Performance comparison of two nucleic acid amplification systems for SARS-CoV-2 detection: A multi-center study

Area of Science:

• Molecular Diagnostics
• Infectious Disease Testing
• COVID-19 Detection

Background:

• Emergence of rapid nucleic acid testing systems to combat COVID-19.
• Limited comparative studies on diagnostic performance versus conventional systems.
• Need for evaluating clinical utility of rapid SARS-CoV-2 detection.

Purpose of the Study:

• Evaluate and compare the clinical diagnostic performance of a rapid nucleic acid detection system against conventional methods for SARS-CoV-2.
• Assess the accuracy, including sensitivity, specificity, and predictive values.
• Analyze the concordance and performance based on viral load.

Main Methods:

• Retrospective analysis of 63,352 oropharyngeal swab results.
• Comparison of sensitivity, specificity, PPV, and NPV between rapid (Daan Gene) and conventional systems.
• Assessment of concordance using OPA, PPA, NPA, and kappa (κ) value.
• Analysis of rapid system sensitivity relative to viral load (Ct values).

Main Results:

• The Daan Gene rapid system demonstrated slightly lower sensitivity (0.86) but equivalent specificity compared to conventional systems (0.979).
• High positive predictive value (PPV) and negative predictive value (NPV) of ≥98.0% for SARS-CoV-2.
• Excellent agreement between Daan Gene and conventional systems (κ = 0.893).
• Daan Gene achieved 99.31% sensitivity for high viral load (Ct < 35) and 50% for low viral load (Ct ≥ 35).

Conclusions:

• Rapid nucleic acid detection systems offer a viable alternative for rapid SARS-CoV-2 identification, particularly in cases with high viral loads.
• The Daan Gene system shows excellent concordance with conventional methods, indicating reliable performance.
• This rapid testing approach can serve as a valuable complement to existing COVID-19 diagnostic strategies.