Sensitivity and identifiability analysis of COVID-19 pandemic models

Modeling county level COVID-19 transmission in the greater St. Louis area: Challenges of uncertainty and identifiability when fitting mechanistic models to time-varying processes

We use a compartmental model with a time-varying transmission parameter to describe county level COVID-19 transmission in the greater St. Louis area of Missouri and investigate the challenges in fitting such a model to time-varying processes. We fit this model to synthetic and real confirmed case and hospital discharge data from May to December 2020 and calculate uncertainties in the resulting parameter estimates. We also explore non-identifiability within the estimated parameter set. We find that the death rate of infectious non-hospitalized individuals, the testing parameter and the initial number of exposed individuals are not identifiable based on an investigation of correlation coefficients between pairs of parameter estimates. We also explore how this non-identifiability ties back into uncertainties in the estimated parameters and find that it inflates uncertainty in the estimates of our time-varying transmission parameter. However, we do find that R0 is not highly affected by non-identifiability of its constituent components and the uncertainties associated with the quantity are smaller than those of the estimated parameters. Parameter values estimated from data will always be associated with some uncertainty and our work highlights the importance of conducting these analyses when fitting such models to real data. Exploring identifiability and uncertainty is crucial in revealing how much we can trust the parameter estimates.

Mathematical Modeling and Short-Term Forecasting of the COVID-19 Epidemic in Bulgaria: SEIRS Model with Vaccination

Data from the World Health Organization indicate that Bulgaria has the second-highest COVID-19 mortality rate in the world and the lowest vaccination rate in the European Union. In this context, to find the crucial epidemiological parameters that characterize the ongoing pandemic in Bulgaria, we introduce an extended SEIRS model with time-dependent coefficients. In addition to this, vaccination and vital dynamics are included in the model. We construct an appropriate Cauchy problem for a system of nonlinear ordinary differential equations and prove that its unique solution possesses some biologically reasonable features. Furthermore, we propose a numerical scheme and give an algorithm for the parameters identification in the obtained discrete problem. We show that the found values are close to the parameters values in the original differential problem. Based on the presented analysis, we develop a strategy for short-term prediction of the spread of the pandemic among the host population. The proposed model, as well as the methods and algorithms for parameters identification and forecasting, could be applied to COVID-19 data in every single country in the world.

Agent-based modeling of COVID-19 outbreaks for New York state and UK: Parameter identification algorithm

This paper uses Covasim, an agent-based model (ABM) of COVID-19, to evaluate and scenarios of epidemic spread in New York State (USA) and the UK. Epidemiological parameters such as contagiousness (virus transmission rate), initial number of infected people, and probability of being tested depend on the region's demographic and geographical features, the containment measures introduced; they are calibrated to data about COVID-19 spread in the region of interest. At the first stage of our study, epidemiological data (numbers of people tested, diagnoses, critical cases, hospitalizations, and deaths) for each of the mentioned regions were analyzed. The data were characterized in terms of seasonality, stationarity, and dependency spaces, and were extrapolated using machine learning techniques to specify unknown epidemiological parameters of the model. At the second stage, the Optuna optimizer based on the tree Parzen estimation method for objective function minimization was applied to determine the model's unknown parameters. The model was validated with the historical data of 2020. The modeled results of COVID-19 spread in New York State and the UK have demonstrated that if the level of testing and containment measures is preserved, the number of positive cases in New York State remain the same during March of 2021, while in the UK it will reduce.