Royal College of Surgeons in Ireland
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Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing [version 2; peer review: 2 approved]

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posted on 2022-03-21, 12:11 authored by Chiara De SantiChiara De Santi, Benson Jacob, Patricia Kroich, Sean Doyle, Rebecca Ward, Brian Li, Owain Donnelly, Amy Dykes, Trisha Neelakant, David Neary, Ross McGuinness, Jacqueline Cafferkey, Kieran RyanKieran Ryan, Veronica Quadu, Killian McGrogan, Alejandro Garcia Leon, Patrick Mallon, Fidelma FitzpatrickFidelma Fitzpatrick, Hilary HumphreysHilary Humphreys, Eoghan De BarraEoghan De Barra, Steven KerriganSteven Kerrigan, Gianpiero CavalleriGianpiero Cavalleri
Introduction: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited. The aim of our study was to assess SalivaDirect as an alternative method for COVID-19 testing.
Methods: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings, respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRp and N1 gene targets in NPS and saliva, respectively.
Results: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833-0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample ( p=0.860). A highly significant correlation (r = 0.475, p<0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens.
Conclusions: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Accurate and less invasive saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.


Royal College of Surgeons in Ireland

Science Foundation Ireland Grant 20/COV/0185.



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Published Citation

De Santi C, et al. Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing [version 2; peer review: 2 approved] HRB Open Res. 2021;4:85.

Publication Date

15 October 2021

PubMed ID



  • School of Pharmacy and Biomolecular Sciences
  • International Health and Tropical Medicine
  • Beaumont Hospital
  • Surgical Affairs
  • Clinical Microbiology
  • FutureNeuro Centre
  • Undergraduate Research


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