Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection

Sci Rep. 2021 Feb 4;11(1):3134. doi: 10.1038/s41598-021-82787-z.


We aimed to test the sensitivity of naso-oropharyngeal saliva and self-administered nasal (SN) swab compared to nasopharyngeal (NP) swab for COVID-19 testing in a large cohort of migrant workers in Singapore. We also tested the utility of next-generation sequencing (NGS) for diagnosis of COVID-19. Saliva, NP and SN swabs were collected from subjects who presented with acute respiratory infection, their asymptomatic roommates, and prior confirmed cases who were undergoing isolation at a community care facility in June 2020. All samples were tested using RT-PCR. SARS-CoV-2 amplicon-based NGS with phylogenetic analysis was done for 30 samples. We recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively. In total, 62.0%, 44.5%, and 37.7% of saliva, NP and SN samples were positive. Cycle threshold (Ct) values were lower during the earlier period of infection across all sample types. The percentage of test-positive saliva was higher than NP and SN swabs. We found a strong correlation between viral genome coverage by NGS and Ct values for SARS-CoV-2. Phylogenetic analyses revealed Clade O and lineage B.6 known to be circulating in Singapore. We found saliva to be a sensitive and viable sample for COVID-19 diagnosis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • COVID-19 / diagnosis*
  • COVID-19 Nucleic Acid Testing*
  • Cohort Studies
  • Female
  • Humans
  • Male
  • Nasal Mucosa / virology*
  • Nasopharynx / virology
  • RNA, Viral / isolation & purification*
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification
  • Saliva / virology*
  • Sensitivity and Specificity
  • Singapore / epidemiology
  • Specimen Handling*


  • RNA, Viral