TY - JOUR
AU - Fagg, Jamie
AU - Beale, Rupert
AU - Futschik, Matthias E.
AU - Turek, Elena
AU - Chapman, David
AU - Halstead, Susan
AU - Jones, Marc V.
AU - Cole-Hamilton, Joanna
AU - Gunson, Rory N.
AU - Sudhanva, Malur
AU - Klapper, Paul E.
AU - VanSteenhouse, Harper
AU - Tunkel, Sarah
AU - Dominiczak, Anna
AU - Fowler, Tom
AU - Peto, Timothy E.A.
PY - 2023
DA - August
TI - Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing
JO - Journal of Clinical Virology
VL - 167
DO - http://dx.doi.org/10.1016/j.jcv.2023.105574
AB - Background: The challenges of rapid upscaling of testing capacity were a major lesson from the COVID-19 pandemic response. The need for process adjustments in high-throughput testing laboratories made sample pooling a challenging option to implement. Objective: This study aimed to evaluate whether pooling samples at source (swab pooling) was as effective as qRT-PCR testing of individuals in identifying cases of SARS-CoV-2 in real-world community testing conditions using the same high-throughput pipeline. Methods: Two cohorts of 10 (Pool10: 1,030 participants and 103 pools) and 6 (Pool6: 1,284 participants and 214 pools) samples per pool were tested for concordance, sensitivity, specificity, and Ct value differences with individual testing as reference. Results: Swab pooling allowed unmodified application of an existing high-throughput SARS-Cov-2 testing pipeline with only marginal loss of accuracy. For Pool10, concordance was 98.1% (95% Confidence interval: 93.3–99.8%), sensitivity was 95.7% (85.5–99.5%), and specificity was 100.0% (93.6–100.0%). For Pool6, concordance was 97.2% (94.0–99.0%), sensitivity was 97.5% (93.7–99.3%), and specificity was 96.4% (87.7–99.6%). Differences of outcomes measure between pool size were not significant. Most positive individual samples, which were not detected in pools, had very low viral concentration. If only individual samples with a viral concentration &gt; 400 copies/ml (i.e. Ct value &lt; 30) were considered positive, the overall sensitivity of pooling increased to 99.5%. Conclusion: The study demonstrated high sensitivity and specificity by swab pooling and the immediate capability of high-throughput laboratories to implement this method making it an option in planning of rapid upscaling of laboratory capacity for future pandemics.
PB - Elsevier
UR - https://eprints.gla.ac.uk/363454/
KW - Coronavirus (COVID-19)
ER