Swab pooling: A new method for large-scale RT-qPCR screening of SARS-CoV-2 avoiding sample dilution

Christoff, Ana Paula; Cruz, Giuliano Netto Flores; Sereia, Aline Fernanda Rodrigues; Boberg, Dellyana Rodrigues; Bastiani, Daniela Carolina de; Yamanaka, Laís Eiko; Fongaro, Gislaine; Stoco, Patrícia Hermes; Bazzo, Maria Luiza; Grisard, Edmundo C.; Hernandes, Camila; Oliveira, Luiz Felipe Valter de

doi:10.1371/journal.pone.0246544

Cited by 29 publications

(29 citation statements)

References 27 publications

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“…4b), and no differences in the distributions of CT values were observed between paired tests stratified by number of swabs (Fig 4c). Taken together, and in agreement with previous studies [46][47][48] , these data strongly argue that swab pooling does not result in any significant loss of PCR test sensitivity.…”

Section: Clinical Performance Of Pooled Screening Testssupporting

confidence: 92%

“…This method requires additional sample manipulation, and results in dilution of viral RNA present in individual samples. Alternatively, tests may be pooled at the time swabs (samples) are taken, by combining multiple swabs from individuals in the same sample tube (swab pooling, also known as cohort pooling, or pooling at source) [46][47][48] . This approach avoids reductions in test sensitivity caused by sample dilution, and disruption of existing laboratory workflows.…”

Section: Mainmentioning

confidence: 99%

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Feasibility and efficacy of mass testing for SARS-CoV-2 in a UK university using swab pooling and PCR

Warne¹,

Enright²,

Metaxaki³

et al. 2021

Preprint

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Transmission of SARS-CoV-2 without symptoms is well described, and may be mitigated by mass testing. Nonetheless, the optimal implementation and quantitative real-world impact of this approach remain unclear. During a period of rising SARS-CoV-2 prevalence, students at the University of Cambridge were enrolled in a voluntary programme of weekly PCR-based asymptomatic screening. Swab pooling by household reduced the total testing capacity required by five-fold, without affecting laboratory workflows or compromising test sensitivity. Participation remained >75% throughout the study period. 299/671 (45%) of students diagnosed with SARS-CoV-2 were either identified or pre-emptively quarantined because of the screening programme. After a negative screening test, the risk of developing COVID-19 over the following 7 days was decreased by 51%. Modelling transmission using parameters from our study suggests a reduction in R0 of up to 31% attributable to weekly screening. We therefore demonstrate the feasibility and efficacy of regular, voluntary mass testing for COVID-19.

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Section: Clinical Performance Of Pooled Screening Testssupporting

confidence: 92%

Section: Mainmentioning

confidence: 99%

Feasibility and efficacy of mass testing for SARS-CoV-2 in a UK university using swab pooling and PCR

Warne¹,

Enright²,

Metaxaki³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…There have been recent reports of screening approaches using pooled RT-qPCR 15 , 16 , sacrificing some sensitivity to vastly increase capacity for PCR testing. These have shown success in practice, but still rely on conventional nasopharyngeal swabs as material.…”

Section: Discussionmentioning

confidence: 99%

Clinical performance and accuracy of a qPCR-based SARS-CoV-2 mass-screening workflow for healthcare-worker surveillance using pooled self-sampled gargling solutions: A cross-sectional study

Olearo

Nörz

Hoffman

et al. 2021

Journal of Infection

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Introduction The large number of asymptomatic SARS-CoV-2 infections necessitates general screening of employees. We evaluate the performance of a SARS-CoV-2 screening program in asymptomatic healthcare-workers (HCW), utilizing self-sampled gargling-solution and sample pooling for RT-qPCR. Methods We conducted a cross-sectional retrospective study to collect real-life data on the performance of a screening-workflow based on automated-pooling and high-throughput qPCR testing over a 3-month-period at the University Hospital Hamburg. Results Matrix validation reveals that lower limit of detection for SARS-CoV-2 RNA in gargling-solution was 180 copies/mL (5-sample-pool). A total of 55,122 self-collected gargle samples (=7,513 HCWs) was analyzed. The median time to result was 8.5 hours (IQR 7.2-10.8). Of 11,192 pools analyzed, 11,041 (98.7%) were negative, 69 (0.6%) were positive and 82 (0.7%) were invalid. Individual testing of pool participants revealed 57 SARS-CoV-2 previously unrecognized infections. All 57 HCWs were either pre-symptomatic or asymptomatic (prevalence 0.76%,CI95%0.58-0.98%). Accuracy based on HCWs with gargle-solution and NP-swab available within 3-day-interval (N=521) was 99.5% (CI95%98.3-99.9%), sensitivity 88.9% (CI95%65.3-98.6%) while specificity 99.8% (CI95%98.9-99.9). Conclusion This workflow was highly effective in identifying SARS-CoV-2 positive HCWs, thereby lowering the potential of inter-HCW and HCW-patient transmissions. Automated-sample-pooling helped to conserve qPCR reagents and represents a promising alternative strategy to antigen testing in mass-screening programs.

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“…Pooled sample testing has been reported by many groups to be successful [ 23–25 ]. There are a variety of different pooling protocols including different number of samples to be included in each pool and various techniques to improve sensitivity in a pooled sample [ 26 , 27 ]. We report that pools of eight individual samples resulted in highly effective and efficient detection of SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 99%

Efficiency of Pooled Surveillance Testing in Academic Labs to Detect and Inhibit Covid-19 Outbreaks

et al. 2021

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Robust surveillance testing is a key strategic plan to prevent COVID-19 outbreaks and slow the spread of the SARS-CoV-2 pandemic; however, limited resources, facilities and time often impair the implementation of a widespread surveillance effort. To mitigate these resource limitations, we employed a strategy of pooling samples, reducing reagent cost and processing time. Through utilizing academic faculty and labs, successful pooled surveillance testing was conducted throughout Fall 2020 semester to detect positive SARS-CoV-2 infections in a population of 4400 students. During the semester, over 25,000 individual COVID status evaluations were made by pooling eight individual samples into one quantitative reverse transcription polymerase chain reaction. This pooled surveillance strategy was highly effective at detecting infection and significantly reduced financial burden and cost by $3.6 million.

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Swab pooling: A new method for large-scale RT-qPCR screening of SARS-CoV-2 avoiding sample dilution

Cited by 29 publications

References 27 publications

Feasibility and efficacy of mass testing for SARS-CoV-2 in a UK university using swab pooling and PCR

Feasibility and efficacy of mass testing for SARS-CoV-2 in a UK university using swab pooling and PCR

Clinical performance and accuracy of a qPCR-based SARS-CoV-2 mass-screening workflow for healthcare-worker surveillance using pooled self-sampled gargling solutions: A cross-sectional study

Efficiency of Pooled Surveillance Testing in Academic Labs to Detect and Inhibit Covid-19 Outbreaks

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