SARS-CoV-2 detection in different respiratory sites: A systematic review and meta-analysis

EBioMedicine. 2020 Sep;59:102903. doi: 10.1016/j.ebiom.2020.102903. Epub 2020 Jul 24.


Background: The accurate detection of SARS-CoV-2 through respiratory sampling is critical for the prevention of further transmission and the timely initiation of treatment for COVID-19. There is a diverse range of SARS-CoV-2 detection rates in reported studies, with uncertainty as to the optimal sampling strategy for COVID-19 diagnosis and monitoring.

Methods: We performed a systematic review and meta-analysis of studies comparing respiratory sampling strategies for the detection of SARS-CoV-2 RNA. The inclusion criteria were studies that assessed at least two respiratory sampling sites (oropharyngeal swab, nasopharyngeal swab, and sputum) in participants with COVID-19. The percentage positive tests were compared between sampling modalities by constructing a Z-test assuming independence and using the standard errors obtained from the random effects meta-analysis.

Findings: From 1039 total studies, we identified 11 studies that met our inclusion criteria, with SARS-CoV-2 testing results from a total of 3442 respiratory tract specimens. Compared to nasopharyngeal swab sampling, sputum testing resulted in significantly higher rates of SARS-CoV-2 RNA detection while oropharyngeal swab testing had lower rates of viral RNA detection. Earlier sampling after symptom onset was associated with improved detection rates, but the differences in SARS-CoV-2 RNA detection by sampling method was consistent regardless of the duration of symptoms.

Interpretation: The results support sputum sampling as a valuable method of COVID-19 diagnosis and monitoring, and highlight the importance of early testing after symptom onset to increase the rates of COVID-19 diagnosis.

Funding: This study was funded in part by the NIH grants U01AI106701 and by the Harvard University for AIDS Research (NIAID 5P30AI060354).

Keywords: COVID-19; Diagnosis; Nasopharyngeal; Oropharyngeal; SARS-CoV-2; Sputum.

Publication types

  • Meta-Analysis
  • Systematic Review

MeSH terms

  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification*
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / virology
  • Databases, Factual
  • Humans
  • Nasopharynx / virology*
  • Oropharynx / virology*
  • Pandemics
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / virology
  • RNA, Viral / metabolism
  • Sputum / virology*


  • RNA, Viral

Supplementary concepts

  • COVID-19
  • severe acute respiratory syndrome coronavirus 2