Optimal Testing Strategy for the Identification of COVID-19 Infections

The systematic identification of infectious, yet unreported, individuals is critical for the containment of the COVID-19 pandemic. We present a strategy for identifying the location, timing and extent of testing that maximizes information gain for such infections. The optimal testing strategy relies on Bayesian experimental design and forecasting epidemic models that account for time dependent interventions. It is applicable at the onset and spreading of the epidemic and can forewarn for a possible recurrence of the disease after relaxation of interventions. We examine its application in Switzerland and show that it can provide timely and systematic guidance for the effective identification of infectious individuals with finite testing resources. The methodology and the open source code are readily adaptable to countries around the world.

[1]  D. Lindley On a Measure of the Information Provided by an Experiment , 1956 .

[2]  Costas Papadimitriou,et al.  Optimal sensor placement methodology for parametric identification of structural systems , 2004 .

[3]  T. Neumann Probability Theory The Logic Of Science , 2016 .

[4]  Jens Niklas Eberhardt,et al.  Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening , 2020, Journal of Clinical Virology.

[5]  P. Koumoutsakos,et al.  Data-driven inference of the reproduction number for COVID-19 before and after interventions for 51 European countries. , 2020, Swiss medical weekly.

[6]  Johannes Haushofer,et al.  Which interventions work best in a pandemic? , 2020, Science.

[7]  P. Koumoutsakos,et al.  Optimal Flow Sensing for Schooling Swimmers , 2020, Biomimetics.

[8]  Brendan Hickey,et al.  Evaluation of Group Testing for SARS-CoV-2 RNA , 2020, medRxiv.

[9]  J. Rocklöv,et al.  The reproductive number of COVID-19 is higher compared to SARS coronavirus , 2020, Journal of travel medicine.

[10]  Robert C. Wolpert,et al.  A Review of the , 1985 .

[11]  Bohn Stafleu van Loghum,et al.  Online … , 2002, LOG IN.

[12]  Anthony N. Pettitt,et al.  A Review of Modern Computational Algorithms for Bayesian Optimal Design , 2016 .

[13]  ThaiBinh Luong,et al.  Modeling Epidemics With Compartmental Models. , 2020, JAMA.

[14]  K. J. Ryan,et al.  Estimating Expected Information Gains for Experimental Designs With Application to the Random Fatigue-Limit Model , 2003 .

[15]  D. Berry Bayesian clinical trials , 2006, Nature Reviews Drug Discovery.

[16]  Xun Huan,et al.  Simulation-based optimal Bayesian experimental design for nonlinear systems , 2011, J. Comput. Phys..

[17]  Costas Papadimitriou,et al.  On prediction error correlation in Bayesian model updating , 2013 .

[18]  Costas Papadimitriou,et al.  Optimal sensor placement for artificial swimmers , 2019, Journal of Fluid Mechanics.

[19]  Andrea du Toit,et al.  Outbreak of a novel coronavirus , 2020, Nature Reviews Microbiology.

[20]  Johannes Zierenberg,et al.  Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions , 2020, Science.

[21]  G. Gao,et al.  A Novel Coronavirus from Patients with Pneumonia in China, 2019 , 2020, The New England journal of medicine.

[22]  J. Ioannidis,et al.  The infection fatality rate of COVID-19 inferred from seroprevalence data , 2020, medRxiv.

[23]  R. Tjian,et al.  Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection , 2020, RNA.

[24]  J. Speagle dynesty: a dynamic nested sampling package for estimating Bayesian posteriors and evidences , 2019, Monthly Notices of the Royal Astronomical Society.

[25]  K. Chaloner,et al.  Bayesian Experimental Design: A Review , 1995 .

[26]  Ruiyun Li,et al.  Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2) , 2020, Science.

[27]  K. Arrow,et al.  Handbook of Mathematical Economics , 1983 .

[28]  D. Adam Special report: The simulations driving the world’s response to COVID-19 , 2020, Nature.

[29]  Patrick Riley,et al.  A Bayesian experimental autonomous researcher for mechanical design , 2020, Science Advances.

[30]  C. Papadimitriou,et al.  The effect of prediction error correlation on optimal sensor placement in structural dynamics , 2012 .