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

  1. Solen Kernéis
  2. Caroline Elie
  3. Jacques Fourgeaud
  4. Laure Choupeaux
  5. Séverine Mercier Delarue
  6. Marie-Laure Alby
  7. Pierre Quentin
  8. Juliette Pavie
  9. Patricia Brazille
  10. Marie Laure Néré
  11. Marine Minier
  12. Audrey Gabassi
  13. Aurélien Gibaud
  14. Sébastien Gauthier
  15. Chrystel Leroy
  16. Etienne Voirin-Mathieu
  17. Claire Poyart
  18. Michel Vidaud
  19. Béatrice Parfait
  20. Constance Delaugerre
  21. Jean-Marc Tréluyer
  22. Jérôme Le Goff
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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-Hôpitaux de Paris Foundation.

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