Estimation of Covid-19 Prevalence Dynamics from Pooled Data

Estimating the prevalence of a disease, such as COVID-19, is necessary for evaluating and mitigating risks of its transmission. Estimates that consider how prevalence changes with time provide more information about these risks but are difficult to obtain due to the necessary survey intensity and commensurate testing costs. Motivated by a dataset on COVID-19, from the University of Notre Dame, we propose pooling and jointly testing multiple samples to reduce testing costs. A nonparametric, hierarchical Bayesian model is used to infer population prevalence from the pooled test results without needing to retest individuals from pools that test positive. This approach is shown to reduce uncertainty compared to individual testing at the same budget and to produce similar estimates compared to individual testing at a much higher budget through simulation studies and an analysis of COVID-19 infections at Notre Dame.