Stochastic transmission in epidemiological models.

Recent empirical evidence suggests that the transmission coefficient in susceptible-exposed-infected-removed-like (SEIR-like) models evolves with time, presenting random patterns, and some stylized facts, such as mean-reversion and jumps. To address such observations we propose the use of jump-diffusion stochastic processes to parameterize the transmission coefficient in an SEIR-like model that accounts for death and time-dependent parameters. We provide a detailed theoretical analysis of the proposed model proving the existence and uniqueness of solutions as well as studying its asymptotic behavior. We also compare the proposed model with some variations possibly including jumps. The forecast performance of the considered models, using reported COVID-19 infections from New York City, is then tested in different scenarios. Despite the simplicity of the epidemiological model, by considering stochastic transmission, the forecasted scenarios were fairly accurate.

Time-dependent vaccine efficacy estimation quantified by a mathematical model.

In this paper we calculate the variation of the estimated vaccine efficacy (VE) due to the time-dependent force of infection resulting from the difference between the moment the Clinical Trial (CT) begins and the peak in the outbreak intensity. Using a simple mathematical model we tested the hypothesis that the time difference between the moment the CT begins and the peak in the outbreak intensity determines substantially different values for VE. We exemplify the method with the case of the VE efficacy estimation for one of the vaccines against the new coronavirus SARS-CoV-2.

Bayesian inference and wind field statistical modeling applied to multiple source estimation.

We present a methodology to identify multiple pollutant sources in the atmosphere that combines a data-driven dispersion model with Bayesian inference and uncertainty quantification. The dispersion model accounts for a realistic wind field based on the output of a multivariate dynamic linear model (DLM), estimated from measured wind components time series. The forward problem solution, described by an adjoint transient advection-diffusion partial differential equation, is then obtained using an appropriately stabilized finite element formulation. The Bayesian inference tool accounts for uncertainty in the concentration data and automatically states the balance between the prior and the likelihood. The source parameters are estimated by a Metropolis in Gibbs Monte Carlo Markov chain (MCMC) algorithm with adaptive steps. The MCMC algorithm is initialized with a maximum a posteriori estimator obtained with particle swarm optimization to accelerate convergence. Finally, the proposed methodology seems to outperform inversion techniques from previous works.

Time-dependent vaccine efficacy estimation quantified by a mathematical model

In this paper we calculate the variation of the estimated vaccine efficacy (VE) due to the time-dependent force of infection resulting from the difference between the moment the Clinical Trial (CT) begins and the peak in the outbreak intensity. Using a simple mathematical model we tested the hypothesis that the time difference between the moment the CT begins and the peak in the outbreak intensity determines substantially different values for VE. We exemplify the method with the case of the VE efficacy estimation for one of the vaccines against the new coronavirus SARS-CoV-2.

On the role of financial support programs in mitigating the SARS-CoV-2 spread in Brazil.

BACKGROUND: During 2020, there were no effective treatments or vaccines against SARS-CoV-2. The most common disease contention measures were social distance (social isolation), the use of face masks and lockdowns. In the beginning, numerous countries have succeeded to control and reduce COVID-19 infections at a high economic cost. Thus, to alleviate such side effects, many countries have implemented socioeconomic programs to fund individuals that lost their jobs and to help endangered businesses to survive. METHODS: We assess the role of a socioeconomic program, so-called "Auxilio Emergencial" (AE), during 2020 as a measure to mitigate the Coronavirus Disease 2019 (COVID-19) outbreak in Brazil. For each Brazilian State, we estimate the time-dependent reproduction number from daily reports of COVID-19 infections and deaths using a Susceptible-Exposed-Infected-Recovered-like (SEIR-like) model. Then, we analyse the correlations between the reproduction number, the amount of individuals receiving governmental aid, and the index of social isolation based on mobile phone information. RESULTS: We observed significant positive correlation values between the average values by the AE and median values of an index accounting for individual mobility. We also observed significantly negative correlation values between the reproduction number and this index on individual mobility. Using the simulations of a susceptible-exposed-infected-removed-like model, if the AE was not operational during the first wave of COVID-19 infections, the accumulated number of infections and deaths could be 6.5 (90% CI: 1.3-21) and 7.9 (90% CI: 1.5-23) times higher, respectively, in comparison with the actual implementation of AE. CONCLUSIONS: Our results suggest that the AE implemented in Brazil had a significant influence on social isolation by allowing those in need to stay at home, which would reduce the expected numbers of infections and deaths.

The impact of COVID-19 vaccination delay: A data-driven modeling analysis for Chicago and New York City.

BACKGROUND: By the beginning of December 2020, some vaccines against COVID-19 already presented efficacy and security, which qualify them to be used in mass vaccination campaigns. Thus, setting up strategies of vaccination became crucial to control the COVID-19 pandemic. METHODS: We use daily COVID-19 reports from Chicago and New York City (NYC) from 01-Mar2020 to 28-Nov-2020 to estimate the parameters of an SEIR-like epidemiological model that accounts for different severity levels. To achieve data adherent predictions, we let the model parameters to be time-dependent. The model is used to forecast different vaccination scenarios, where the campaign starts at different dates, from 01-Oct-2020 to 01-Apr-2021. To generate realistic scenarios, disease control strategies are implemented whenever the number of predicted daily hospitalizations reaches a preset threshold. RESULTS: The model reproduces the empirical data with remarkable accuracy. Delaying the vaccination severely affects the mortality, hospitalization, and recovery projections. In Chicago, the disease spread was under control, reducing the mortality increment as the start of the vaccination was postponed. In NYC, the number of cases was increasing, thus, the estimated model predicted a much larger impact, despite the implementation of contention measures. The earlier the vaccination campaign begins, the larger is its potential impact in reducing the COVID-19 cases, as well as in the hospitalizations and deaths. Moreover, the rate at which cases, hospitalizations and deaths increase with the delay in the vaccination beginning strongly depends on the shape of the incidence of infection in each city.

Uncertainty quantification and atmospheric source estimation with a discrepancy-based and a state-dependent adaptative MCMC.

We address the source characterization of atmospheric releases using adaptive strategies in Bayesian inference in combination with the numerical solution of the dispersion problem by a stabilized finite element method and uncertainty quantification in the measurements. The adaptive techniques accelerate the convergence of Monte Carlo Markov Chain (MCMC) algorithms, leading to accurate reconstructions of the source parameters. Such accuracy is illustrated by the comparison with results from previous works. Moreover, the technique used to simulate the corresponding dispersion problem allowed us to introduce relevant meteorological information. The uncertainty quantification also improves the quality of reconstructions. Numerical examples using data from the Copenhagen experimental campaign illustrate the effectiveness of the proposed methodology. We found errors in reconstructions ranging from 0.11% to 8.67% of the size of the search region, which is similar to results found in previous works using deterministic techniques, with comparable computational time.

Estimating, monitoring, and forecasting COVID-19 epidemics: a spatiotemporal approach applied to NYC data.

We propose a susceptible-exposed-infective-recovered-type (SEIR-type) meta-population model to simulate and monitor the (COVID-19) epidemic evolution. The basic model consists of seven categories, namely, susceptible (S), exposed (E), three infective classes, recovered (R), and deceased (D). We define these categories for n age and sex groups in m different spatial locations. Therefore, the resulting model contains all epidemiological classes for each age group, sex, and location. The mixing between them is accomplished by means of time-dependent infection rate matrices. The model is calibrated with the curve of daily new infections in New York City and its boroughs, including census data, and the proportions of infections, hospitalizations, and deaths for each age range. We finally obtain a model that matches the reported curves and predicts accurate infection information for different locations and age classes.

Source characterization of airborne pollutant emissions by hybrid metaheuristic/gradient-based optimization techniques.

We propose a methodology to estimate single and multiple emission sources of atmospheric contaminants. It combines hybrid metaheuristic/gradient-descent optimization techniques and Tikhonov-type regularization. The dispersion problem is solved by the Galerkin/Least-squares finite element formulation, which allows more realistic modeling. The accuracy of the proposed inversion model is tested under different contexts with experimental data. To identify single and multiple emissions, we use experimental field data. We consider different configurations for both the Tikhonov-type functional and optimization techniques. Several single and composite data misfit functions are tested. We also use a discrepancy-based choice rule for the regularization parameter. The resulting inversion tool is highly versatile and presents accurate results under different contexts with a competitive computational cost.