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Impact of COVID-19 pre-test probability on positive predictive value of high cycle threshold SARS-CoV-2 real-time reverse transcription PCR test results

Published online by Cambridge University Press:  09 August 2021

Jonathan B. Gubbay*
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Division of Infectious Diseases, Department of Paediatrics, The Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada M5G 1X8.
Heather Rilkoff
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
Heather L. Kristjanson
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
Jessica D. Forbes
Affiliation:
Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Michelle Murti
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, Canada M5T 3M7
AliReza Eshaghi
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
George Broukhanski
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Antoine Corbeil
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Nahuel Fittipaldi
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Jessica P. Hopkins
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, Canada M5T 3M7 Department of Health Research Methods, Evidence, and Impact, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
Erik Kristjanson
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
Julianne V. Kus
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Liane Macdonald
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON, Canada M5T 3M7
Anna Majury
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Pathology and Molecular Medicine, Queens University, 88 Stuart Street, Kingston, Ontario, Canada K7L 3N6
Gustavo V Mallo
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
Tony Mazzulli
Affiliation:
Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8 Department of Microbiology, Sinai Health/University Health Network, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
Roberto G. Melano
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Romy Olsha
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
Stephen J. Perusini
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1
Vanessa Tran
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Vanessa G Allen
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
Samir N Patel
Affiliation:
Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada M5G 1M1 Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8
*
* Corresponding Author: Jonathan B. Gubbay, Public Health Ontario, 661 University Avenue, Toronto, Ontario, Canada, M5G 1M1, Phone: +1 647-792-3170, Fax: +1 416-235-5800, Email: jonathan.gubbay@oahpp.ca

Abstract

Objectives

Performance characteristics of SARS-CoV-2 nucleic acid detection assays are understudied within contexts of low pre-test probability, including screening asymptomatic persons without epidemiological links to confirmed cases, or asymptomatic surveillance testing. SARS-CoV-2 detection without symptoms may represent presymptomatic or asymptomatic infection, resolved infection with persistent RNA shedding, or a false positive test. This study assessed positive predictive value of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) assays by retesting positive specimens from five pre-test probability groups ranging from high to low with an alternate assay.

Methods

A total of 122 rRT-PCR positive specimens collected from unique patients between March and July 2020 were retested using a laboratory-developed nested RT-PCR assay targeting the RNA-dependent RNA polymerase (RdRp) gene followed by Sanger sequencing.

Results

Significantly fewer (15.6%) positive results in the lowest pre-test probability group (facilities with institution-wide screening having ≤ 3 positive asymptomatic cases) were reproduced with the nested RdRp gene RT-PCR assay than in each of the four groups with higher pre-test probability (individual group range 50·0% to 85·0%).

Conclusions

Large-scale SARS-CoV-2 screening testing initiatives among low pre-test probability populations should be evaluated thoroughly prior to implementation given the risk of false positives and consequent potential for harm at the individual and population level.

Type
Original Article
Copyright
© 2021 by The Society for Healthcare Epidemiology of America. All rights reserved.

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Impact of COVID-19 pre-test probability on positive predictive value of high cycle threshold SARS-CoV-2 real-time reverse transcription PCR test results
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