Testing qPCR positive, negative and inconclusive COVID-19 clinical samples using digital PCR

Background

In response to the global outbreak of coronavirus disease 2019 (COVID-19) there is a high demand for sensitive, accurate and consistent tests. Although RT-qPCR has served as the standard of care diagnostic test for the detection of SARS-CoV-2 infection, RT-dPCR (reverse transcription digital PCR) has recently been shown to outperform the traditional method in terms of sensitivity and accuracy.(1,2)

False negative and questionable negative rates using the current screening methodologies (RT-qPCR) have varied over the course of the pandemic and have been reported to be as high as 20%.(3,4) Because of this, asymptomatic patients are at an elevated risk of unknowingly spreading the disease. In addition to the need for more sensitive screening methods, a technology enabling higher accuracy will be critical for screening in determining more accurate rates of re-infection.

A highly sensitive, orthogonal test method to help resolve questionable negatives will increase overall testing accuracy and may also help reduce community transmission. The Combinati Absolute Q with its industry leading accuracy is ideally suited for the disambiguation of questionable negative test outcomes.

The goal of this study was to compare the results obtained using the CDC RT-qPCR assay with a dPCR test on a series of clinical samples. In collaboration with USC Clinical Laboratories, Molecular Pathology at University of Southern California, nucleic acids extracted  from 19 clinical specimens from individuals who tested negative or were diagnosed with COVID-19 were tested on the Combinati Absolute Q dPCR Platform using the |Q|™ SARS-CoV-2 Triplex Assay.

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  1. Suo T, Liu X, Guo M, et al. ddPCR: a more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens. medRxiv. March 2020:2020.02.29.20029439. doi:10.1101/2020.02.29.20029439
  2. Dong L, Zhou J, Niu C, et al. Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR. medRxiv. March 2020:2020.03.14.20036129. doi:10.1101/2020.03.14.20036129
  3. Woloshin, Steven, et al. “False Negative Tests for SARS-CoV-2 Infection – Challenges and Implications: NEJM.” New England Journal of Medicine, 22 May 2020, www.nejm.org/doi/full/10.1056/NEJMp2015897.
  4. Yu F, et al., “Quantitative Detection and Viral Load Analysis of SARS-CoV-2in Infected Patients”, Clin Infect Dis, 2020

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