Characteristics of SARS-CoV-2 testing for rapid diagnosis of COVID-19 during the initial stages of a global pandemic

Guthrie, Jennifer L.; Chen, Allison J.; Budhram, Dalton R.; Cronin, Kirby; Peci, Adriana; Nelson, Paul; Mallo, Gustavo V.; Broukhanski, George; Murti, Michelle; Majury, Anna; Mazzulli, Tony; Allen, Vanessa G.; Patel, Samir N.; Kus, Julianne V.; Tran, Vanessa; Gubbay, Jonathan B.

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.