Validation and deployment of a direct saliva real-time RT-PCR test on pooled samples for COVID-19 surveillance testing

PLoS One. 2021 Dec 30;16(12):e0261956. doi: 10.1371/journal.pone.0261956. eCollection 2021.

Abstract

A direct, real-time reverse transcriptase PCR test on pooled saliva was validated in 2,786 participants against oropharyngeal swabs. Among asymptomatic/pre-symptomatic participants, the test was found to be in 99.21% agreement and 45% more sensitive than contemporaneous oropharyngeal swabs. The test was then used for surveillance testing on 44,242 saliva samples from asymptomatic participants. Those whose saliva showed evidence of SARS-CoV-2 within 50 cycles of amplification were referred for confirmatory testing, with 87% of those tested by nasal swab within 72 hours receiving a positive diagnostic result on Abbott ID NOW or real-time PCR platforms. Median Ct values on the saliva PCR for those with a positive and negative confirmatory tests was 30.67 and 35.92 respectively, however, binary logistic regression analysis of the saliva Ct values indicates that Ct thresholds as high as 47 may be useful in a surveillance setting. Overall, data indicate that direct RT-PCR testing of pooled saliva samples is an effective method of SARS-CoV-2 surveillance.

Publication types

  • Validation Study

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 Nucleic Acid Testing / methods*
  • Carrier State / diagnosis*
  • Diagnostic Tests, Routine / methods*
  • Humans
  • Real-Time Polymerase Chain Reaction / methods*
  • Saliva / virology*
  • Sensitivity and Specificity

Grants and funding

The author(s) received no specific funding for this work.