1. Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.
- Author
-
Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, and Grubaugh ND
- Subjects
- Betacoronavirus isolation & purification, COVID-19, COVID-19 Testing, Clinical Laboratory Techniques statistics & numerical data, Coronavirus Infections epidemiology, Genetic Variation, Genome, Viral, Humans, Molecular Probe Techniques statistics & numerical data, Pandemics, Pneumonia, Viral epidemiology, RNA genetics, RNA Probes genetics, Reverse Transcriptase Polymerase Chain Reaction statistics & numerical data, SARS-CoV-2, Sensitivity and Specificity, Betacoronavirus genetics, Clinical Laboratory Techniques methods, Coronavirus Infections diagnosis, Coronavirus Infections virology, Pneumonia, Viral diagnosis, Pneumonia, Viral virology, RNA, Viral analysis, RNA, Viral genetics, Reverse Transcriptase Polymerase Chain Reaction methods
- Abstract
The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse transcription-PCR (RT-qPCR) assays are being used by clinical, research and public health laboratories. However, it is currently unclear whether results from different tests are comparable. Our goal was to make independent evaluations of primer-probe sets used in four common SARS-CoV-2 diagnostic assays. From our comparisons of RT-qPCR analytical efficiency and sensitivity, we show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 viral RNA copies per reaction. The exception for this is the RdRp-SARSr (Charité) confirmatory primer-probe set which has low sensitivity, probably due to a mismatch to circulating SARS-CoV-2 in the reverse primer. We did not find evidence for background amplification with pre-COVID-19 samples or recent SARS-CoV-2 evolution decreasing sensitivity. Our recommendation for SARS-CoV-2 diagnostic testing is to select an assay with high sensitivity and that is regionally used, to ease comparability between outcomes.
- Published
- 2020
- Full Text
- View/download PDF