High-sensitivity SARS-CoV-2 group testing by digital PCR among symptomatic patients in hospital settings
Background: 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.
Methods: 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.
Results: 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.
Journal of Clinical Virology 141, 104895 (2021)
Citation
@article{martin2021,
author = {Martin, Alexandra and Storto, Alexandre and Le Hingrat,
Quentin and Collin, Gilles and André, Barbara and Mallory, Allison
and Dangla, Rémi and Descamps, Diane and Visseaux, Benoit and
Gossner, Olivier},
title = {High-Sensitivity {SARS-CoV-2} Group Testing by Digital {PCR}
Among Symptomatic Patients in Hospital Settings},
journal = {Journal of Clinical Virology},
volume = {141},
pages = {104895},
date = {2021},
url = {https://gossner.me/papers/high-sensitivity-sars-cov-2-group-testing-by-digital-pcr-among-symptomatic-patients.html},
doi = {10.1016/j.jcv.2021.104895},
langid = {en},
abstract = {Background: 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. Methods: 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. Results: 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.}
}