Prospective Study Comparing Deep Throat Saliva With Other Respiratory Tract Specimens in the Diagnosis of Novel Coronavirus Disease 2019

J Infect Dis. 2020 Oct 13;222(10):1612-1619. doi: 10.1093/infdis/jiaa487.


Background: Self-collected specimens have been advocated to avoid infectious exposure to healthcare workers. Self-induced sputum in those with a productive cough and saliva in those without a productive cough have been proposed, but sensitivity remains uncertain.

Methods: We performed a prospective study in 2 regional hospitals in Hong Kong.

Results: We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. Deep throat saliva had the lowest overall reverse-transcriptase polymerase chain reaction (RT-PCR)-positive rate (68.7% vs 89.4% [sputum] and 80.9% [pooled NP and throat swabs]) and the lowest viral ribonucleic acid (RNA) concentration (mean log copy/mL 3.54 vs 5.03 [sputum] and 4.63 [pooled NP and throat swabs]). Analyses with respect to time from symptom onset and severity also revealed similar results. Virus yields of DTS correlated with that of sputum (Pearson correlation index 0.76; 95% confidence interval, 0.62-0.86). We estimated that the overall false-negative rate of DTS could be as high as 31.3% and increased 2.7 times among patients without sputum.

Conclusions: Deep throat saliva produced the lowest viral RNA concentration and RT-PCR-positive rate compared with conventional respiratory specimens in all phases of illness. Self-collected sputum should be the choice for patients with sputum.

Keywords: COVID-19; SARS-CoV-2; coronavirus; diagnosis; saliva.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Betacoronavirus / genetics*
  • COVID-19
  • COVID-19 Testing
  • COVID-19 Vaccines
  • Clinical Laboratory Techniques* / methods
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / virology
  • Female
  • Hong Kong / epidemiology
  • Humans
  • Male
  • Middle Aged
  • Nasopharynx / virology*
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / virology
  • Prospective Studies
  • RNA, Viral / genetics
  • Real-Time Polymerase Chain Reaction
  • Reverse Transcriptase Polymerase Chain Reaction
  • SARS-CoV-2
  • Saliva / virology*
  • Specimen Handling / methods
  • Sputum / virology*
  • Young Adult


  • COVID-19 Vaccines
  • Covid-19 aAPC vaccine
  • RNA, Viral