Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2

Catherine A Hogan; Malaya K Sahoo; ChunHong Huang; Natasha Garamani; Bryan Stevens; James Zehnder; Benjamin A Pinsky

doi:10.1016/j.jcv.2020.104383

Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2

J Clin Virol. 2020 Jun:127:104383. doi: 10.1016/j.jcv.2020.104383. Epub 2020 Apr 24.

Authors

Catherine A Hogan¹, Malaya K Sahoo², ChunHong Huang², Natasha Garamani², Bryan Stevens¹, James Zehnder², Benjamin A Pinsky³

Affiliations

¹ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA.
² Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
³ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: bpinsky@stanford.edu.

Abstract

Background: Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and there is a need to assess their test performance relative to one another.

Objectives: The aim of this study was to compare the test performance of the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene.

Study design: We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient.

Results: A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6.

Conclusion: The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.

Keywords: Laboratory-developed test; Panther fusion; QIAsymphony; SARS-CoV-2.

Publication types

Comparative Study

MeSH terms

Betacoronavirus / genetics
COVID-19
Coronavirus Envelope Proteins
Coronavirus Infections / diagnosis*
Humans
Molecular Diagnostic Techniques / methods*
Molecular Diagnostic Techniques / standards*
Nasopharynx / virology
Pandemics
Pneumonia, Viral / diagnosis*
Reagent Kits, Diagnostic / standards*
Reproducibility of Results
SARS-CoV-2
Viral Envelope Proteins / genetics
Viral Envelope Proteins / isolation & purification*

Substances

Coronavirus Envelope Proteins
Reagent Kits, Diagnostic
Viral Envelope Proteins
envelope protein, SARS-CoV-2