Accuracy of antigen and nucleic acid amplification testing on saliva and naopharyngeal samples for detection of SARS-CoV-2 in ambulatory care

Background: Nasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the current standard diagnostic test for of coronavirus disease 2019 (COVID-19). However, the NAAT technique is lengthy and nasopharyngeal sampling requires trained personnel. Saliva NAAT represents an interesting alternative but diagnostic performances vary widely between studies. Objective: To assess 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), as compared to nasopharyngeal NAAT. Design: Prospective participant enrollment from 19 October through 18 December 2020. Setting: Two community COVID-19 screening centers in Paris, France. Participants: 1452 ambulatory children and adults referred for SARS-CoV-2 testing. Interventions: NAAT on a saliva sample (performed with three different protocols for pre-processing, amplification and detection of SARS-CoV-2) and Ag testing on a nasopharyngeal sample. Measurements: Performance of saliva NAAT and nasopharyngeal Ag testing. Results: Overall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was of 94% (95% CI, 86% to 98%), 23% (CI, 14% to 35%), 94% (CI, 88% to 97%) and 96% (CI, 91% to 99%) for the nasopharyngeal Ag test and the three different protocols of saliva NAAT, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals. Limitations: Few children (n=122, 8%) were included. Conclusion: In the ambulatory setting, diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT seems similar to that of nasopharyngeal NAAT, subject to strict compliance with specific pre-processing and amplification protocols. Registration number: NCT04578509 Funding Sources: French Ministry of Health and the Assistance Publique-Hopitaux de Paris Foundation.