High-sensitivity SARS-CoV-2 group testing by digital PCR among symptomatic patients in hospital settings

• Published in: Journal of clinical virology Vol. 141; p. 104895
• Main Authors: Martin, Alexandra, Storto, Alexandre, Le Hingrat, Quentin, Collin, Gilles, André, Barbara, Mallory, Allison, Dangla, Rémi, Descamps, Diane, Visseaux, Benoit, Gossner, Olivier
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2021
• Subjects: COVID-19; Digital PCR; Group testing; Hospitals; Humans; Pandemics; Polymerase Chain Reaction; RT-PCR; Sample pooling; SARS-CoV-2; Sensitivity and Specificity; COVID-19; SARS-CoV-2; Digital PCR; Sample pooling; Group testing; RT-PCR
• DOI: 10.1016/j.jcv.2021.104895
• ISSN: 1386-6532

•SARS-CoV-2 RT-PCR testing is central to follow disease spread.•Group testing expand testing capabilities but present some sensitivity concerns.•Digital PCR on group of 16 to 32 demonstrated similar sensitivity to individual RT-PCR.•Digital PCR reduced reagent needs, up to 80%, costs and increased testing capabilities. Worldwide demand for SARS-CoV-2 RT-PCR testing is still high as testing remains central to follow the disease spread and vaccine efficacy. Group testing has been proposed as a solution to expand testing capabilities but sensitivity concerns may limit its impact on the management of the pandemic. Digital PCR (RT-dPCR) has been shown to be highly sensitive and could help by providing larger testing capabilities without compromising sensitivity. We implemented RT-dPCR based COVID-19 group testing on a commercially available system and assay (naica® system from Stilla Technologies) and investigated the sensitivity of the method in real life conditions of a university hospital in Paris, France, in May 2020. We tested the protocol in a direct comparison with reference RT-PCR testing on 448 samples split into groups of 8, 16 and 32 samples for RT-dPCR analysis. Individual RT-PCR testing identified 25/448 positive samples. Using 56 groups of 8, RT-dPCR identified 23 groups as positive, corresponding to 26 positive samples by individual PCR (positive percentage agreement 95.2% [95% confidence interval: 76.2–99.9%]) and including 2 samples not detected by individual RT-PCR but confirmed positive by further investigation. 15 of 28 groups of 16 tested positive, corresponding to 25 positive samples by individual PCR (positive percentage agreement 87.5% [95% confidence interval: 61.7–98.4%]). 14 groups of 32 were fully concordant with individual PCR testing but will need to be confirmed on larger datasets. Our proposed approach of group testing by digital PCR has similar diagnostic sensitivity compared to individual RT-PCR testing for group up to 16 samples. This approach reduces the quantity of reagent needed by up to 80% while reducing costs and increasing capabilities of testing up to 10-fold.