Comparison of the analytical sensitivity of three real time PCR kits used in the detection of the SARS-CoV-2

Background: COVID-19 infection is diagnosed by a real-time Reverse transcriptase Polymerase chain reaction (RT-PCR), which can detect the presence of the SARS-CoV-2 virus as early as day one of symptoms. However, the performance of these kits can vary widely. We assessed the performance of three different PCR kits from different manufacturers used for diagnosis of COVID-19 in Sri Lanka.

Methods: The performance of two PCR kits were compared to the Da An gene PCR kit in a total of 68 samples. The known positive samples were from the patients admitted to the National Hospital of Infectious Diseases. The performance was evaluated in samples with a ct value >35 (n=30), samples which were positive with ct values of the samples between 30 to 35 (n=10), those that gave an inconclusive result (n=8) and those that were negative (n=20).

Results: The three PCR kits had highly varied sensitivity for the positive with high ct values (>35) and lower ct values (ct values 30-35). For instance, the 3rd kit (RealStar® SARS-CoV-2 RT-PCR Kit 1.0), only detected 6/10 (60%) of samples with ct values between 30 to 35. The GeneFinder™ and the RealStar® SARS-CoV-2 RT-PCR Kit 1.0, both showed low sensitivity for positive samples with high ct values (>35, suggesting low viral loads), with the GeneFinder™ giving positives for only 1/30 (3.3%) samples and the RealStar® SARS-CoV-2 RT-PCR Kit 1.0 giving positives for only 8/20 (26.7%) of samples.

Conclusions: PCR kits vary in sensitivity and it is crucial that PCR kits are thoroughly evaluated prior to using them and kits with higher sensitivity should be used in the compatible machine for optimum results.