Test Agreement between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges

• Type of Material: Article
• Authors: Kari Broder, Emory University; Ahmed Babiker, Emory University; Charles Myers, Emory University; Terri White, Emory University; Heather Jones, Emory University; John Cardella, Emory University; Eileen Burd, Emory University; Charles Hill, Emory University; Colleen Kraft, Emory University
• Language: English
• Date: 2020-08-01
• Publisher: AMER SOC MICROBIOLOGY
• Publication Version: Final Published Version
• Copyright Statement: © 2020 American Society for Microbiology.
• Final Published Version (URL): http://dx.doi.org/10.1128/JCM.01187-20
• Title of Journal or Parent Work: JOURNAL OF CLINICAL MICROBIOLOGY
• Volume: 58
• Issue: 8
• Keywords: Life Sciences & Biomedicine; virology; diagnostics; RT-PCR; Microbiology; SARS-CoV-2; COVID-19; Science & Technology
• Research Categories: Biology, Microbiology; Biology, Virology

Abstract

The SARS-CoV-2 pandemic has changed the face of the globe and upended the daily lives of billions. In an effort to bring mass testing to as many as possible, multiple diagnostic tests, including molecular, antigen detection, and serological assays, have been rapidly developed. Under U.S. Food and Drug Administration (FDA) Emergency Use Authorization (EUA), several reverse transcription-PCR (RT-PCR) assays have reached U.S. laboratories, each with its own testing capacity and proprietary methods (1, 2). Multiple logistical challenges have required laboratories to validate and implement multiple platforms for testing, but data on positive percent agreement across platforms are limited. Our institution utilizes the Roche Cobas 6800 SARS-CoV-2 assay, the Cepheid GeneXpert Xpress SARS-CoV-2 assay, and a laboratory-developed test (LDT) based on a modified CDC protocol, but there is no gold standard for the diagnostic accuracy of these assays. Thus, our objective was to determine the degree of agreement between two tests by running the same samples across both platforms and comparing the cycle threshold (CT) values (E target to E target) among samples with high (>30) CT values, corresponding to lower viral loads. We collected 35 positive (positivity determined per assay instructions) nasopharyngeal samples with an E target CT value of ≥30 on the Roche Cobas 6800 assay; those samples then underwent secondary testing on the Cepheid GeneXpert assay within 3 days of initial testing.