Modelling pooling strategies for SARS-CoV-2 testing in a university setting
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Abstract
Background: Pre-symptomatic and asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are important elements in the coronavirus disease 2019 (COVID-19) pandemic, and there remains a reliance on testing to manage the spread of the disease. In the UK, many universities opened for blended learning for the 2020-2021 academic year, with a mixture of face to face and online teaching.
Methods: In this study we present a simulation framework to evaluate the effectiveness of different mass testing strategies within a university setting, across a range of transmission scenarios.
Results: The sensitivity of 5x pooled RT-qPCR tests appears to be higher than testing using the lateral flow device with relatively little loss compared to single RT-qPCR tests, and is improved by pooling by social cluster. The range of strategies that we evaluated give comparable results for estimating prevalence.
Conclusions: Pooling tests by known social structures, such as student households can substantially improve the cost effectiveness of RT-qPCR tests. We also note that routine recording of quantitative RT-qPCR results would facilitate future modelling studies.
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SciScore for 10.1101/2021.01.19.20248560: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We determined the cost of sample collection to be £3.47 (comprising of saliva sampling funnel (£1.86; Isohelix), collection tube (£1.42; Isohelix), storage tube, and pipette tip (£0.19)) and the cost of a PCR test to be £12.46 (based on 1 extraction using QIAsymphony® (QIAGEN) kits at £4.46 per sample, and one PCR reaction using the Altona SARS-CoV-2 RealStar RT-PCR Kit 1.0 at £8.00 per sample. QIAsymphony®suggested: (Miami University Biorepository Core Facility, RRID:SCR_017816)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the …SciScore for 10.1101/2021.01.19.20248560: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We determined the cost of sample collection to be £3.47 (comprising of saliva sampling funnel (£1.86; Isohelix), collection tube (£1.42; Isohelix), storage tube, and pipette tip (£0.19)) and the cost of a PCR test to be £12.46 (based on 1 extraction using QIAsymphony® (QIAGEN) kits at £4.46 per sample, and one PCR reaction using the Altona SARS-CoV-2 RealStar RT-PCR Kit 1.0 at £8.00 per sample. QIAsymphony®suggested: (Miami University Biorepository Core Facility, RRID:SCR_017816)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:A key limitation of the costing analysis is that the logistics and time required to pool samples using maximal bin packing was not considered. It’s likely that the most realistic way to achieve pooling by living circle would be for samples to be submitted together and grouped within the lab according to when they are submitted. The true cost per PPV of pooling is therefore likely to be affected by the limitations of implementing pooling. Similarly, practical considerations within the laboratory infrastructure do place limitations on the complexity of the sample grouping strategies. Per-individual follow-up testing within positive pools improves the specificity of test results but can become costly as prevalence increases. Outbreaks have been seen to be controlled within university settings (e.g. 27) which suggests that structural measures are effective and it is unlikely that prevalence will ever be particularly high at any given point5. Given that close contacts of positive cases are advised to self-isolate regardless of their test status, follow-up testing of positive pools may provide unactionable information when then pools are composed of social contacts. However, the value of testing the contacts of infected individuals has recently been shown in other simulations28, where it was suggested that testing of contacts is likely to identify substantially more true negatives than false negatives. Changes in the ratio of cost of sampling compared to cost of PCR test will affec...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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