Fagg, J; Beale, R; Futschik, ME; Turek, E; Chapman, D; Halstead, S; Jones, M; ... Fowler, T; + view all Fagg, J; Beale, R; Futschik, ME; Turek, E; Chapman, D; Halstead, S; Jones, M; Cole-Hamilton, J; Gunson, R; Sudhanva, M; Klapper, PE; Vansteenhouse, H; Tunkel, S; Dominiczak, A; Peto, TE; Fowler, T; - view fewer (2023) Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing. Journal of Clinical Virology , 167 , Article 105574. 10.1016/j.jcv.2023.105574.

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Abstract

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 > 400 copies/ml (i.e. Ct value < 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.

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