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

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 commercial...

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Autores principales: Williams, Eloise, Bond, Katherine, Chong, Brian, Giltrap, Dawn, Eaton, Malcolm, Kyriakou, Peter, Calvert, Peter, Zhang, Bowen, Siwan, Mahendra, Howden, Benjamin, Druce, Julian, Catton, Mike, Williamson, Deborah A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Published by Elsevier B.V. on behalf of Royal College of Pathologists of Australasia. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462582/
https://www.ncbi.nlm.nih.gov/pubmed/32943228
http://dx.doi.org/10.1016/j.pathol.2020.08.004
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author Williams, Eloise
Bond, Katherine
Chong, Brian
Giltrap, Dawn
Eaton, Malcolm
Kyriakou, Peter
Calvert, Peter
Zhang, Bowen
Siwan, Mahendra
Howden, Benjamin
Druce, Julian
Catton, Mike
Williamson, Deborah A.
author_facet Williams, Eloise
Bond, Katherine
Chong, Brian
Giltrap, Dawn
Eaton, Malcolm
Kyriakou, Peter
Calvert, Peter
Zhang, Bowen
Siwan, Mahendra
Howden, Benjamin
Druce, Julian
Catton, Mike
Williamson, Deborah A.
author_sort Williams, Eloise
collection PubMed
description 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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spelling pubmed-74625822020-09-02 Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory Williams, Eloise Bond, Katherine Chong, Brian Giltrap, Dawn Eaton, Malcolm Kyriakou, Peter Calvert, Peter Zhang, Bowen Siwan, Mahendra Howden, Benjamin Druce, Julian Catton, Mike Williamson, Deborah A. Pathology Focus on SARS-Cov-2 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. Published by Elsevier B.V. on behalf of Royal College of Pathologists of Australasia. 2020-12 2020-09-01 /pmc/articles/PMC7462582/ /pubmed/32943228 http://dx.doi.org/10.1016/j.pathol.2020.08.004 Text en Crown Copyright © 2020 Published by Elsevier B.V. on behalf of Royal College of Pathologists of Australasia. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Focus on SARS-Cov-2
Williams, Eloise
Bond, Katherine
Chong, Brian
Giltrap, Dawn
Eaton, Malcolm
Kyriakou, Peter
Calvert, Peter
Zhang, Bowen
Siwan, Mahendra
Howden, Benjamin
Druce, Julian
Catton, Mike
Williamson, Deborah A.
Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory
title Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory
title_full Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory
title_fullStr Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory
title_full_unstemmed Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory
title_short Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory
title_sort implementation and evaluation of a novel real-time multiplex assay for sars-cov-2: in-field learnings from a clinical microbiology laboratory
topic Focus on SARS-Cov-2
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462582/
https://www.ncbi.nlm.nih.gov/pubmed/32943228
http://dx.doi.org/10.1016/j.pathol.2020.08.004
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