Pooled testing of traced contacts under superspreading dynamics

Testing is recommended for all close contacts of confirmed COVID-19 patients. However, existing pooled testing methods are oblivious to the circumstances of contagion provided by contact tracing. Here, we build upon a well-known semi-adaptive pooled testing method, Dorfman’s method with imperfect tests, and derive a simple pooled testing method based on dynamic programming that is specifically designed to use information provided by contact tracing. Experiments using a variety of reproduction numbers and dispersion levels, including those estimated in the context of the COVID-19 pandemic, show that the pools found using our method result in a significantly lower number of tests than those found using Dorfman’s method. Our method provides the greatest competitive advantage when the number of contacts of an infected individual is small, or the distribution of secondary infections is highly overdispersed. Moreover, it maintains this competitive advantage under imperfect contact tracing and significant levels of dilution.Author summary: Due to the emergence of COVID-19, pooled testing has gained significant attention as a method for allocating testing resources more efficiently. In this context, the majority of existing pooled testing methods for the identification of infected individuals are agnostic to the circumstances of contagion. However, individuals for whom a test is ordered are usually traced contacts of an infectious person—they are secondary infections. As a result, their infection statuses are correlated. In this work, we propose a novel pooled testing method that makes explicit use of epidemic parameters describing the distribution of secondary infections. Our method partitions an infected individual’s contacts into pools whose sizes make more efficient use of the available tests. Extensive simulations under a variety of epidemiological conditions informed by the COVID-19 literature show that our method can significantly decrease the expected number of tests under superspreading dynamics, i.e., when the distribution of secondary infections exhibits high variance. The simulations also show that our method maintains its advantageous performance under imperfect conditions, such as significant dilution effects or incomplete contact tracing.