Analysis of multistage pooling studies of biological specimens for estimating disease incidence and prevalence

The testing of pooled samples of biological specimens for the purpose of estimating disease prevalence may be more cost effective than testing individual samples, particularly if the prevalence of disease is low. Multistage pooling studies involve testing pools and then sequentially subdividing and testing the positive pools. A simple estimator of disease prevalence and its variance are derived for general multistage pooling studies and are shown to be natural generalizations of Thompson's (1962) original estimators for single-stage pooling studies. The reduction in variance associated with each additional stage is calibrated. The results are extended to estimating disease incidence rates. The methods are used to estimate HIV incidence rates from a prevalence study of early HIV infection using a PCR assay for HIV RNA.