A four specimen-pooling scheme reliably detects SARS-CoV-2 and influenza viruses using the BioFire FilmArray Respiratory Panel 2.1

Abstract

The COVID-19 pandemic required increased testing capacity, enabling rapid case identification and effective contract tracing to reduce transmission of disease. The BioFire FilmArray is a fully automated nucleic acid amplification test system providing specificity and sensitivity associated with gold standard molecular methods. The FilmArray Respiratory Panel 2.1 targets 22 viral and bacterial pathogens, including SARS-CoV-2 and influenza virus. While each panel provides a robust output of information regarding pathogen detection, the specimen throughput is low. This study evaluates the FilmArray Respiratory Panel 2.1 using 33 pools of contrived nasal samples and 22 pools of clinical nasopharyngeal specimens to determine the feasibility of increasing testing capacity, while maintaining detection of both SARS-CoV-2 and influenza virus. We observed 100% detection and 90% positive agreement for SARS-CoV-2 and 98% detection and 95% positive agreement for influenza viruses with pools of contrived or clinical specimens, respectively. While discordant results were mainly attributed to loss in sensitivity, the sensitivity of the pooling assay was well within accepted limits of detection for a nucleic acid amplification test. Overall, this study provides evidence supporting the use of pooling patient specimens, one in four with the FilmArray Respiratory Panel 2.1 for the detection of SARS-CoV-2 and influenza virus.

Figure 1

Sensitivity of the FilmArray RP2.1 for the detection of SARS-CoV-2 after specimen pooling. One contrived sample containing, 200, 400, 600, 800 or 1000 E copies/ml, was equally mixed with three negative contrived samples, with the exception of the last sample, which was equally mixed with nine negative contrived samples. The FilmArray RP2.1 was used to detect the presence of SARS-CoV-2. Each bar denotes a separate pool. Each pool was tested in triplicate and the mean and standard error are presented.

Figure 2

Detection of challenge respiratory viruses using the FilmArray RP2.1 after specimen pooling. A contrived-clinical sample containing a low (~ Ct 35) or moderate (~ Ct 30) concentration of either Flu A, FluB, RSV, RV, OC43, and 229E was equally mixed with three negative contrived-clinical samples. Each pool was tested in triplicate and the mean and standard error are presented.

Figure 3

Detection of SARS-CoV-2 and challenge respiratory viruses after a four specimen-pooling strategy using the FilmArray RP2.1. A contrived-clinical sample containing 1000 E copies/ml or 1.35 × 10⁶ E copies/ml of SARS-CoV-2 was equally mixed with three contrived samples containing (A) high (~ Ct 25), (B) moderate (~ Ct 30), or (C) low (~ Ct 35) amounts of either Flu A, FluB, RSV, RV, OC43, and 229E. The FilmArray RP2.1 was employed to detect the presence of SARS-CoV-2. Each coloured set denotes a separate pool. Each pool was tested in triplicate and the mean and standard error are presented.