Parallel testing of 241 clinical nasopharyngeal swabs for the detection of SARS-CoV-2 virus on the Cepheid Xpert Xpress SARS-CoV-2 and the Roche cobas SARS-CoV-2 assays

What is it about?

At our institution (National University Health System, Singapore), the Cepheid Xpert Xpress SARS-CoV-2 (herein referred as the Xpert; Cepheid, California, USA) and the Roche cobas SARS-CoV-2 (herein referred as the cobas; Roche Molecular Systems, New Jersey, USA) assays are deployed interchangeably to meet the national testing demand for SARS-CoV-2. To date, existing comparative studies on the Xpert and cobas assays relied on retesting of residual positive samples that were initially detected by the cobas assay. This may lead to the exclusion of positive samples near the detection limit of the Xpert assay, which the cobas assay may fail to detect. To address the concern, we assayed 241 fresh clinical nasopharyngeal (NP) swab samples in parallel on both the Xpert and the cobas assays to allow for a head-to-head comparative analysis. After testing, there was 95% agreement between the assays for both negative and positive clinical samples, suggesting comparable diagnostic performance. However, our results show that the Xpert assay has higher sensitivity compared to the cobas assay, with the former detecting six additional cases among the low positives. Therefore, retesting of the samples using the Xpert assay should be considered when the SARS-CoV-2 results do not correlate with the patients’ clinical presentations to ensure that the detection of samples with low levels of SARS-CoV-2 viral RNA is not overlooked.

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