Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory

Eloise Williams; Katherine Bond; Brian Chong; Dawn Giltrap; Malcolm Eaton; Peter Kyriakou; Peter Calvert; Bowen Zhang; Mahendra Siwan; Benjamin Howden; Julian Druce; Mike Catton; Deborah A Williamson

doi:10.1016/j.pathol.2020.08.004

Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory

Pathology. 2020 Dec;52(7):754-759. doi: 10.1016/j.pathol.2020.08.004. Epub 2020 Sep 1.

Authors

Affiliations

¹ Department of Microbiology, Royal Melbourne Hospital, Melbourne, Vic, Australia. Electronic address: eloise.williams@mh.org.au.
² Department of Microbiology, Royal Melbourne Hospital, Melbourne, Vic, Australia.
³ Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.
⁴ Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.
⁵ Department of Microbiology, Royal Melbourne Hospital, Melbourne, Vic, Australia; Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.

Abstract

The unprecedented scale of testing required to effectively control the coronavirus disease (COVID-19) pandemic has necessitated urgent implementation of rapid testing in clinical microbiology laboratories. To date, there are limited data available on the analytical performance of emerging commercially available assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and integration of these assays into laboratory workflows. Here, we performed a prospective validation study of a commercially available assay, the AusDiagnostics Coronavirus Typing (8-well) assay. Respiratory tract samples for SARS-CoV-2 testing were collected between 1 March and 25 March 2020. All positive samples and a random subset of negative samples were sent to a reference laboratory for confirmation. In total, 2673 samples were analysed using the Coronavirus Typing assay. The predominant sample type was a combined nasopharyngeal/throat swab (2640/2673; 98.8%). Fifty-four patients were positive for SARS-CoV-2 (2.0%) using the Coronavirus Typing assay; 53/54 (98.1%) positive results and 621/621 (100%) negative results were concordant with the reference laboratory. Compared to the reference laboratory gold standard, sensitivity of the Coronavirus Typing assay for SARS-CoV-2 was 100% (95% CI 93.2-100%), specificity 99.8% (95% CI 99.1-100%), positive predictive value 98.1% (95% CI 90.2-99.7%) and negative predictive value 100% (95% CI 99.4-100%). In many countries, standard regulatory requirements for the introduction of new assays have been replaced by emergency authorisations and it is critical that laboratories share their post-market validation experiences, as the consequences of widespread introduction of a suboptimal assay for SARS-CoV-2 are profound. Here, we share our in-field experience, and encourage other laboratories to follow suit.

Keywords: COVID-19; Coronavirus; PCR; SARS-CoV-2; diagnostics; molecular microbiology; severe acute respiratory virus.

Publication types

Validation Study

MeSH terms

Adult
COVID-19 / diagnosis*
COVID-19 Nucleic Acid Testing / methods*
Female
Humans
Male
Middle Aged
Multiplex Polymerase Chain Reaction / methods*
SARS-CoV-2
Sensitivity and Specificity
Workflow