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

Published:September 01, 2020DOI:https://doi.org/10.1016/j.pathol.2020.08.004

      Summary

      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 In many countries, standard regulatory requirements for the introduction of new assays have been replaced by emergency authorisations and it is critical that laboratories share their post-market validation experiences, as the consequences of widespread introduction of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.

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      References

        • Zhu N.
        • Zhang D.
        • Wang W.
        • et al.
        A novel coronavirus from patients with pneumonia in China, 2019.
        N Engl J Med. 2020; 382: 727-733
        • Corman V.M.
        • Landt O.
        • Kaiser M.
        • et al.
        Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR.
        Euro Surveill. 2020; 25: 2000045
        • Reusken C.
        • Broberg E.K.
        • Haagmans B.
        • et al.
        Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020.
        Euro Surveill. 2020; 25: 2000082
        • Centers for Disease Control and Prevention
        CDC 2019 Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel.
        Centers for Disease Control and Prevention, Atlanta2020
        • Chu D.K.W.
        • Pan Y.
        • Cheng S.M.S.
        • et al.
        Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia.
        Clin Chem. 2020; 66: 549-555
        • Pfefferle S.
        • Reucher S.
        • Norz D.
        • et al.
        Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system.
        Euro Surveill. 2020; 25: 2000152
        • Sharfstein J.M.
        • Becker S.J.
        • Mello M.M.
        Diagnostic testing for the novel coronavirus.
        JAMA. 2020; Mar 9; (online ahead of print)
      1. Australian Government. Therapeutic Goods (Medical Devices–Novel Coronavirus) (Emergency) Exemption 2020. Cited 12 Apr 2020. https://www.legislation.gov.au/Details/F2020N00015.

      2. Australian Government. Therapeutic Goods (Medical Devices - Accredited Pathology Laboratories (COVID-19 Emergency) Exemption 2020. Cited 12 Apr 2020. https://www.legislation.gov.au/Details/F2020N00032.

      3. Australian Government Department of Health, Therapeutic Goods Administration. COVID-19 test kits included on the ARTG for legal supply in Australia. Cited 12 Apr 2020. https://www.tga.gov.au/covid-19-test-kits-included-artg-legal-supply-australia.

        • Konrad R.
        • Eberle U.
        • Dangel A.
        • et al.
        Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020.
        Euro Surveill. 2020; 25: 2000173
        • National Pathology Accreditation Advisory Council
        Requirements for Quality Control, External Quality Assurance and Method Evaluation.
        (Sixth Edition 2018). Australian Government Department of Health, Canberra2018
        • Rojek A.
        • Dutch M.
        • Camilleri D.
        • et al.
        Early clinical response to a high consequence infectious disease outbreak at the Royal Melbourne Hospital Emergency Department - insights from COVID-19.
        Med J Aust. 2020; (Mar 16: (online ahead of print))
        • Victorian Department of Health and Human Services
        Coronavirus Disease 2019 (COVID-19): Case and Contact Management Guidelines for Health Services and General Practitioners.
        (Version 15, 2020) Victoria State Government Health and Human Services, Melbourne2020
        • National Pathology Accreditation Advisory Council
        Requirements for the Development and Use of In-House In Vitro Diagnostic Medical Devices (IVDs).
        (Fourth Edition, 2018). Australian Government Department of Health,, Canberra2018
      4. Public Health Laboratory Network. PHLN guidance on laboratory testing for SARS-CoV-2 (the virus that causes COVID-19). Cited 12 Apr 2020. https://www.health.gov.au/resources/publications/phln-guidance-on-laboratory-testing-for-sars-cov-2-the-virus-that-causes-covid-19.

        • Caly L.
        • Druce J.
        • Roberts J.
        • et al.
        Isolation and rapid sharing of the 2019 novel coronavirus (SARS-CoV-2) from the first diagnostics of COVID-19 in Australia.
        Med J Aust. 2020; 212: 459-462
        • Ng Y.
        • Li Z.
        • Chua Y.X.
        • et al.
        Evaluation of the effectiveness of surveillance and containment measures for the first 100 patients with COVID-19 in Singapore - January 2-February 29, 2020.
        MMWR. 2020; 69: 307-311
        • Spiteri G.
        • Fielding J.
        • Diercke M.
        • et al.
        First cases of coronavirus disease 2019 (COVID-19) in the WHO European region, 24 January to 21 February 2020.
        Euro Surveill. 2020; 25: 2000178
        • Onder G.
        • Rezza G.
        • Brusaferro S.
        Case-fatality rate and characteristics of patients dying in relation to COVID-19 in Italy.
        JAMA. 2020; Mar 23; (online ahead of print)
        • World Health Organization
        Coronavirus Disease 2019 (COVID-19) Situation Report - 42, 2 March 2020.
        World Health Organization, Geneva2020
        • World Health Organization
        Coronavirus Disease 2019 (COVID-19) Situation Report - 66, 26 March 2020.
        World Health Organization, Geneva2020
      5. Australian Government Department of Health. Government response to the COVID-19 outbreak. Cited 12 Apr 2020. https://www.health.gov.au/news/health-alerts/novel-coronavirus-2019-ncov-health-alert/government-response-to-the-covid-19-outbreak.

        • To K.K.
        • Tsang O.T.
        • Leung W.S.
        • et al.
        Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study.
        Lancet Infect Dis. 2020; 20: 565-574
        • Kim J.Y.
        • Ko J.H.
        • Kim Y.
        • et al.
        Viral load kinetics of SARS-CoV-2 infection in first two patients in Korea.
        J Kor Med Sci. 2020; 35: e86
        • Zou L.
        • Ruan F.
        • Huang M.
        • et al.
        SARS-CoV-2 Viral load in upper respiratory specimens of infected patients.
        N Engl J Med. 2020; 382: 1177-1179
        • Li Q.
        • Guan X.
        • Wu P.
        • et al.
        Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia.
        N Eng J Med. 2020; 382: 1199-1207
        • Pung R.
        • Chiew C.J.
        • Young B.E.
        • et al.
        Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures.
        Lancet. 2020; 395: 1039-1046
        • Chan J.F.-W.
        • Yuan S.
        • Kok K.-H.
        • et al.
        A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster.
        Lancet. 2020; 395: 514-523
        • Meunier D.
        • Woodford N.
        • Hopkins K.L.
        Evaluation of the AusDiagnostics MT CRE EU assay for the detection of carbapenemase genes and transferable colistin resistance determinants mcr-1/-2 in MDR Gram-negative bacteria.
        J Antimicrob Chemother. 2018; 73: 3355-3358
        • Binnicker M.J.
        Emergence of a novel coronavirus disease (COVID-19) and the importance of diagnostic testing: why partnership between clinical laboratories, public health agencies, and industry is essential to control the outbreak.
        Clin Chem. 2020; 66: 664-666
        • Poston J.T.
        • Patel B.K.
        • Davis A.M.
        Management of critically ill adults with COVID-19.
        JAMA. 2020; Mar 26; (online ahead of print)
        • Murthy S.
        • Gomersall C.D.
        • Fowler R.A.
        Care for critically ill patients with COVID-19.
        JAMA. 2020; Mar 11; (online ahead of print)
        • Curtis J.R.
        • Kross E.K.
        • Stapleton R.D.
        The importance of addressing advance care planning and decisions about do-not-resuscitate orders during novel coronavirus 2019 (COVID-19).
        JAMA. 2020; Mar 27; (online ahead of print)