Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples

Eis‐Hübinger, Anna Maria; Hönemann, Mario; Wenzel, Jürgen J.; Berger, Annemarie; Widera, Marek; Schmidt, Bárbara; Aldabbagh, Souhaib; Marx, Benjamin; Streeck, Hendrik; Ciesek, Sandra; Liebert, Uwe G.; Huzly, Daniela; Hengel, Hartmut; Panning, Marcus

doi:10.1016/j.jcv.2020.104381

Cited by 53 publications

(55 citation statements)

References 9 publications

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“…The pooling method was validated for nCov tests by many laboratories [2][3][4][5][6][7][8][9][10][11][12][13][14][15]. However, the following questions remained open, which we address in this paper.…”

Section: Introductionmentioning

confidence: 99%

Pooling of coronavirus tests under unknown prevalence

Pikovski

2020

Epidemiol. Infect.

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Diagnostic testing for the novel coronavirus is an important tool to fight the coronavirus disease (Covid-19) pandemic. However, testing capacities are limited. A modified testing protocol, whereby a number of probes are ‘pooled’ (i.e. grouped), is known to increase the capacity for testing. Here, we model pooled testing with a double-average model, which we think to be close to reality for Covid-19 testing. The optimal pool size and the effect of test errors are considered. The results show that the best pool size is three to five, under reasonable assumptions. Pool testing even reduces the number of false positives in the absence of dilution effects.

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Section: Introductionmentioning

confidence: 99%

Pooling of coronavirus tests under unknown prevalence

Pikovski

2020

Epidemiol. Infect.

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“…Results from these pooling methods support that pooled screening strategy can be pursued to increase testing throughput, limit use of reagents, and increase overall testing e ciency [6,7] at an expected slight loss of sensitivity for direct clinical sample pooling. The same could be attained with no loss of sensitivity for RNA pooling.…”

Section: Discussionmentioning

confidence: 69%

“…Sample pooling (mixing of samples and testing at a single pool, and subsequent individual testing needed only if the pool tests positive) has been used as an attractive method for community monitoring of infectious diseases as it requires no additional training, equipment, or materials [4][5][6]. The key principles for successful application of group testing involve knowledge of the limit-of-detection, sensitivity, and speci city of the assay, and the prevalence of disease in a given population (7,8).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Sample Pooling for Screening of SARS-CoV-2

Mulu

Alemayehu

Alemu

et al. 2020

Preprint

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Background: The coronavirus disease (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability efficient method is urgently needed.Objectives: To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2 Methods: Direct clinical sample and NA pooling approach was used for the standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 targeting the envelop (E) and open reading frame (ORF1ab) genomic region of the virus. In this approach, experimental pools were created using SARS CoV-2 positive clinical samples spiked with up to 9 negative samples prior to NA extraction step to have a final extraction volume of 200μL (maximum dilution factor of 10). Viral NA was also subsequently extracted from each pool and tested using the SARS CoV-2 RT-PCR assay.Results: We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the ct value of the original sample, corresponding to high, medium, and low SARS CoV-2 viral copies/reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend poling of 4 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 4 in 1 was expected to retain accuracy of the test irrespective of the ct value (relative ribonucleic acid RNA copy number) of the sample spiked and result in a 237% increase in testing efficiency. Conclusions: The approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community.

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“…A selection of presumed clinically feasible and optimal multi-stage schemes P3S3, P9S3, P4S2 and P16S3 was made. Also, the schemes P32S2, P10S2 and the matrix scheme were considered as they appeared in earlier literature [6,7]. MATPLOTLIB was used to plot their improvement factors for prevalence rates between 0% and 30%.…”

Section: Evaluation Of Testing Schemesmentioning

confidence: 99%

“…We determined the improvement factor of P3S2, P9S3, P4S2 and P16S4 for prevalence rates up to 30% (Figure 3 A+B) and compared results with previously described schemes, namely the two-stage testing schemes with pool sizes of 10 (P10S2, [6]), or 32 (P32S2, [5]). We also assessed the matrix testing scheme [7] using a matrix of 96 samples (12x8) that groups samples in rows (8 pools comprising 12 samples) and columns (12 pools comprising 8 samples) a method that has also been used for epitope mapping in immunology research application [8].…”

Section: Performance Of Presumed Clinically Feasible Group Testing Scmentioning

confidence: 99%

Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening

Eberhardt

Breuckmann

Eberhardt³

2020

Preprint

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189Manuscript: 2442 Abstract Background:SARS-CoV-2 test kits are in critical shortage in many countries. This limits large-scale population testing and hinders the effort to identify and isolate infected individuals. Objectives:Herein, we developed and evaluated multi-stage group testing schemes that test samples in groups of various pool sizes in multiple stages. Through this approach, groups of negative samples can be eliminated with a single test, avoiding the need for individual testing and achieving considerable savings of resources. Study design:We designed and parameterized various multi-stage testing schemes and compared their efficiency at different prevalence rates using computer simulations. Results:We found that three-stage testing schemes with pool sizes of maximum 16 samples can test up to three and seven times as many individuals with the same number of test kits for prevalence rates of around 5% and 1%, respectively. We propose an adaptive approach, where the optimal testing scheme is selected based on the expected prevalence rate. Conclusion:These group testing schemes could lead to a major reduction in the number of testing kits required and help improve large-scale population testing in general and in the context of the current COVID-19 pandemic.

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Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples

Cited by 53 publications

References 9 publications

Pooling of coronavirus tests under unknown prevalence

Pooling of coronavirus tests under unknown prevalence

Evaluation of Sample Pooling for Screening of SARS-CoV-2

Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening

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