Validation of GeneXpert testing for SARS-CoV-2 RNA in eight hospital laboratories in Oman

Abstract

In response to the current COVID-19 pandemic, numerous commercial assays have been developed for the detection of SARS-CoV-2 for use in the clinical diagnostic laboratories. To date, there is limited comparison of testing methods performed in different hospital laboratory sites. The aims of the study were to evaluate the analytical performance of Cepheid Xpert Xpress SARS-CoV-2 when compared to RT-PCR. This is a cross-sectional study. A total of 155 nasopharyngeal swabs were taken in duplicate from patients presenting with suspected COVID-19 to 8 hospitals in Oman. One swab was tested by the hospital laboratory and the duplicate swab was sent to the national Central Public Health Laboratory (CPHL) for testing. We compared the analytical performance of the commercially available point of care Cepheid Xpert Xpress SARS-CoV-2 assay which was used in the 8 different hospitals with assays including Liferiver, Sansure, TIB MOL BIOL, Kingfisher and COBAS 6800 by Roche which were performed at the CPHL. Testing of the duplicate swabs revealed excellent agreement of results with the viral loads of Ct values ranging from 16-43 for the E gene, 18-44 for the N gene and 17-44 for the ORF gene using the Liferiver assay. The overall sample sensitivity and specificity of the Cepheid Xpert Xpress SARS-CoV-2 assay were both 100% and there was 100% agreement across specimens. We conclude that the rapid GeneXpert and RT-PCR kits assessed in this study may be used for routine diagnostic testing of COVID-19 patients by experienced clinical microbiology diagnostic laboratories. Our results highlight the importance of rapid molecular testing at different sites within a country in a public health emergency.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; comparison; coronavirus.

Figure 1

scatter diagram showing the regression line of Ct values between the Xpert Xpress and Liferiver SARS-CoV-2 assays and the target viral genes for the positive samples; A) Xpert E gene Ct vs Liferiver E gene Ct, B) Xpert N gene Ct vs Liferiver N gene Ct, C) Xpert E gene Ct vs Xpert N gene Ct, D) Liferiver E gene Ct vs Liferiver N gene Ct, E) Liferiver E gene Ct vs Liferiver ORF gene Ct, F) Liferiver N gene Ct vs Liferiver N gene Ct, G) Xpert E gene Ct vs Liferiver ORF gene Ct, H) Xpert N gene Ct vs Liferiver ORF gene Ct; The regression equation, correlation coefficient (r) and p values are shown; The solid line represents the regression and the broken lines represent the 95% confidence levels