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      Clinical Evaluation of the GeneXpert® Xpert® Xpress SARS-CoV-2/Flu/RSV Combination Test

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          Abstract

          The Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV combination test received emergency use authorization approval by the United States Food and Drug Administration in December 2020, and Health Canada approval in January 2021. The performance characteristics of the GeneXpert Xpert Xpress SARS-CoV-2/Flu/RSV combination test were assessed at Lakeridge Health Oshawa and the National Microbiology Laboratory of Canada. The combination test was compared to the Xpert SARS-CoV-2 and Xpert Flu/RSV assays, and the BioFire FilmArray Respiratory Panel 2.1 (RP2.1) test kit. Materials evaluated were serial dilutions of chemically-inactivated SARS-CoV-2 and remnant clinical specimens (nasal or nasopharyngeal swabs) collected from patients. The limit of detection (LOD) for the SARS-CoV-2 component of the Xpert SARS-CoV-2/Flu/RSV combination test was determined to be <100 viral copies/mL when using chemically-inactivated SARS-CoV-2. In total, 86 clinical positive and 51 clinical negative samples were used for this study, with mixtures of clinical positives being used to mimic coinfection and screen for competitive inhibition. The combination test showed a high percent agreement with the Xpert SARS-CoV-2 and Xpert Flu/RSV tests, as well as the BioFire FilmArray RP2.1. Based on the findings from this study and a growing body of research, the Xpert SARS-CoV-2/Flu/RSV combination test will serve as an effective replacement for the Xpert SARS-CoV-2 and Xpert Flu/RSV assays.

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          Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2

          Wei Zhen, Elizabeth Smith, Ryhana Manji … (2020)
          Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread across the globe. As part of the worldwide response, many molecular diagnostic platforms have been granted emergency use authorization (EUA) by the Food and Drug Administration (FDA) to identify SARS-CoV-2 positive patients. Our objective was to evaluate three sample-to-answer molecular diagnostic platforms (Cepheid Xpert Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW COVID-19 [ID NOW], and GenMark ePlex SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients.
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            Multi-center evaluation of cepheid xpert® xpress SARS-CoV-2 point-of-care test during the SARS-CoV-2 pandemic

            Femke Wolters, Jeroen van de Bovenkamp, Bart van den Bosch … (2020)
            Background With the outbreak of SARS-CoV-2, rapid diagnostics are paramount to contain the current pandemic. The routinely used realtime RT-PCR is sensitive, specific and able to process large batches of samples. However, turnaround time is long and in cases where fast obtained results are critical, molecular point of care tests (POCT) can be an alternative. Here we report on a multicenter evaluation of the Cepheid Xpert Xpress SARS-CoV-2 point-of-care test. Study design The Xpert Xpress SARS-CoV-2 assay was evaluated against the routine in-house real-time RT-PCR assays in three medical microbiology laboratories in The Netherlands. A sensitivity and specificity panel was tested consisting of a dilution series of SARS-CoV-2 and ten samples containing SARS-CoV-2 and a range of other seasonal respiratory viruses. Additionally, 58 samples of patients positive for SARS-CoV-2 with different viral loads and 30 tested negative samples in all three Dutch laboratories using an in-house RT-PCR, were evaluated using Cepheids Xpert Xpress SARS-CoV-2 cartridges. Results Xpert Xpress SARS-CoV-2 point of care test showed equal performance compared to routine in-house testing with a limit of detection (LOD) of 8.26 copies/mL. Other seasonal respiratory viruses were not detected. In clinical samples Xpert Xpress SARS-CoV-2 reaches an agreement of 100 % compared to all in-house RT-PCRs Conclusion Cepheids GeneXpert Xpert Xpress SARS-CoV-2 is a valuable addition for laboratories in situations where rapid and accurate diagnostics are of the essence.
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              Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays

              Angelica Moran, Kathleen G Beavis, Scott Matushek … (2020)
              LETTER Severe acute respiratory syndrome coronavirus 2 (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 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 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 (CT ) 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, CT 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 agreement, CT values were lower in the 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 specimens, as testing was limited to 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.
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                Author and article information

                Journal
                Title: Journal of Clinical Virology Plus
                Publisher: Published by Elsevier Ltd.
                ISSN (Print): 2667-0380
                ISSN (Electronic): 2667-0380
                Publication date PMC-release: 12 April 2021
                Publication date (Electronic): 12 April 2021
                Electronic Location Identifier: 100014
                Affiliations
                [1 ]Laboratory Medicine and Infection Prevention and Control, Lakeridge Health, L1G 2B9, Oshawa, Ontario, Canada
                [2 ]Ontario Tech University, L1G 0C5, Oshawa, Ontario, Canada
                [3 ]Ontario Health, Toronto, Ontario, Canada
                [4 ]Bacterial Pathogens Division, National Microbiology Laboratory, Canadian Science Centre for Human and Animal Health, R3E 3R2, Public Health Agency of Canada, Winnipeg, Canada
                [5 ]Department of Medical Microbiology and Infectious Diseases, University of Manitoba, R3E 0W2, Winnipeg, Canada
                [6 ]National HIV and Retrovirology Laboratories, National Microbiology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, R3E 3L5, Winnipeg, Canada
                Author notes
                [* ]Correspondence.
                Article
                Publisher Item ID: S2667-0380(21)00006-5 Publisher ID: 100014
                DOI: 10.1016/j.jcvp.2021.100014
                PMC ID: 8040320
                SO-VID: db372543-8dd5-481d-a84c-2424f50067a9
                Copyright © © 2021 Published by Elsevier Ltd.
                License:

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                Date received : 3 March 2021
                Date revision received : 7 April 2021
                Date accepted : 8 April 2021
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