Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies.

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).

Stable and Robust Sampling Strategies for Compressive Imaging.

In many signal processing applications, one wishes to acquire images that are sparse in transform domains such as spatial finite differences or wavelets using frequency domain samples. For such applications, overwhelming empirical evidence suggests that superior image reconstruction can be obtained through variable density sampling strategies that concentrate on lower frequencies. The wavelet and Fourier transform domains are not incoherent because low-order wavelets and low-order frequencies are correlated, so compressive sensing theory does not immediately imply sampling strategies and reconstruction guarantees. In this paper, we turn to a more refined notion of coherence-the so-called local coherence-measuring for each sensing vector separately how correlated it is to the sparsity basis. For Fourier measurements and Haar wavelet sparsity, the local coherence can be controlled and bounded explicitly, so for matrices comprised of frequencies sampled from a suitable inverse square power-law density, we can prove the restricted isometry property with near-optimal embedding dimensions. Consequently, the variable-density sampling strategy we provide allows for image reconstructions that are stable to sparsity defects and robust to measurement noise. Our results cover both reconstruction by ℓ1-minimization and total variation minimization. The local coherence framework developed in this paper should be of independent interest, as it implies that for optimal sparse recovery results, it suffices to have bounded average coherence from sensing basis to sparsity basis-as opposed to bounded maximal coherence-as long as the sampling strategy is adapted accordingly.