COVIDStrategyCalculator: A software to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation

Abstract

While large-scale vaccination campaigns against SARS-CoV-2 are rolled out at the time of writing, non-pharmaceutical interventions (NPIs), including the isolation of infected individuals and quarantine of exposed individuals, remain central measures to contain the spread of SARS-CoV-2. Strategies that combine NPIs with innovative SARS-CoV-2 testing strategies may increase containment efficacy and help to shorten quarantine durations. We developed a user-friendly software tool that implements a recently published stochastic within-host viral dynamics model that captures temporal attributes of the viral infection, such as test sensitivity, infectiousness, and the occurrence of symptoms. Based on this model, the software allows to evaluate the efficacy of user-defined, arbitrary NPI and testing strategies in reducing the transmission potential in different contexts. The software thus enables decision makers to explore NPI strategies and perform hypothesis testing, e.g., with regard to the utilization of novel diagnostics or with regard to containing novel virus variants.

Keywords: COVID; PCR; RDT; SARS-CoV-2; antigen; non-pharmaceutic intervention; public health; software; strategy; testing.

Figure 1

Intra-host viral dynamics (A) Stochastic transit compartment model of intra-host viral dynamics. Model details are provided in an associated article. (B–D) Model simulation with regard to time-dependent (B) virus detectability by PCR, (C) infectiousness, and (D) the probability of experiencing symptoms.

Figure 2

Screenshot of the COVIDStrategyCalculator The main window consists of four components: time course trajectories (1), test efficacy reports (2), a result log (3), and user input (4). Reported results include the simulation settings, the pre- and post-procedure probability of infectiousness, as well as the efficacy estimates, depicted as “% relative risk” and the “% risk reduction.”

Figure 3

User input panels of the COVIDStrategyCalculator (A) Zoom-in on the NPI configuration window. (B) Model parameter input tab. (C) Prevalence estimator input tab. Details of the usage and meaning of the different input fields are provided in the text.