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Kernéis S, Elie C, Fourgeaud J, Choupeaux L, Delarue SM, Alby ML, Quentin P, Pavie J, Brazille P, Néré ML, Minier M, Gabassi A, Gibaud A, Gauthier S, Leroy C, Voirin-Mathieu E, Poyart C, Vidaud M, Parfait B, Delaugerre C, Tréluyer JM, LeGoff J. Accuracy of saliva and nasopharyngeal sampling for detection of SARS-CoV-2 in community screening: a multicentric cohort study. Eur J Clin Microbiol Infect Dis 2021; 40:2379-2388. [PMID: 34342768 PMCID: PMC8329409 DOI: 10.1007/s10096-021-04327-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/27/2021] [Indexed: 01/07/2023]
Abstract
Nasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the standard diagnostic test of coronavirus disease 2019. Our objectives were to assess, in real-life conditions, the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambulatory care. This was a prospective cohort study from 19 October through 18 December 2020 in two community COVID-19 screening centers in Paris, France. Two nasopharyngeal swabs and one saliva sample were simultaneously collected. Diagnostic accuracies of nasopharyngeal Ag testing and of three saliva NAAT methods were assessed as compared to nasopharyngeal NAAT. A total of 1452 ambulatory children and adults were included. Overall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was 94%, 23%, 96%, and 94% for the three different protocols of saliva NAAT and for the nasopharyngeal Ag test, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals. Diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT is similar to that of nasopharyngeal NAAT, subject to compliance with specific protocols for saliva. Registration number: NCT04578509.
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Affiliation(s)
- Solen Kernéis
- Université de Paris, INSERM, IAME, 75018, Paris, France.
- Equipe de Prévention du Risque Infectieux, AP-HP, Hôpital Bichat, 46 rue Henri Huchard, 75018, Paris, France.
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion, 75015, Paris, France.
| | - Caroline Elie
- Clinical Research Unit / Clinical Investigation Center, APHP, Necker-Enfants Malades Hospital, 75015, Paris, France
- EA 7323 Pharmacologie Et Thérapeutique de L'enfant Et de La Femme Enceinte, Université de Paris, 75015, Paris, France
| | - Jacques Fourgeaud
- Virologie, AP-HP, Hôpital Necker-Enfants Malades, 75015, Paris, France
- Equipe Hospitalo-Universitaire 7328, Prise en Charge Des Anomalies Congénitales Et de Leur Traitement, Institut Imagine, Université de Paris, 75015, Paris, France
| | - Laure Choupeaux
- Clinical Research Unit / Clinical Investigation Center, APHP, Necker-Enfants Malades Hospital, 75015, Paris, France
| | | | - Marie-Laure Alby
- Centre de Dépistage COVISAN 13 14 15, Communauté Professionnelle de Territoire de Santé, 75014, Paris, France
| | - Pierre Quentin
- Centre de Dépistage COVISAN 13 14 15, Communauté Professionnelle de Territoire de Santé, 75014, Paris, France
| | - Juliette Pavie
- Immuno-Infectiologie, AP-HP, Hôtel Dieu, 75004, Paris, France
- Centre de Dépistage COVISAN, AP-HP, Hôtel Dieu, 75004, Paris, France
| | - Patricia Brazille
- Centre de Dépistage COVISAN, AP-HP, Hôtel Dieu, 75004, Paris, France
- Espace Santé Jeunes - Unité Guy Môquet, AP-HP, Hôtel Dieu, 75004, Paris, France
| | | | - Marine Minier
- Virologie, AP-HP, Hôpital Saint Louis, 75010, Paris, France
| | - Audrey Gabassi
- Virologie, AP-HP, Hôpital Saint Louis, 75010, Paris, France
| | | | - Sébastien Gauthier
- Centre de Ressources Biologiques - Site Cochin, AP-HP, Fédération des CRB/PRB D'AP-HP. Centre-Université de Paris, Hôpital Cochin, 75014, Paris, France
| | | | - Etienne Voirin-Mathieu
- Plateforme SeqOIA, AP-HP, 75014, Paris, France
- Virologie, Hôpital Cochin, AP-HP, 75014, Paris, France
| | - Claire Poyart
- Université de Paris, INSERM, Institut Cochin, 1016, F-75014, Paris, France
- Bactériologie, AP-HP Centre, Hôpital Cochin, 75014, Paris, France
| | - Michel Vidaud
- Plateforme SeqOIA, AP-HP, 75014, Paris, France
- Université de Paris, INSERM, Institut Cochin, 1016, F-75014, Paris, France
| | - Béatrice Parfait
- Centre de Ressources Biologiques - Site Cochin, AP-HP, Fédération des CRB/PRB D'AP-HP. Centre-Université de Paris, Hôpital Cochin, 75014, Paris, France
| | - Constance Delaugerre
- Virologie, AP-HP, Hôpital Saint Louis, 75010, Paris, France
- Université de Paris, INSERM, U944, F-75010, Paris, France
| | - Jean-Marc Tréluyer
- Clinical Research Unit / Clinical Investigation Center, APHP, Necker-Enfants Malades Hospital, 75015, Paris, France
- EA 7323 Pharmacologie Et Thérapeutique de L'enfant Et de La Femme Enceinte, Université de Paris, 75015, Paris, France
| | - Jérôme LeGoff
- Virologie, AP-HP, Hôpital Saint Louis, 75010, Paris, France
- Equipe INSIGHT, Université de Paris, INSERM, U976, F-75010, Paris, France
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LeGoff J, Kernéis S, Elie C, Mercier-Delarue S, Gastli N, Choupeaux L, Fourgeaud J, Alby ML, Quentin P, Pavie J, Brazille P, Néré ML, Minier M, Gabassi A, Leroy C, Parfait B, Tréluyer JM, Delaugerre C. Evaluation of a saliva molecular point of care for the detection of SARS-CoV-2 in ambulatory care. Sci Rep 2021; 11:21126. [PMID: 34702867 PMCID: PMC8548486 DOI: 10.1038/s41598-021-00560-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Rapid identification of SARS-CoV-2-infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swabs. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Overall, 117 of the 1718 participants (7%) tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97%, respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference tests, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. The detection of SARS-CoV-2 in crude saliva samples with an RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing. Registration number: NCT04578509.
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Affiliation(s)
- Jérôme LeGoff
- Virologie, AP-HP, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010, Paris, France. .,INSERM, Equipe INSIGHT, U976, 75010, Université de Paris, Paris, France.
| | - Solen Kernéis
- INSERM, IAME, Université de Paris, 75018, Paris, France.,Equipe de Prévention du Risque Infectieux, AP-HP, Hôpital Bichat, 75018, Paris, France.,Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion, 75015, Paris, France
| | - Caroline Elie
- Clinical Research Unit / Clinical Investigation Center, APHP, Necker-Enfants Malades Hospital, 75015, Paris, France.,EA 7323 Pharmacologie et Thérapeutique de l'enfant et de la Femme Enceinte, Université de Paris, 75015, Paris, France
| | | | - Nabil Gastli
- Plateforme Covid IDF, AP-HP Centre, 75014, Paris, France
| | - Laure Choupeaux
- Clinical Research Unit / Clinical Investigation Center, APHP, Necker-Enfants Malades Hospital, 75015, Paris, France
| | - Jacques Fourgeaud
- Virologie, AP-HP, Hôpital Necker-Enfants Malades, 75015, Paris, France
| | - Marie-Laure Alby
- Centre de Dépistage COVISAN 13 14 15, Communauté Professionnelle de Territoire de Santé, 75014, Paris, France
| | - Pierre Quentin
- Centre de Dépistage COVISAN 13 14 15, Communauté Professionnelle de Territoire de Santé, 75014, Paris, France
| | - Juliette Pavie
- Immuno-Infectiologie, AP-HP, Hôtel Dieu, 75004, Paris, France.,Centre de Dépistage COVISAN, AP-HP, Hôtel-Dieu, 75004, Paris, France
| | - Patricia Brazille
- Immuno-Infectiologie, AP-HP, Hôtel Dieu, 75004, Paris, France.,Centre de Dépistage COVISAN, AP-HP, Hôtel-Dieu, 75004, Paris, France
| | - Marie Laure Néré
- Virologie, AP-HP, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010, Paris, France
| | - Marine Minier
- Virologie, AP-HP, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010, Paris, France
| | - Audrey Gabassi
- Virologie, AP-HP, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010, Paris, France
| | - Chrystel Leroy
- Plateforme Covid IDF, AP-HP Centre, 75014, Paris, France.,Plateforme SeqOIA, AP-HP, 75014, Paris, France
| | - Béatrice Parfait
- Centre de Ressources Biologiques, Hôpital Cochin, 75014, Paris, France
| | - Jean-Marc Tréluyer
- Clinical Research Unit / Clinical Investigation Center, APHP, Necker-Enfants Malades Hospital, 75015, Paris, France.,EA 7323 Pharmacologie et Thérapeutique de l'enfant et de la Femme Enceinte, Université de Paris, 75015, Paris, France
| | - Constance Delaugerre
- Virologie, AP-HP, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010, Paris, France.,INSERM, U944, 75010, Université de Paris, Paris, France
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