Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays.

LETTER

Severe acute respiratory syndrome coronavirus 2 (n class="Species">SARS-CoV-2), a novel coronavirus responsible for a December 2019 outbreak in Wuhan, China, causes a syndrome characterized by fever, cough, and dyspnea progressing to acute respiratory distress syndrome (1). SARS-CoV-2 quickly spread to other countries, with the new coronavirus disease 2019 (COVID-19) declared a pandemic in March 2020 (2–4). Rapid testing for SARS-CoV-2 is important for epidemiological tracking and institution of quarantine procedures (5). The clinical description of COVID-19 continues to evolve; with transmission by asymptomatic individuals reported (6–8), widespread testing is necessary.

Multiple reverse transcription-PCR (RT-PCR) assays have received emergency use authorization from the U.S. Food and Drug Administration. The Roche cobas SARS-CoV-2 assay is a qualitative test that detects n class="Species">SARS-CoV-2-specific ORF1 and part of the E gene, conserved across sarbecoviruses, including SARS-CoV-2 (9). The Cepheid Xpert Xpress SARS-CoV-2 assay also detects the pan-sarbecovirus E gene but detects the N2 region of the N gene as its SARS-CoV-2-specific target (10). This report compares results from specimens tested with both assays.

Eight nasal and 95 nasopharyngeal specimens were collected from inpatients and ambulatory n class="Species">patients at the University of Chicago. Samples were tested by the Roche cobas SARS-CoV-2 assay on the cobas 6800 system (Roche Molecular Systems, Branchburg, NJ) and by the Cepheid Xpert Xpress SARS-CoV-2 assay on the GeneXpert system (Cepheid, Sunnyvale, CA). Of these 103 specimens, 42 tested positive and 60 tested negative with both systems, for an agreement of 99%. Testing was repeated on the single specimen with discrepant results. For this specimen, the Roche assay was repeatedly negative for SARS-CoV-2. The initial Cepheid assay result was positive for SARS-CoV-2, though the cycle threshold (C) values for detection of the E gene were 0.0 (negative) and 42.0 (low positivity) for the N gene. Repeat Cepheid testing was negative for both targets. These results suggest that SARS-CoV-2 was present at a very low concentration, near the detection limit of the Cepheid assay.

For the 42 positive samples, C values for the E gene ranged from 15.05 to 39.75 (mean, 26.35; standard deviation [SD], 6.69) for the Roche assay and 13.6 to 38.2 (mean, 24.8; SD, 7.1) for the Cepheid assay. By Bland-Altman analysis to assess agreemeene">nt, C values were lower in the n class="Chemical">Cepheid assay for 37 of 42 samples (mean difference, –1.57; 95% limits of agreement, –5.34, 2.20). This might be due to differences in primer sequences for the E gene, reagents, or amplification conditions.

Limitations of this study include the small sample size of SARS-CoV-2-positive specimeene">ns, as testing was limited to n class="Species">patients within our institution. The assays also detect different SARS-CoV-2-specific genes, which may lead to false-negative results if a mutation prevents primer binding. The Cepheid assay is a 45-min random-access assay, with throughput dependent on the number of instrument slots. The Roche platform is batch based, accommodating 90 samples/run every 90 min. As each run requires up to 3 h and 45 min, throughput is approximately 1 result per minute. Overall, the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 assays show excellent agreement (>99%), and their combined usage can be tailored to maximize SARS-CoV-2 testing.