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

Abstract

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.

Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care

“…Finally, our study con rmed, as previously 19 , the good performance of saliva RT-PCR and nasopharyngeal antigen testing as reliable alternative strategies to detect SARS-CoV-2 in both symptomatic and asymptomatic individuals in the ambulatory setting. Further work is needed to optimize an assay combining collected saliva and rapid point-of-care isothermal detection of SARS-CoV-2 RNA.…”

“…Self-collected saliva is non-invasive and easy to collect and thus more suitable for mass-screening than nasopharyngeal sampling [11][12][13][14] . Recent meta-analyses assessed performances of saliva RT-PCR tests for the diagnosis of COVID-19 [15][16][17][18] and we recently con rmed in a large prospective study the excellent sensitivity of saliva RT-PCR, as compared to nasopharyngeal RT-PCR, for the detection of SARS-CoV-2 in community screening centers 19 .…”

“…Informed consent was obtained from all subjects or, if subjects were under 18, from a parent and/or legal guardian. All adults and children, either symptomatic or asymptomatic, referred to the two participating COVISAN centers, Paris, France, were eligible as described previously 19 . In accordance with EasyCoV® assay manufacturer instructions of (SkillCell-Alcen, Jarry, France), performances of saliva RT-LAMP were estimated on saliva tested in screening centers, immediately after collection (< 5 minutes) or stored immediately at 4°C and then tested within a maximal 90 minutes interval after collection.…”

Accuracy of novel antigen rapid diagnostics for SARS-CoV-2: A living systematic review and meta-analysis

“…At the end of the data extraction process, 37 studies were still in preprint form [4,171,173,174,177,180,190,192,201,204,205,207,211,[214][215][216]218,220,222,223,225,227,231,233,234,238,240,244,247,253,257,265,267,284,287,290,293]. All studies were written in English, except for 2 in Spanish [175,280].…”

“…Median Ct values differed in symptomatic and asymptomatic patients. For those studies where it was possible to extract a median Ct value, it ranged from 20.5 to 27.0 in symptomatic patients [170,207,226,258,271,272] and from 27.2 to 30.5 in asymptomatic patients [170,201,258].…”