Open AccessCharacteristics of SARS-CoV-2 testing for rapid diagnosis of COVID-19 during the initial stages of a global pandemic
Author(s) -
Jennifer L. Guthrie,
Allison J. Chen,
Dalton Budhram,
Kirby Cronin,
Adriana Peci,
Paul Nelson,
Gustavo V. Mallo,
George Broukhanski,
Michelle Murti,
Anna Majury,
Tony Mazzulli,
Vanessa Allen,
Samir N. Patel,
Julianne V. Kus,
Vanessa Tran,
Jonathan B. Gubbay
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0253941
Subject(s) - concordance , covid-19 , asymptomatic , medicine , pandemic , diagnostic test , predictive value , predictive value of tests , pathology , emergency medicine , disease , infectious disease (medical specialty) , outbreak
Accurate SARS-CoV-2 diagnosis is essential to guide prevention and control of COVID-19. Here we examine SARS-CoV-2 molecular-based test performance characteristics and summarize case-level data related to COVID-19 diagnosis. From January 11 through April 22, 2020, Public Health Ontario conducted SARS-CoV-2 testing of 86,942 specimens collected from 80,354 individuals, primarily using real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods. We analyzed test results across specimen types and for individuals with multiple same-day and multi-day collected specimens. Nasopharyngeal compared to throat swabs had a higher positivity (8.8% vs. 4.8%) and an adjusted estimate 2.9 C t lower (SE = 0.5, p <0.001). Same-day specimens showed high concordance (98.8%), and the median C t of multi-day specimens increased over time. Symptomatic cases had rRT-PCR results with an adjusted estimate 3.0 C t (SE = 0.5, p <0.001) lower than asymptomatic/pre-symptomatic cases. Overall test sensitivity was 84.6%, with a negative predictive value of 95.5%. Molecular testing is the mainstay of SARS-CoV-2 diagnosis and testing protocols will continue to be dynamic and iteratively modified as more is learned about this emerging pathogen.