Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type

Abstract

14The advent of the COVID-19 pandemic in the United States created a unique situation 15 where multiple molecular diagnostic assays with various indications for use in the detection of 16 SARS-CoV-2 rapidly received Emergency Use Authorization by the FDA, were validated by 17 laboratories and utilized clinically, all within a period of a few weeks. We compared the 18 performance of four of these assays that were being evaluated for use at our institution: Abbott 19 RealTime m2000 SARS-CoV-2 Assay, DiaSorin Simplexa COVID-19 Direct, Cepheid Xpert 20 Xpress SARS-CoV-2 and Abbott ID NOW COVID-19. Nasopharyngeal and nasal specimens 21 were collected from 88 ED and hospital-admitted patients and tested by the four methods in 22 parallel to compare performance. ID NOW performance stood out as significantly worse than 23 the other three assays despite demonstrating comparable analytic sensitivity. Further study 24 determined that the use of a foam nasal swab compared to a nylon flocked nasopharyngeal swab, 25 as well as use in a population chronically vs. acutely positive for SARS-CoV-2, were significant 26 factors in the poor comparable performance. 27 and with different turnaround time needs demanded that laboratories implement more than one 36 type of NAAT to respond to the crisis. 37SARS-CoV-2 testing in our laboratory began with the CDC EUA assay performed on 38 Abbott m2000, but due to that assay's significant throughput constraints (24 specimens in 8 39 hours), we quickly verified and switched to the Abbott RealTime SARS-CoV-2 EUA Assay 40 (m2000) once released (94 specimens in ~8 hours). Although this assay provided capacity for 41 our outpatient testing needs, we also verified the DiaSorin Simplexa COVID-19 Direct 42 (Simplexa) assay, capable of resulting 8 specimens in 90 minutes, and used this assay as a rapid 43 turn-around time (TAT) option for our inpatient and emergency department (ED) populations. 44 Within a few weeks, additional SARS-CoV-2 NAAT options emerged that were specifically 45 designed for rapid testing of patients in the point of care setting: the Cepheid Xpert Xpress 46 SARS-CoV-2 (Xpert) assay, which could provide results in 45 minutes, and the Abbott ID NOW 47 82Dilutions were prepared from ZeptoMetrix inactivated SARS-CoV-2 virus (1.70 x 10 5 83 TCID50/ml) that was internally quantified to 10 9.62 copies/mL relative to a standard curve of 84 AccuPlex™ SARS-CoV-2 Reference Material (SeraCare) constructed on the m2000 assay. From 85 that stock, dilutions were made in VTM (1,042, 521, 260, 130, 65 and 32.5 copies/mL) and 86 tested on the m2000, Simplexa, and Xpert SARS-CoV-2 assays. A separate set of ZeptoMetrix 87 dilutions in VTM were made so that when added to the 2.5 ml of elution buffer in the ID NOW 88 receiver cup, equivalent concentrations were achieved (1,042, 522, 262, 105 and 53 copies/mL). 89In this way, the concentrations of viral copies in the ID NOW buffer were equivalent to the VTM 90 dilutions used for the other three instruments. Five replicates at each dilution wer...

Point of Care Nucleic Acid Testing for SARS-CoV-2 in Hospitalized Patients: A Clinical Validation Trial and Implementation Study

“…A number of near-patient tests have been described. Some have not performed well, 12 and none have undergone testing under rigorous clinical trial conditions with real-world data on the impact on patient management. 13 , 14 , 15 , 16 , 17 Thorough, prospective evaluation for a high-consequence pathogen such as SARS-CoV-2 is particularly important, given the risks related to false positives or negatives in the hospital setting.…”

Relative Sensitivity of ID NOW and RT-PCR for Detection of SARS-CoV-2 in an Ambulatory Population: Clinical Evaluation, Systematic Review and Meta-analysis

“…The use of "convenience samples," particularly populations including patients who have been hospitalized after a diagnosis of COVID-19, may include more patients who are past their period of peak viral load compared to a sample of ambulatory patients first presenting for evaluation-such as those in our study who appeared for testing because of recent symptom onset. The two studies that met inclusion criteria for our review which had the lowest positive percent agreement between ID NOW and RT-PCR both included hospitalized patients, 13,17 although another study with very low concordance did not. 14 The conclusions from our clinical study are limited by a relatively small number of positive cases; nonetheless the high level of agreement with RT-PCR suggests that ID NOW is highly effective at identifying, or excluding, SARS-CoV-2 in a symptomatic ambulatory patient population.…”

“…These results are consistent with the studies in our systematic review that showed discordance among assays to be most frequent when Ct values were relatively high (see Supplemental Materials). 3,4,[13][14][15][16] The ID NOW instructions for use (IFU, https://www.fda.gov/media/136525/download) have changed over time, but generally have called for samples to be tested no later than one hour after specimen acquisition and kept at room temperature during that period. The changes in the IFU have made it difficult to assess if published studies provided sufficient information to allow a determination that conformation to instructions for use was followed sufficiently.…”