Tuberculosis remains a high burden for Human society despite considerable investments in its control. Unique features in the history of infection and transmission dynamics of tuberculosis pose serious limitations on the direct interpretation of surveillance data and call for models that incorporate latent processes and simulate specific interventions. A transmission model was adjusted to the dataset of active tuberculosis cases reported in Portugal between 2002 and 2009. We estimated key transmission parameters from the data (i.e. time to diagnosis, treatment length, default proportion, proportion of pulmonary TB cases). Using the adjusted model to the Portuguese case, we estimated the total burden of tuberculosis in Portugal. We further performed sensitivity analysis to heterogeneities in susceptibility to infection and exposure intensity. We calculated a mean time to diagnose of 2.81 months and treatment length of 8.80 months in Portugal. The proportion defaulting treatment was calculated as 0.04 and the proportion of pulmonary cases as 0.75. Using these values, we estimated a TB burden of 1.6 million infected persons, corresponding to more than 15% of the Portuguese population. We further described the sensitivity of these estimates to heterogeneity. We showed that the model reproduces well the observed dynamics of the Portuguese data, thus demonstrating its adequacy for devising control strategies for TB and predicting the effects of interventions.

In this paper, we present an age-structured SEIR model that uses contact patterns to reflect the physical distance measures implemented in Portugal to control the COVID-19 pandemic. By using these matrices and proper estimates for the parameters in the model, we were able to ascertain the impact of mitigation strategies employed in the past. Results show that the March 2020 lockdown had an impact on disease transmission, bringing the effective reproduction number ($\mathcal{R}\left(t\right)$) below 1. We estimate that there was an increase in the transmission after the initial lift of the measures on 6 May 2020 that resulted in a second wave that was curbed by the October and November measures. December 2020 saw an increase in the transmission reaching an $\mathcal{R}\left(t\right)$ = 1.45 in early January 2021. Simulations indicate that the lockdown imposed on the 15 January 2021 might reduce the intensive care unit (ICU) demand to below 200 cases in early April if it lasts at least 2 months. As it stands, the model was capable of projecting the number of individuals in each infection phase for each age group and moment in time.

We study—with existence and unicity results—a variant of the SIR model for an infectious disease incorporating both the possibility of a death outcome—in a short period of time—and a regime switch that can account for the mitigation measures used to control the spreading of the infections, such as a total lockdown. This model is parametrised by three parameters: the basic reproduction number, the mortality rate of the infected, and the duration of the disease. We discuss a particular example of application to Portuguese COVID-19 data in two short periods just after the start of the epidemic in 4 March 2020, with the first two cases dated that day. We propose a simple and effective method for the estimation of the main parameters of the disease, namely, the basic reproduction number and the mortality rate of the infected. We correct these estimated values to take into account the asymptomatic non-diagnosed members of the population. We compare the outcome of the model in the cases of the existence, or not, of a regime switch, and under three different scenarios, with a remarkable agreement between model and data deaths in the case of our basis scenario. In a final short remark, we deal with the existence of symmetries for the proposed model.

In diseases with long-term immunity, vaccination is known to increase the average age at infection as a result of the decrease in the pathogen circulation. This implies that a vaccination campaign can have negative effects when a disease is more costly (financial or health-related costs) for higher ages. This work considers an age-structured population transmission model with imperfect vaccination. We aim to compare the social and individual costs of vaccination, assuming that disease costs are age-dependent, while the disease's dynamic is age-independent. A model for pathogen deterministic dynamics in a population consisting of juveniles and adults, assumed to be rational agents, is introduced. The parameter region for which vaccination has a positive social impact is fully characterized and the Nash equilibrium of the vaccination game is obtained. Finally, collective strategies designed to promote voluntary vaccination, without compromising social welfare, are discussed.