What is the role of nucleic acid amplification testing (NAAT) in the diagnosis of coronavirus disease 2019 (COVID-19), and what are the best means of collecting samples?

Updated: Jun 18, 2021
  • Author: James J Dunn, PhD, D(ABMM), MT(ASCP); more...
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The currently recommended modality for the diagnosis of acute or current SARS-CoV-2 infection is a nucleic acid amplification test (NAAT) that detects one or more RNA gene targets specific to the virus. [7]  Symptomatic patients, individuals with known or suspected COVID-19 exposure, and persons from an area with high disease prevalence can be tested with this method. [4] IDSA guidelines also suggest that patients who initially test negative, but in whom there is a high clinical suspicion of COVID-19, should receive an additional NAAT, which is estimated to increase the sensitivity of the test by 17%. [4]

Presently, there are five SARS-CoV-2 assays that have EUA approval for the testing of asymptomatic patients or for use as part of community surveillance. [9] It is important, however, to test only asymptomatic patients with high pretest probability of having SARS-CoV-2, since this decreases the frequency of false negatives by increasing the negative predictive value (NPV). [10]

A recommendation from the IDSA published December 23, 2020, suggests that for SARS-CoV-2 RNA testing, collection of an NP swab, an MT swab, an anterior nasal swab, saliva, or a combined anterior nasal/OP swab yields more accurate results than does obtainment of an OP swab alone, when symptoms indicate the presence of COVID-19. However, the recommendation was marked as conditional, with very low evidence certainty. [11, 12]

A literature review by Butler-Laporte et al suggested that saliva samples provide sensitivity and specificity comparable to NP swabs in SARS-CoV-2 NAATs. Pooled sensitivity for saliva and NP swabs were found to be 83.2% versus 84.8%, respectively, while pooled specificity was 99.2% versus 98.9%, respectively. The investigators indicated that larger-scale research is needed into NAAT accuracy when saliva is used. [13]

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