ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 and has quickly become a worldwide pandemic. In response, many diagnostic manufacturers have developed molecular assays for SARS-CoV-2 under the Food and Drug Administration (FDA) Emergency Use Authorization (EUA) pathway. This study compared three of these assays, the Hologic Panther Fusion SARS-CoV-2 assay (Fusion), the Hologic Aptima SARS-CoV-2 assay (Aptima), and the BioFire Defense COVID-19 test (BioFire), to determine analytical and clinical performance as well as workflow. All three assays showed similar limits of detection (LODs) using inactivated virus, with 100% detection, ranging from 500 to 1,000 genome equivalents/ml, whereas use of a quantified RNA transcript standard showed the same trend but had values ranging from 62.5 to 125 copies/ml, confirming variability in absolute quantification of reference standards. The clinical correlation found that the Fusion and BioFire assays had a positive percent agreement (PPA) of 98.7%, followed by the Aptima assay at 94.7%, compared to the consensus result. All three assays exhibited 100% negative percent agreement (NPA). Analysis of discordant results revealed that all four samples missed by the Aptima assay had cycle threshold (Ct ) values of >37 by the Fusion assay. In conclusion, while all three assays showed similar relative LODs, we showed differences in absolute LODs depending on which standard was employed. In addition, the Fusion and BioFire assays showed better clinical performance, while the Aptima assay showed a modest decrease in overall PPA. These findings should be kept in mind when making platform testing decisions.
Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , COVID-19 , COVID-19 Testing , Humans , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2 , United States , United States Food and Drug AdministrationABSTRACT
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. We found that Xpert Xpress had the lowest limit of detection (100% detection at 100 copies/ml), followed by ePlex (100% detection at 1,000 copies/ml), and ID NOW (20,000 copies/ml). Xpert Xpress also had highest positive percent agreement (PPA) compared to our reference standard (98.3%) followed by ePlex (91.4%) and ID NOW (87.7%). All three assays showed 100% negative percent agreement (NPA). In the workflow analysis, ID NOW produced the lowest time to result per specimen (â¼17 min) compared to Xpert Xpress (â¼46 min) and ePlex (â¼1.5 h), but what ID NOW gained in rapid results, it lost in analytical and clinical performance. ePlex had the longest time to results and showed a slight improvement in PPA over ID NOW. Information about the clinical and analytical performance of these assays, as well as workflow, will be critical in making informed and timely decisions on testing platforms.
Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19 , COVID-19 Testing , Child , Child, Preschool , Coronavirus Infections/virology , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Pandemics , Pneumonia, Viral/virology , SARS-CoV-2 , Sensitivity and Specificity , Workflow , Young AdultABSTRACT
From 2009 to 2015, the laboratories of the 19-hospital North Shore-LIJ Health System experienced 5 threatened interruptions in service and supported 2 regional health-care providers with threatened interruptions in their laboratory service. We report our strategies to maintain laboratory performance during these events, drawing upon the strengths of our integrated laboratory service line. Established in 2009, the laboratory service line has unified medical and administrative leadership and system-wide divisional structure, quality management, and standardization of operations and procedures. Among many benefits, this governance structure enabled the laboratories to respond to a series of unexpected events. Specifically, at our various service sites, the laboratories dealt with pandemic (2009), 2 floods (2010, 2012), 2 fires (2010, 2015), and laboratory floor subsidence (2013). We were also asked to provide support for a regional physician network facing abrupt loss of testing services from closure of another regional clinical laboratory (2010) and to intervene for a non-health system hospital threatened with closure owing to noncompliance of laboratory operations (2012). In all but a single instance, patient care was served without interruption in service. In the last instance, fire interrupted laboratory services for 30 minutes. We conclude that in a large integrated health system, threats to continuous laboratory operations are not infrequent when measured on an annual basis. While most threats are from external physical circumstances, some emanate from unexpected administrative events. A strong laboratory governance mechanism that includes unified medical and administrative leadership across the entirety of the laboratory service line enables successful responses to these threats.
