Inconclusive results of SARS-CoV2 RT-qPCR: To retest or not?

Abstract

Background: Reverse transcription-quantitative PCR (RT-qPCR) is widely used to detect SARS-CoV-2 infections. A small proportion (3-5%) of the samples turn out to be inconclusive which are difficult to interpret and require repeat testing. Methods: This study utilizing RT-qPCR for SARS-CoV-2 collected data from the viral RNA extracted using Maccura Mag-Bind RNA from NPOP specimen, then amplified and quantified using Maccura SARS-CoV-2 Fluorescent PCR kit. The data with inconclusive interpretation and re-test results were selected and further analysed. Results: The retrospective analysis of 247 inconclusive samples that were retested was included in the study. Among the inconclusive results from the first test, 80% of samples which expressed SARS-CoV-2 N and E genes (without ORF1ab gene) turned out to be positive in the repeat test (p < 0.001), while 55% of samples that had only one gene expressed initially, were positive on repeat testing. The E gene was detected (without N and ORF1ab gene) in nine samples, of which seven were negative on re-testing. Conclusions: Our study suggests that it is beneficial to repeat the SARS-CoV-2 RT-qPCR test, especially when two genes are expressed, while detection of only E gene in the first test can be regarded as negative.