Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription-Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19

J Clin Microbiol. 2020 Aug 24;58(9):e01438-20. doi: 10.1128/JCM.01438-20. Print 2020 Aug 24.

Abstract

The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity.

Keywords: RT-LAMP; RT-qPCR; SARS-CoV-2; antigen test; saliva.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Antigens, Viral / analysis
  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification
  • COVID-19
  • COVID-19 Testing
  • Clinical Laboratory Techniques* / methods
  • Clinical Laboratory Techniques* / standards
  • Clinical Laboratory Techniques* / statistics & numerical data
  • Coronavirus Infections / diagnosis*
  • Female
  • Humans
  • Immunoassay* / methods
  • Immunoassay* / standards
  • Immunoassay* / statistics & numerical data
  • Male
  • Middle Aged
  • Nucleic Acid Amplification Techniques* / methods
  • Nucleic Acid Amplification Techniques* / standards
  • Nucleic Acid Amplification Techniques* / statistics & numerical data
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • RNA, Viral / analysis
  • RNA, Viral / genetics
  • SARS-CoV-2
  • Saliva / virology*
  • Sensitivity and Specificity
  • Specimen Handling
  • Young Adult

Substances

  • Antigens, Viral
  • RNA, Viral