Comparison of next generation diagnostic systems (NGDS) for the detection of SARS‐CoV‐2

Introduction The World Health Organization (WHO) declared coronavirus disease 2019 (COVID‐19) a pandemic in March 2020. Initially, supply chain disruptions and increased demand for testing led to shortages of critical laboratory reagents and inadequate testing capacity. Thus, alternative means of biosample collection and testing were essential to overcome these obstacles and reduce viral transmission. This study aimed to 1) compare the sensitivity and specificity of Cepheid GeneXpert® IV and BioFire® FilmArray® 2.0 next generation detection systems to detect SARS‐CoV‐2, 2) evaluate the performance of both platforms using different biospecimen types, and 3) assess saline as an alternative to viral transport media (VTM) for sample collection. Methods A total of 1,080 specimens consisting of nasopharyngeal (NP) swabs in VTM, NP swabs in saline, nasal swabs, oropharyngeal (OP) swabs, and saliva were collected from 216 enrollees. Limit of detection (LoD) assays, NP VTM and NP saline concordance, and saliva testing were performed on the BioFire® FilmArray® 2.0 Respiratory Panel 2.1 and Cepheid GeneXpert® Xpress SARS‐CoV‐2/Flu/RSV assays. Results LoD and comparative testing demonstrated increased sensitivity with the Cepheid compared with the BioFire® in detecting SARS‐CoV‐2 in NP VTM and saline, nasal, and OP swabs. Conversely, saliva testing on the Cepheid showed statistically significant lower sensitivity compared to the BioFire®. Finally, NP swabs in saline showed no significant difference compared with NP swabs in VTM on both platforms. Conclusion The Cepheid and BioFire® NGDS are viable options to address a variety of public health needs providing rapid and reliable, point‐of‐care testing using a variety of clinical matrices. Limit of detection (LoD) and comparative testing, performed on BioFire® FilmArray® and Cepheid GeneXpert® Xpress, demonstrated increased sensitivity with the Cepheid compared with the BioFire® in detecting SARS‐CoV‐2 in NP VTM and saline, nasal, and OP swabs. Conversely, saliva testing on the Cepheid showed statistically significant lower sensitivity compared with the BioFire®. Finally, NP swabs in saline showed no significant difference comparedwith NP swabs in VTM on both platforms. The Cepheid and BioFire® NGDS are viable options to address a variety of public health needs providing rapid and reliable, point‐of‐care testing using a variety of clinical matrices.