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Verdun, C.M.* ; Fuchs, T.* ; Harar, P.* ; Elbrächter, D.* ; Fischer, D.S. ; Berner, J.* ; Grohs, P.* ; Theis, F.J. ; Krahmer, F.*

Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies.

Front. Publ. Health 9:583377 (2021)
Publ. Version/Full Text DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Background: Due to the ongoing COVID-19 pandemic, demand for diagnostic testing has increased drastically, resulting in shortages of necessary materials to conduct the tests and overwhelming the capacity of testing laboratories. The supply scarcity and capacity limits affect test administration: priority must be given to hospitalized patients and symptomatic individuals, which can prevent the identification of asymptomatic and presymptomatic individuals and hence effective tracking and tracing policies. We describe optimized group testing strategies applicable to SARS-CoV-2 tests in scenarios tailored to the current COVID-19 pandemic and assess significant gains compared to individual testing. Methods: We account for biochemically realistic scenarios in the context of dilution effects on SARS-CoV-2 samples and consider evidence on specificity and sensitivity of PCR-based tests for the novel coronavirus. Because of the current uncertainty and the temporal and spatial changes in the prevalence regime, we provide analysis for several realistic scenarios and propose fast and reliable strategies for massive testing procedures. Key Findings: We find significant efficiency gaps between different group testing strategies in realistic scenarios for SARS-CoV-2 testing, highlighting the need for an informed decision of the pooling protocol depending on estimated prevalence, target specificity, and high- vs. low-risk population. For example, using one of the presented methods, all 1.47 million inhabitants of Munich, Germany, could be tested using only around 141 thousand tests if the infection rate is below 0.4% is assumed. Using 1 million tests, the 6.69 million inhabitants from the city of Rio de Janeiro, Brazil, could be tested as long as the infection rate does not exceed 1%. Moreover, we provide an interactive web application, available at www.grouptexting.com, for visualizing the different strategies and designing pooling schemes according to specific prevalence scenarios and test configurations. Interpretation: Altogether, this work may help provide a basis for an efficient upscaling of current testing procedures, which takes the population heterogeneity into account and is fine-grained towards the desired study populations, e.g., mild/asymptomatic individuals vs. symptomatic ones but also mixtures thereof. Funding: German Science Foundation (DFG), German Federal Ministry of Education and Research (BMBF), Chan Zuckerberg Initiative DAF, and Austrian Science Fund (FWF).
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Covid-19 ; Rt-pcr ; Sars-cov-2 ; Group Testing ; Informative Testing ; Pooling; Defective Members
ISSN (print) / ISBN 2296-2565
e-ISSN 2296-2565
Journal Frontiers in Public Health
Quellenangaben Volume: 9, Issue: , Pages: , Article Number: 583377 Supplement: ,
Publisher Frontiers
Publishing Place Lausanne
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants Joachim Herz Stiftung
German Science Foundation
BMBF
Chan Zuckerberg Initiative DAF (advised fund of Silicon Valley Community Foundation)
Austrian Science Fund (FWF)
German research foundation (DFG) fellowship through the Graduate School of Quantitative Biosciences Munich (QBM)
German Science Foundation (DFG)