow School of Dentistry of USC, Los Angeles, California, USA.,Corresponding author
| | - Sibel Dincer
- Clinical Assistant Professor of Dentistry, Division of Biomedical Sciences, Herman Ostrow School of Dentistry of USC, Los Angeles, California, USA
| | - Mahvash Navazesh
- Executive Associate Dean for Academic, Faculty & Student Affairs, Division of Periodontology, Diagnostic Sciences & Dental Hygiene, Professor of Diagnostic Sciences, Herman Ostrow School of Dentistry of USC, Los Angeles, California, USA
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6
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Saliva versus Upper Respiratory Swabs: Equivalent for Severe Acute Respiratory Syndrome Coronavirus 2 University Screening while Saliva Positivity Is Prolonged After Symptom Onset in Coronavirus Disease 2019 Hospitalized Patients. J Mol Diagn 2022; 24:727-737. [PMID: 35489695 PMCID: PMC9044746 DOI: 10.1016/j.jmoldx.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/25/2022] [Accepted: 03/30/2022] [Indexed: 11/22/2022] Open
Abstract
Reopening of schools and workplaces during the ongoing coronavirus disease 2019 (COVID-19) pandemic requires affordable and convenient population-wide screening methods. Although upper respiratory swab is considered the preferable specimen for testing, saliva offers several advantages, such as easier collection and lower cost. In this study, we compared the performance of saliva with upper respiratory swab for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. Paired saliva and anterior nares specimens were collected from a largely asymptomatic cohort of students, faculty, and staff from the University of Pennsylvania. Paired saliva and combined nasopharyngeal/oropharyngeal (NP/OP) specimens were also collected from hospitalized patients with symptomatic COVID-19 following confirmatory testing. All study samples were tested by real-time PCR in the Hospital of the University of Pennsylvania. In the university cohort, positivity rates were 37 of 2500 for saliva (sensitivity, 86.1%) and 36 of 2500 for anterior nares (sensitivity, 83.7%), with an overall agreement of 99.6%. In the hospital study cohort, positivity rates were 35 of 49 for saliva (sensitivity, 89.3%) and 28 of 49 for NP/OP (sensitivity, 75.8%), with an overall agreement of 75.6%. A larger proportion of saliva than NP/OP samples tested positive after 4 days of symptom onset in hospitalized patients. Our results show that saliva has an acceptable sensitivity and is comparable to upper respiratory swab, supporting the use of saliva for SARS-CoV-2 detection in both symptomatic and asymptomatic populations.
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7
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Lopes JIF, da Costa Silva CA, Cunha RG, Soares AM, Lopes MED, da Conceição Neto OC, Alves ADR, da Costa Nunes Pimentel Coelho WL, Amorim Filho L, Amado Leon LA. A Large Cohort Study of SARS-CoV-2 Detection in Saliva: A Non-Invasive Alternative Diagnostic Test for Patients with Bleeding Disorders. Viruses 2021; 13:v13122361. [PMID: 34960630 PMCID: PMC8707508 DOI: 10.3390/v13122361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023] Open
Abstract
Diagnosis of SARS-CoV-2 infections is mostly based on the nasopharyngeal swabs (NPS). However, this collection is invasive and uncomfortable, especially for children and patients with coagulopathies, whose NPS collection often causes bleeding. Thus, the aim of this study was to evaluate the usefulness and accuracy of saliva for the diagnosis of COVID-19 in patients presenting bleeding disorders. Samples of NPS, oropharyngeal swabs (OPS), and saliva were collected simultaneously from 1159 hospitalized patients with hematological diseases and from 524 healthcare workers, both symptomatic and asymptomatic for SARS-CoV-2. All samples were evaluated for SARS-CoV-2 by qRT-PCR. SARS-CoV-2 was detected in NPS, OPS and saliva from 16.9%, 14.4% and 15.6% individuals, respectively. Tests in saliva showed sensitivity, specificity, and overall agreement of 73.3%, 96.9% and 92.7% (=0.74), respectively. Salivary tests had good accuracy (AUC = 0.7) for discriminating negative and positive qRT-PCR for SARS-CoV-2. Higher sensitivity was observed in symptomatic than in non-symptomatic patients, as well as in healthy subjects than in patients with hematological disease, in both OPS and saliva. The mean viral load in NPS was significantly higher than in OPS and in saliva samples (p < 0.001). Saliva is a good diagnostic tool to detect SARS-CoV-2, especially among patients symptomatic for COVID-19, and is a valuable specimen for mass screening of hospitalized patients with hematological diseases, especially for those that with bleeding disorders.
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Affiliation(s)
- Josiane Iole França Lopes
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
- Laboratório de Desenvolvimento Tecnológico em Virologia, Oswaldo Cruz Institute/Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-900, Brazil; (A.D.R.A.); (W.L.d.C.N.P.C.)
| | - Carlos Alexandre da Costa Silva
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
| | - Rodrigo Guimarães Cunha
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
| | - Alexandra Martins Soares
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
| | - Maria Esther Duarte Lopes
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
| | - Orlando Carlos da Conceição Neto
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
| | - Arthur Daniel Rocha Alves
- Laboratório de Desenvolvimento Tecnológico em Virologia, Oswaldo Cruz Institute/Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-900, Brazil; (A.D.R.A.); (W.L.d.C.N.P.C.)
| | - Wagner Luis da Costa Nunes Pimentel Coelho
- Laboratório de Desenvolvimento Tecnológico em Virologia, Oswaldo Cruz Institute/Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-900, Brazil; (A.D.R.A.); (W.L.d.C.N.P.C.)
| | - Luiz Amorim Filho
- Instituto de Hematologia Arthur de Siqueira Cavalcanti/Hemorio, Rua Frei Caneca, 8, Centro, Rio de Janeiro CEP 20211-030, Brazil; (J.I.F.L.); (C.A.d.C.S.); (R.G.C.); (A.M.S.); (M.E.D.L.); (O.C.d.C.N.); (L.A.F.)
| | - Luciane Almeida Amado Leon
- Laboratório de Desenvolvimento Tecnológico em Virologia, Oswaldo Cruz Institute/Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro CEP 21040-900, Brazil; (A.D.R.A.); (W.L.d.C.N.P.C.)
- Correspondence: ; Tel.: +55-(21)-2562-1876
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8
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Alemany A, Millat-Martinez P, Ouchi D, Corbacho-Monné M, Bordoy AE, Esteban C, Hernández Á, Casañ C, Gonzalez V, Costes G, Capdevila-Jáuregui M, Torrano-Soler P, San José A, Ara J, Prat N, Clotet B, Bassat Q, Gimenez M, Blanco I, Baro B, Mitjà O. Self-collected mid-nasal swabs and saliva specimens, compared with nasopharyngeal swabs, for SARS-CoV-2 detection in mild COVID-19 patients. J Infect 2021; 83:709-737. [PMID: 34537322 PMCID: PMC8444446 DOI: 10.1016/j.jinf.2021.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Andrea Alemany
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain; Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | | | - Dan Ouchi
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | | | - Antoni E Bordoy
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Cristina Esteban
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Águeda Hernández
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Cristina Casañ
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Victoria Gonzalez
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Gèlia Costes
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | | | | | - Alba San José
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain
| | - Jordi Ara
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Núria Prat
- Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Bonaventura Clotet
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain; Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Universitat de Vic-Universitat Central de Catalunya (UVIC-UCC), Vic, Spain
| | - Quique Bassat
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain; Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Montserrat Gimenez
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain
| | - Ignacio Blanco
- Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Gerència Territorial Metropolitana Nord, Institut Català de la Salut, Barcelona, Spain
| | - Bàrbara Baro
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
| | - Oriol Mitjà
- Fight AIDS and Infectious Diseases Foundation, Badalona, Spain; Hospital Universitari Germans Trias i Pujol, Barcelona Institute for Global Health, Rosselló, 132, Badalona 08036, Spain; Lihir Medical Centre, International SOS Clinic, Lihir Island, Papua New Guinea
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9
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Migueres M, Vellas C, Abravanel F, Da Silva I, Dimeglio C, Ferrer V, Raymond S, Mansuy JM, Izopet J. Testing individual and pooled saliva samples for sars-cov-2 nucleic acid: a prospective study. Diagn Microbiol Infect Dis 2021; 101:115478. [PMID: 34364098 PMCID: PMC8279932 DOI: 10.1016/j.diagmicrobio.2021.115478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022]
Abstract
Control of the rapid spread of the SARS-CoV-2 virus requires efficient testing. We collected paired nasopharyngeal swab (NPs) and saliva samples from 303 subjects (52.8% symptomatic) at a drive-through testing center; 18% of whom tested positive. The NPs, salivas and five saliva pools were tested for SARS-CoV-2 RNA using the Aptima™ assay and a laboratory-developed test (LDT) on the Panther-Fusion™ Hologic® platform. The saliva sensitivity was 80% (LDT) and 87.5% (Aptima™) whereas that of NPs was 96.4% in both assays. The pooled saliva sensitivity of 72.7% (LDT) and 75% (Aptima™) was not significantly different of that of individual saliva testing. Saliva specimens appear to be suitable for sensitive non-invasive assays to detect SARS-CoV-2 nucleic acid; pooling them for a single test will improve laboratory throughput.
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Affiliation(s)
- Marion Migueres
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse, France; Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - Camille Vellas
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse, France; Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Florence Abravanel
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse, France; Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Chloé Dimeglio
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France
| | - Venicia Ferrer
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France
| | - Stéphanie Raymond
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse, France; Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Jacques Izopet
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse, France; Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
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10
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Hiroi S, Kubota-Koketsu R, Sasaki T, Morikawa S, Motomura K, Nakayama EE, Okuno Y, Shioda T. Infectivity assay for detection of SARS-CoV-2 in samples from patients with COVID-19. J Med Virol 2021; 93:5917-5923. [PMID: 34139026 PMCID: PMC8426682 DOI: 10.1002/jmv.27145] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/15/2021] [Accepted: 06/09/2021] [Indexed: 12/23/2022]
Abstract
Since the coronavirus disease 2019 (COVID-19) outbreak, laboratory diagnosis has mainly been conducted using reverse-transcription polymerase chain reaction (RT-PCR). Detecting the presence of an infectious virus in the collected sample is essential to analyze if a person can transmit infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there have been no quantitative investigations conducted for infectious SARS-CoV-2 in clinical samples. Therefore, in the present study, a rapid and simple focus-forming assay using the peroxidase-antiperoxidase technique was developed to quantify infectious SARS-CoV-2 titers in 119 samples (n = 52, nasopharyngeal swabs [NPS]; n = 67, saliva) from patients with COVID-19. Furthermore, the study findings were compared with the cycle threshold (Ct) values of real-time RT-PCR. The infectious virus titers in NPS samples and Ct values were inversely correlated, and no infectious virus could be detected when the Ct value exceeded 30. In contrast, a low correlation was observed between the infectious virus titers in saliva and Ct values (r = -0.261, p = 0.027). Furthermore, the infectious virus titers in the saliva were significantly lower than those in the NPS samples. Ten days after the onset of COVID-19 symptoms, the infectious virus was undetectable, and Ct values were more than 30 in NSP and saliva samples. The results indicate that patients whose symptoms subsided 10 days after onset, with Ct values more than 30 in NSP and saliva samples, were less likely to infect others.
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Affiliation(s)
- Satoshi Hiroi
- Division of Microbiology, Virology Section, Osaka Institute of Public Health, Osaka, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tadahiro Sasaki
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Saeko Morikawa
- Division of Microbiology, Virology Section, Osaka Institute of Public Health, Osaka, Japan
| | - Kazushi Motomura
- Division of Microbiology, Virology Section, Osaka Institute of Public Health, Osaka, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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11
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Evaluation of RNA Extraction-Free Method for Detection of SARS-CoV-2 in Salivary Samples for Mass Screening for COVID-19. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568350. [PMID: 34327228 PMCID: PMC8245243 DOI: 10.1155/2021/5568350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/15/2021] [Indexed: 12/28/2022]
Abstract
In this COVID-19 pandemic, there is a dire need for cost-effective and less time-consuming alternatives for SARS-CoV-2 testing. The RNA extraction-free method for detecting SARS-CoV-2 in saliva is a promising option. This study found that it has high sensitivity (85.34%), specificity (95.04%), and was comparable to the gold standard nasopharyngeal swab (NPS) sample tests. The method showed good agreement between salivary and NPS samples, with a kappa coefficient of 0.797. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fisher Applied Biosystems showed high sensitivity, positive predictive value (PPV), and negative predictive value (NPV) but also showed a higher percentage of invalid reports. On the other hand, the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples, and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction-free method for salivary sample serves as an effective alternative screening method for COVID-19.
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12
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Ibrahimi N, Delaunay-Moisan A, Hill C, Le Teuff G, Rupprecht JF, Thuret JY, Chaltiel D, Potier MC. Screening for SARS-CoV-2 by RT-PCR: Saliva or nasopharyngeal swab? Rapid review and meta-analysis. PLoS One 2021; 16:e0253007. [PMID: 34111196 PMCID: PMC8191978 DOI: 10.1371/journal.pone.0253007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Diagnosis of COVID-19 in symptomatic patients and screening of populations for SARS-CoV-2 infection require access to straightforward, low-cost and high-throughput testing. The recommended nasopharyngeal swab tests are limited by the need of trained professionals and specific consumables and this procedure is poorly accepted as a screening method In contrast, saliva sampling can be self-administered. METHODS In order to compare saliva and nasopharyngeal/oropharyngeal samples for the detection of SARS-CoV-2, we designed a meta-analysis searching in PubMed up to December 29th, 2020 with the key words "(SARS-CoV-2 OR COVID-19 OR COVID19) AND (salivary OR saliva OR oral fluid)) NOT (review[Publication Type]) NOT (PrePrint[Publication Type])" applying the following criteria: records published in peer reviewed scientific journals, in English, with at least 15 nasopharyngeal/orapharyngeal swabs and saliva paired samples tested by RT-PCR, studies with available raw data including numbers of positive and negative tests with the two sampling methods. For all studies, concordance and sensitivity were calculated and then pooled in a random-effects model. FINDINGS A total of 377 studies were retrieved, of which 50 were eligible, reporting on 16,473 pairs of nasopharyngeal/oropharyngeal and saliva samples. Meta-analysis showed high concordance, 92.5% (95%CI: 89.5-94.7), across studies and pooled sensitivities of 86.5% (95%CI: 83.4-89.1) and 92.0% (95%CI: 89.1-94.2) from saliva and nasopharyngeal/oropharyngeal swabs respectively. Heterogeneity across studies was 72.0% for saliva and 85.0% for nasopharyngeal/oropharyngeal swabs. INTERPRETATION Our meta-analysis strongly suggests that saliva could be used for frequent testing of COVID-19 patients and "en masse" screening of populations.
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Affiliation(s)
- Nusaïbah Ibrahimi
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Agnès Delaunay-Moisan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette Cedex, France
| | - Catherine Hill
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Gwénaël Le Teuff
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean-François Rupprecht
- Aix Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, Turing Center for Living Systems, Marseille, France
| | - Jean-Yves Thuret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette Cedex, France
| | - Dan Chaltiel
- Service de Biostatistique et d’Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Marie-Claude Potier
- Institut du Cerveau (ICM), CNRS UMR 7225 – Inserm U1127, Sorbonne Université, Paris, France
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Caixeta DC, Oliveira SW, Cardoso-Sousa L, Cunha TM, Goulart LR, Martins MM, Marin LM, Jardim ACG, Siqueira WL, Sabino-Silva R. One-Year Update on Salivary Diagnostic of COVID-19. Front Public Health 2021; 9:589564. [PMID: 34150692 PMCID: PMC8210583 DOI: 10.3389/fpubh.2021.589564] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/31/2021] [Indexed: 01/19/2023] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) is a global health problem, which is challenging healthcare worldwide. In this critical review, we discussed the advantages and limitations in the implementation of salivary diagnostic platforms of COVID-19. The diagnostic test of COVID-19 by invasive nasopharyngeal collection is uncomfortable for patients and requires specialized training of healthcare professionals in order to obtain an appropriate collection of samples. Additionally, these professionals are in close contact with infected patients or suspected cases of COVID-19, leading to an increased contamination risk for frontline healthcare workers. Although there is a colossal demand for novel diagnostic platforms with non-invasive and self-collection samples of COVID-19, the implementation of the salivary platforms has not been implemented for extensive scale testing. Up to date, several cross-section and clinical trial studies published in the last 12 months support the potential of detecting SARS-CoV-2 RNA in saliva as a biomarker for COVID-19, providing a self-collection, non-invasive, safe, and comfortable procedure. Therefore, the salivary diagnosis is suitable to protect healthcare professionals and other frontline workers and may encourage patients to get tested due to its advantages over the current invasive methods. The detection of SARS-CoV-2 in saliva was substantial also in patients with a negative nasopharyngeal swab, indicating the presence of false negative results. Furthermore, we expect that salivary diagnostic devices for COVID-19 will continue to be used with austerity without excluding traditional gold standard specimens to detect SARS-CoV-2.
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Affiliation(s)
- Douglas Carvalho Caixeta
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
| | - Stephanie Wutke Oliveira
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
- School of Dentistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Leia Cardoso-Sousa
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
| | | | - Luiz Ricardo Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Mario Machado Martins
- Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Lina Maria Marin
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Science, Federal University of Uberlandia, Uberlandia, Brazil
- São Paulo State University, Institute of Biosciences, Humanities and Exact Sciences, São José Do Rio Preto, Brazil
| | | | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Brazil
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14
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Performance of Saliva Specimens for the Molecular Detection of SARS-CoV-2 in the Community Setting: Does Sample Collection Method Matter? J Clin Microbiol 2021; 59:JCM.03033-20. [PMID: 33419948 PMCID: PMC8092755 DOI: 10.1128/jcm.03033-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Data on the performance of saliva specimens for diagnosing coronavirus disease 2019 (COVID-19) in ambulatory patients are scarce and inconsistent. We assessed saliva-based specimens for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcriptase PCR (RT-PCR) in the community setting and compared three different collection methods. This prospective study was conducted in three primary care centers. RT-PCR was performed on paired nasopharyngeal swabs (NPS) and saliva samples collected from outpatients with a broad clinical spectrum of illness. To assess differences in collection methods, saliva specimens were obtained in a different way in each of the participating centers: supervised collection (SVC), oropharyngeal washing (OPW), and self-collection (SC). Pairs of NPS and saliva samples from 577 patients (median age, 39 years; 44% men; 42% asymptomatic) were collected and tested, and 120 (20.8%) gave positive results. The overall agreement with NPS results and kappa coefficients (κ) for saliva samples obtained by SVC, OPW, and SC were 95% (κ = 0.85), 93.4% (κ = 0.76), and 93.3% (κ = 0.76), respectively. The sensitivities (95% confidence intervals [95% CI]) of the saliva specimens ranged from 86% (72.6% to 93.7%) for SVC to 66.7% (50.4% to 80%) for SC samples. Sensitivity was higher for samples with lower cycle threshold (CT ) values. The best RT-PCR performance was observed for SVC, with sensitivities (95% CI) of 100% (85.9% to 100%) in symptomatic individuals and 88.9% (50.7% to 99.4%) in asymptomatic individuals at CT values of ≤30. We conclude that saliva is an acceptable specimen for the detection of SARS-CoV-2 in the community setting. Specimens collected under supervision perform comparably to NPS and can effectively identify individuals at higher risk of transmission under real-life conditions.
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