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

Abstract

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 a number of realistic scenarios and propose fast and reliable strategies for massive testing procedures. 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%.Interpretation: Altogether this work may help provide a basis for efficient upscaling of current testing procedures, taking the population heterogeneity into account and fine grained towards the desired study populations, e.g. cross-sectional versus health-care workers and adapted mixtures thereof.

Pooling saliva to increase SARS-CoV-2 testing capacity

“…While pooling of samples has been widely proposed as a way to expand testing capacity for large scale screening 9 – 11 , there has been limited empirical evidence on pooling performance to properly inform projections of both feasibility and cost-effectiveness. Therefore, we investigated the potential of pooling saliva for SARS-CoV-2 detection in the laboratory setting, then used our findings to inform a model exploring the benefits of pooled sample testing at different rates of virus prevalence in the population.…”

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

“…Various approaches (such as array testing [23]) have been proposed for the pooling of samples for COVID-19 testing [23][24][25][26]. Optimum pool size and approach depend on factors such as the prevalence of the COVID-19 in the population, and the sensitivity of the test utilized [23,27]. dPCR, which has shown to have higher sensitivity in comparison to RT-PCR, has been proposed as an alternative for testing pooled samples [28].…”

“…Hi-throughput pooled tests [23][24][25][26][27][28] Pooled sequencing using barcodes [93] Commercial platforms-Hi-throughput RT-PCR [220] Alternative reagents and protocols. for diagnostic testing to augment shortages and supply chain constraints during pandemic peak [22] Extraction-free protocols to augment shortage of RNA extraction kits for amplification-based tests [154][155][156][157][158][159] for sequencing-based tests [160] Drive-through collection of respiratory samples [142] At-home self-collection of clinical samples to augment conventional sample collection formats [147,149] Antibody tests to measure seroprevalence of SARS-CoV-2 antibodies and understand the extent of community transmission [133,134] Large scale population-wide screening for identification of asymptomatic cases in low-prevalence regions [23,25,26] Screening for infections at clinics/doctor's offices, airports, borders, etc.…”

COVID-19 prevalence estimation by random sampling in population - optimal sample pooling under varying assumptions about true prevalence

“…1. A thorough discussion on group testing algorithms and their merit in testing for SARS-CoV-2 is available in [7].…”

“…Pooling strategies, also called group testing, effectively increase the test capacity and reduces the required number of RT-PCR-based tests. For SARS-CoV-2 pooling has been estimated to potentially reduce costs by 69% [6], use ten-fold fewer tests [7] and clearing 20 times the number of people from isolation with the same number of tests [8]. Note that I will not discuss pooling of SARS-CoV-2 antibody-based tests, since there is currently not enough information about how pooling affects test parameters.…”