NAAT nasopharyngeal smears remain the gold standard for diagnosing SARS-CoV-2

A systematic review and meta-analysis published in the Journal of Clinical Microbiology showed that nasopharyngeal (NP) swabs are the superior method for diagnosing SARS-CoV-2.

The authors of the study searched the available literature in publication databases up to October 1, 2020 for studies on alternative nucleic acid amplification tests (NAAT) for SARS-CoV-2. Their search, which returned 1253 unique citations, included NAAT analyzes performed on saliva (n = 25), nasal (n = 11), oropharyngeal (n = 6), or nasal / oropharyngeal swabs (n = 4).

The saliva studies included 4528 paired saliva and NP specimens (with the exception of 2 studies in which nasal / oropharyngeal specimens were used as a comparison). 88% of the tests (95% CI, 81-93) detected positive SARS-CoV-2 saliva samples, which was similar to the results of paired NP samples (94%; 95% CI, 90-98). However, the double positivity rate showed relatively poor test agreement (79%; 95% CI, 71-86) and significant heterogeneity (I2, 88.6%).

Stratified according to saliva collection methods, studies on cough or deep neck samples showed a higher positivity (94%; 95% CI, 87-99) than studies in which no collection method was given (86%; 95% CI, 78-92). Studies in which saliva was not preprocessed showed significantly lower positivity rates (60%; 95% CI, 49-70) than those for which the nucleic acid extraction step was performed (89%; 95% CI, 83% -94%).

The studies that used oral swabs had a positivity rate of 84% (95% CI, 57-100), similar to studies that used paired NP swabs (88%; 95% CI, 73-98) , but they showed a low dual positivity rate (68%; 95% CI, 36-93).

The researchers compared midturbinate or anterior nasal swabs with NP swabs in 11 studies. Midturbinate or anterior nasal swabs had a lower positivity rate (82%; 95% CI, 73-90) than the NP smears (98%; 95% CI, 96-100), had a lower two-swab agreement (79%; 95%) %) CI, 69-88) and high heterogeneity (I2, 87%). Stratified by type, the anterior nostrils outperformed the specimens (90%; 95% CI, 84-94) of the nasal midturbinates (84%; 95% CI, 65-97).

These nasal swab studies performed worse in patients with a low viral load (<1000 copies / ml; 61%; 95% CI, 40-79) than in those with a high viral load (85%; 95% CI, 82-). 91).

Nasal swab tests performed by health care workers gave fewer positive results (68%; 95% CI, 47-86) than self-administered tests (93%; 95% CI, 85-98).

These data should be interpreted with caution as study populations and laboratory procedures varied widely between studies. There was also little consensus on sampling methods or laboratory procedures that should be streamlined and standardized to ensure optimal virus detection.

The study’s authors concluded that their review of head-to-head comparisons of SARS-CoV-2 diagnostic sampling indicated that the NAAT NP swab remained the most effective method and that testing for COVID-19 was im Saliva might be the next best option.


Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of salivary, oropharyngeal, and nasal swabs for the molecular detection of SARS-CoV-2: a systematic review and meta-analysis. J Clin Microbiol. Published online January 27, 2021. doi: 10.1128 / JCM.02881-20

This article originally appeared on Infectious Disease Advisor

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