The COVID-19 pandemic highlighted the importance of non-traditional data sources, such as mobile phone data, to inform effective public health interventions and monitor adherence to such measures. Previous studies showed how socioeconomic characteristics shaped population response during restrictions and how repeated interventions eroded adherence over time. Less is known about how different population strata changed their response to repeated interventions and how this impacted the resulting mobility network. We study population response during the first and second infection waves of the COVID-19 pandemic in Chile and Spain. Via spatial lag and regression models, we investigate the adherence to mobility interventions at the municipality level in Chile, highlighting the significant role of wealth, labor structure, COVID-19 incidence, and network metrics characterizing business-as-usual municipality connectivity in shaping mobility changes during the two waves. We assess network structural similarities in the two periods by defining mobility hotspots and traveling probabilities in the two countries. As a proof of concept, we simulate and compare outcomes of an epidemic diffusion occurring in the two waves. While differences exist between factors associated with mobility reduction across waves in Chile, underscoring the dynamic nature of population response, our analysis reveals the resilience of the mobility network across the two waves. We test the robustness of our findings recovering similar results for Spain. Finally, epidemic modeling suggests that historical mobility data from past waves can be leveraged to inform future disease spatial invasion models in repeated interventions. This study highlights the value of historical mobile phone data for building pandemic preparedness and lessens the need for real-time data streams for risk assessment and outbreak response. Our work provides valuable insights into the complex interplay of factors driving mobility across repeated interventions, aiding in developing targeted mitigation strategies.

We present Epydemix, an open-source Python package for the development and calibration of stochastic compartmental epidemic models. The framework supports flexible model structures that incorporate demographic information, age-stratified contact matrices, and dynamic public health interventions. A key feature of Epydemix is its integration of Approximate Bayesian Computation (ABC) techniques to perform parameter inference and model calibration through comparison between observed and simulated data. The package offers a range of ABC methods such as simple rejection sampling, simulation-budget-constrained rejection, and Sequential Monte Carlo (ABC-SMC). Epydemix is modular, and supports ABC-based calibration both for models defined within the package and for those developed externally. To demonstrate the computational framework capabilities, we discuss usage examples that include (i) simulating an intervention-driven model with time-varying parameters, and (ii) benchmarking calibration performance using synthetic epidemic data. We further illustrate the use of the package in a retrospective case study that includes scenario projections under alternative intervention assumptions. By lowering the barrier for the implementation of computational and inference approaches, Epydemix makes epidemic modeling more accessible to a wider range of users, from academic researchers to public health professionals.

The initial rollout of COVID-19 vaccines has been challenged by logistical issues, limited availability of doses, scarce healthcare capacity, spotty acceptance, and the emergence of variants of concern. Non-pharmaceutical interventions (NPIs) have been critical to support these phases. However, vaccines may have prompted behavioural relaxation, potentially reducing NPIs adherence. Epidemic models have explored this phenomenon, but they have not been validated against data. Moreover, recent surveys provide conflicting results on the matter. The extent of behavioural relaxation induced by COVID-19 vaccines is still unclear. Here, we aim to study this phenomenon in four regions. We implement five realistic epidemic models which include age structure, multiple virus strains, NPIs, and vaccinations. One of the models acts as a baseline, while the others extend it including different behavioural relaxation mechanisms. First, we calibrate the baseline model and run counterfactual scenarios to quantify the impact of vaccinations and NPIs. Our results confirm the critical role of both in reducing infection and mortality rates. Second, using different metrics, we calibrate the behavioural models and compare them to each other and to the baseline. Including behavioural relaxation leads to a better fit of weekly deaths in three regions. However, the improvements are limited to a [Formula: see text] reduction in weighted mean absolute percentage errors and these gains are generally offset by models' increased complexity. Overall, we do not find clear signs of behavioural relaxation induced by COVID-19 vaccines on weekly deaths. Furthermore, our results suggest that if this phenomenon occurred, it generally involved only a minority of the population. Our work contributes to the retrospective validation of epidemic models developed amid the COVID-19 Pandemic and underscores the issue of non-identifiability of complex social mechanisms.

We analyze the effectiveness of the first six months of vaccination campaign against SARS-CoV-2 in Italy by using a computational epidemic model which takes into account demographic, mobility, vaccines data, as well as estimates of the introduction and spreading of the more transmissible Alpha variant. We consider six sub-national regions and study the effect of vaccines in terms of number of averted deaths, infections, and reduction in the Infection Fatality Rate (IFR) with respect to counterfactual scenarios with the actual non-pharmaceuticals interventions but no vaccine administration. Furthermore, we compare the effectiveness in counterfactual scenarios with different vaccines allocation strategies and vaccination rates. Our results show that, as of 2021/07/05, vaccines averted 29, 350 (IQR: [16, 454-42, 826]) deaths and 4, 256, 332 (IQR: [1, 675, 564-6, 980, 070]) infections and a new pandemic wave in the country. During the same period, they achieved a -22.2% (IQR: [-31.4%; -13.9%]) IFR reduction. We show that a campaign that would have strictly prioritized age groups at higher risk of dying from COVID-19, besides frontline workers and the fragile population, would have implied additional benefits both in terms of avoided fatalities and reduction in the IFR. Strategies targeting the most active age groups would have prevented a higher number of infections but would have been associated with more deaths. Finally, we study the effects of different vaccination intake scenarios by rescaling the number of available doses in the time period under study to those administered in other countries of reference. The modeling framework can be applied to other countries to provide a mechanistic characterization of vaccination campaigns worldwide.

The promise of efficacious vaccines against SARS-CoV-2 is fulfilled and vaccination campaigns have started worldwide. However, the fight against the pandemic is far from over. Here, we propose an age-structured compartmental model to study the interplay of disease transmission, vaccines rollout, and behavioural dynamics. We investigate, via in-silico simulations, individual and societal behavioural changes, possibly induced by the start of the vaccination campaigns, and manifested as a relaxation in the adoption of non-pharmaceutical interventions. We explore different vaccination rollout speeds, prioritization strategies, vaccine efficacy, as well as multiple behavioural responses. We apply our model to six countries worldwide (Egypt, Peru, Serbia, Ukraine, Canada, and Italy), selected to sample diverse socio-demographic and socio-economic contexts. To isolate the effects of age-structures and contacts patterns from the particular pandemic history of each location, we first study the model considering the same hypothetical initial epidemic scenario in all countries. We then calibrate the model using real epidemiological and mobility data for the different countries. Our findings suggest that early relaxation of safe behaviours can jeopardize the benefits brought by the vaccine in the short term: a fast vaccine distribution and policies aimed at keeping high compliance of individual safe behaviours are key to mitigate disease resurgence.

In this work, we aim to determine the main factors driving self-initiated behavioral changes during the seasonal flu.To this end, we designed and deployed a questionnaire via Influweb, a Web platform for participatory surveillance in Italy, during the 2017 -18 and 2018 -19 seasons.We collected 599 surveys completed by 434 users.The data provide socio-demographic information, level of concerns about the flu, past experience with illnesses, and the type of behavioral changes voluntarily implemented by each participant.We describe each response with a set of features and divide them in three target categories.These describe those that report i) no (26%), ii) only moderately (36%), iii) significant (38%) changes in behaviors.In these settings, we adopt machine learning algorithms to investigate the extent to which target variables can be predicted by looking only at the set of features.Notably, 66% of the samples in the category describing more significant changes in behaviors are correctly classified through Gradient Boosted Trees.Furthermore, we investigate the importance of each feature in the classification task and uncover complex relationships between individuals' characteristics and their attitude towards behavioral change.We find that intensity, recency of past illnesses, perceived susceptibility to and perceived severity of an infection are the most significant features in the classification task and are associated to significant changes in behaviors.Overall, the research contributes to the small set of empirical studies devoted to the data-driven characterization of behavioral changes induced by infectious diseases. Author summaryHuman behavior and infectious diseases are linked by a feedback loop.While individuals might change their behavior as a response to an epidemic, such changes might influence the spreading itself.So far, our understanding and characterization of behavioral changes induced by diseases has been strongly limited by the lack of empirical data.As result, the vast majority of research has been focused on theoretical, what if, scenarios.In this work, we collected a unique dataset comprised of 599 surveys submitted by 434 users to the participatory surveillance platform Influweb over the 2017 -18 and 2018 -19 flu seasons.