Abstract
Estimates of the reproductive number for novel pathogens such as severe acute respiratory syndrome coronavirus 2 are essential for understanding the potential trajectory of the epidemic and the level of intervention that is needed to bring the epidemic under control. However, most methods for estimating the basic reproductive number (R0) and time-varying effective reproductive number (Rt) assume that the fraction of cases detected and reported is constant through time. We explore the impact of secular changes in diagnostic testing and reporting on estimates of R0 and Rt using simulated data. We then compare these patterns to data on reported cases of coronavirus disease and testing practices from different states in the United States from March 4 to August 30, 2020. We find that changes in testing practices and delays in reporting can result in biased estimates of R0 and Rt. Examination of changes in the daily number of tests conducted and the percent of patients testing positive may be helpful for identifying the potential direction of bias. Changes in diagnostic testing and reporting processes should be monitored and taken into consideration when interpreting estimates of the reproductive number of coronavirus disease.
Highlights
The initial stages of the COVID-19 epidemic in the United States (US) were characterized by difficulties in delivering and administering diagnostic tests [1]
Based on our simulations (Table S1, Fig. S1), the likelihood and degree to which R0 and reproductive number (Rt) are biased depends on the manner in which diagnostic testing practices and reporting changes over time
When the fraction of incident cases detected and reported is constant over time and testing capacity scales with the number of “true” cases, the number of confirmed positive cases provides an unbiased estimate of R0, despite possible delays in the reporting process (Fig. 1A, Fig. S2)
Summary
The initial stages of the COVID-19 epidemic in the United States (US) were characterized by difficulties in delivering and administering diagnostic tests [1]. All initial and confirmatory testing needed to be carried out by the CDC, which led to reporting delays and capacity issues early in the epidemic [4, 5]. Tests were only administered to individuals with a history of travel to certain countries or known contact with a positive case. By the time testing capacity increased, state and local health departments were faced with heavy demand for COVID-19 testing. Individuals meeting specific criteria could receive a test, and these criteria have varied from state to state and over time (see Supporting Information (SI) Dataset)
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