A deterministic compartmental model for the transition between variants in the spread of Covid-19 in Italy
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ABSTRACT:
SUBMITTER: Saviano M
PROVIDER: S-EPMC10645303 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:Novel Covid-19 has had a huge impact on the world's population since December 2019. The very rapid spreading of the virus worldwide, with its heavy toll of death and overload of the healthcare systems, induced the scientific community to focus on understanding, monitoring and foreseeing the epidemic evolution, weighing up the impact of different containment measures. An immense literature was produced in few months. Many papers were focused on predicting the peak features through a variety of different models. In the present paper, combining the surveillance data-set with data on mobility and testing, we develop a deterministic compartment model aimed at performing a retrospective analysis to understand the main modifications occurred to the characteristic parameters that regulate the epidemic spreading. We find that, besides self-protective behaviors, a reduction of susceptibility should have occurred in order to explain the fast descent of the epidemic after the peak. A sensitivity analysis of the basic reproduction number, in response to variations of the epidemiological parameters that can be influenced by policy-makers, shows the primary importance of a rigid isolation procedure for the diagnosed cases, combined with an intensive effort in performing extended testing campaigns. Future scenarios depend on the ability to protect the population from the injection of new cases from abroad, and to pursue in applying rigid self-protective measures.
| S-EPMC7647079 | biostudies-literature
Project description:Although the Covid-19 pandemic is still ongoing, the environmental factors beyond virus transmission are only partially known. This statistical study has the aim to identify the key factors that have affected the virus spread during the early phase of pandemic in Italy, among a wide set of potential determinants concerning demographics, environmental pollution and climate. Because of its heterogeneity in pollution levels and climate conditions, Italy provides an ideal scenario for an ecological study. Moreover, the selected period excludes important confounding factors, as different virus variants, restriction policies or vaccines. The short-term relationship between the infection maximum increase and demographic, pollution and meteo-climatic parameters was investigated, including both winter-spring and summer 2020 data, also focusing separately on the two seasonal periods and on North vs Centre-South. Among main results, the importance of population size confirmed social distancing as a key management option. The pollution hazardous role undoubtedly emerged, as NO2 affected infection increase in all the studied scenarios, PM2.5 manifested its impact in North of Italy, while O3 always showed a protective action. Whereas higher temperatures were beneficial, especially in the cold season with also wind and relative humidity, solar irradiance was always relevant, revealing several significant interactions with other co-factors. Presented findings address the importance of the environment in Sars-CoV-2 spread and indicated that special carefulness should be taken in crowded areas, especially if they are highly polluted and weakly exposed to sun. The results suggest that containment of future epidemics similar to Covid-19 could be supported by reducing environmental pollution, achieving safer social habits and promoting preventive health care for better immune system response, as an only comprehensive strategy.
| S-EPMC10079324 | biostudies-literature
Project description:The last year of Covid-19 pandemic has been characterized by the continuous chase between the vaccination campaign and the appearance of new variants that puts further obstacles to the possibility of eradicating the virus and returning to normality in a short period. In the present paper we develop a deterministic compartmental model to describe the evolution of the Covid-19 in Italy as a combined effect of vaccination campaign, new variant spreading and mobility restrictions. Particular attention is given to the mechanism of waning immunity, appropriately timed with respect to the effective progress of the vaccination campaign in Italy. We perform a retrospective analysis in order to explore the role that different mechanisms, such as behavioral changes, variation of the population mobility, seasonal variability of the virus infectivity, and spreading of new variants have had in shaping the epidemiological curve. We find that, in the large time window considered, the most relevant mechanism is the seasonal variation in the stability of the virus, followed by the awareness mechanism, that induces individuals to increase/relax self-protective measures when the number of active cases increases/decreases. The appearance of the Delta variant and the mobility variations have had instead only marginal effects. In absence of vaccines the emerging scenario would have been dramatic with a percentage difference in the number of total infections and total deaths, in both cases, larger than fifty per cent. The model also predicts the appearance of a more contagious variant (the Omicron variant) and its becoming dominant in January 2022.
| S-EPMC9269459 | biostudies-literature
Project description:BackgroundThe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in China at the end of 2019 and it has since spread in few months all over the World. Italy was one of the first Western countries who faced the health emergency and is one of the countries most severely affected by the pandemic. The diffusion of Coronavirus disease 2019 (COVID-19) in Italy has followed a peculiar spatial pattern, however the attention of the scientific community has so far focussed almost exclusively on the prediction of the evolution of the disease over time.MethodsOfficial freely available data about the number of infected at the finest possible level of spatial areal aggregation (Italian provinces) are used to model the spatio-temporal distribution of COVID-19 infections at local level. An endemic-epidemic time-series mixed-effects generalized linear model for areal disease counts has been implemented to understand and predict spatio-temporal diffusion of the phenomenon.ResultsThree subcomponents characterize the fitted model. The first describes the transmission of the illness within provinces; the second accounts for the transmission between nearby provinces; the third is related to the evolution of the disease over time. At the local level, the provinces first concerned by containment measures are those that are not affected by the effects of spatial neighbours. On the other hand, the component accounting for the spatial interaction with surrounding areas is prevalent for provinces that are strongly involved by contagions. Moreover, the proposed model provides good forecasts for the number of infections at local level while controlling for delayed reporting.ConclusionsA strong evidence is found that strict control measures implemented in some provinces efficiently break contagions and limit the spread to nearby areas. While containment policies may potentially be more effective if planned considering the peculiarities of local territories, the effective and homogeneous enforcement of control measures at national level is needed to prevent the disease control being delayed or missed as a whole. This may also apply at international level where, as it is for the European Union or the United States, the internal border checks among states have largely been abolished.
| S-EPMC7509829 | biostudies-literature
Project description:IntroductionThe complex dynamics of the coronavirus disease 2019 (COVID-19) pandemic has made obtaining reliable long-term forecasts of the disease progression difficult. Simple mechanistic models with deterministic parameters are useful for short-term predictions but have ultimately been unsuccessful in extrapolating the trajectory of the pandemic because of unmodelled dynamics and the unrealistic level of certainty that is assumed in the predictions.Methods and analysisWe propose a 22-compartment epidemiological model that includes compartments not previously considered concurrently, to account for the effects of vaccination, asymptomatic individuals, inadequate access to hospital care, post-acute COVID-19 and recovery with long-term health complications. Additionally, new connections between compartments introduce new dynamics to the system and provide a framework to study the sensitivity of model outputs to several concurrent effects, including temporary immunity, vaccination rate and vaccine effectiveness. Subject to data availability for a given region, we discuss a means by which population demographics (age, comorbidity, socioeconomic status, sex and geographical location) and clinically relevant information (different variants, different vaccines) can be incorporated within the 22-compartment framework. Considering a probabilistic interpretation of the parameters allows the model's predictions to reflect the current state of uncertainty about the model parameters and model states. We propose the use of a sparse Bayesian learning algorithm for parameter calibration and model selection. This methodology considers a combination of prescribed parameter prior distributions for parameters that are known to be essential to the modelled dynamics and automatic relevance determination priors for parameters whose relevance is questionable. This is useful as it helps prevent overfitting the available epidemiological data when calibrating the parameters of the proposed model. Population-level administrative health data will serve as partial observations of the model states.Ethics and disseminationApproved by Carleton University's Research Ethics Board-B (clearance ID: 114596). Results will be made available through future publication.
| S-EPMC8914398 | biostudies-literature
Project description:The practicality of administrative measures for covid-19 prevention is crucially based on quantitative information on impacts of various covid-19 transmission influencing elements, including social distancing, contact tracing, medical facilities, vaccine inoculation, etc. A scientific approach of obtaining such quantitative information is based on epidemic models of SIR family. The fundamental SIR model consists of S-susceptible, I-infected, and R-recovered from infected compartmental populations. To obtain the desired quantitative information, these compartmental populations are estimated for varying metaphoric parametric values of various transmission influencing elements, as mentioned above. This paper introduces a new model, named SEIRRPV model, which, in addition to the S and I populations, consists of the E-exposed, Re -recovered from exposed, R-recovered from infected, P-passed away, and V-vaccinated populations. Availing of this additional information, the proposed SEIRRPV model helps in further strengthening the practicality of the administrative measures. The proposed SEIRRPV model is nonlinear and stochastic, requiring a nonlinear estimator to obtain the compartmental populations. This paper uses cubature Kalman filter (CKF) for the nonlinear estimation, which is known for providing an appreciably good accuracy at a fairly small computational demand. The proposed SEIRRPV model, for the first time, stochastically considers the exposed, infected, and vaccinated populations in a single model. The paper also analyzes the non-negativity, epidemic equilibrium, uniqueness, boundary condition, reproduction rate, sensitivity, and local and global stability in disease-free and endemic conditions for the proposed SEIRRPV model. Finally, the performance of the proposed SEIRRPV model is validated for real-data of covid-19 outbreak.
| S-EPMC9968492 | biostudies-literature
Project description:We consider the family of edge-based compartmental models for epidemic spread developed in Miller et al. (J R Soc Interface 9(70):890-906, 2012). These models allow for a range of complex behaviors, and in particular allow us to explicitly incorporate duration of a contact into our mathematical models. Our focus here is to identify conditions under which simpler models may be substituted for more detailed models, and in so doing we define a hierarchy of epidemic models. In particular we provide conditions under which it is appropriate to use the standard mass action SIR model, and we show what happens when these conditions fail. Using our hierarchy, we provide a procedure leading to the choice of the appropriate model for a given population. Our result about the convergence of models to the mass action model gives clear, rigorous conditions under which the mass action model is accurate.
| S-EPMC3552133 | biostudies-literature
Project description: Not available
| S-EPMC9114753 | biostudies-literature
Project description:BackgroundIn the context of the fourth wave of the COVID-19 pandemic in Italy, which occurred in correspondence with the outbreak of the Omicron variant, it became fundamental to assess differences in the risk of severe disease between the Omicron variant and the earlier SARS-CoV-2 variants that were still in circulation despite Omicron becoming prevalent.MethodsWe collected data on 2,267 genotyped PCR-positive swab tests and assessed whether the presence of symptoms, risk of hospitalization, and recovery times were significantly different between Omicron and the earlier variants. Multivariable models adjusted for sex, age class, citizenship, comorbidities, and symptomatology allowed assessing the difference in outcomes between Omicron and the earlier variants according to vaccination status and timing of administration.ResultsCompared to the earlier variants in the same period, Omicron was less symptomatic, resulted in fewer hospital admissions for those who were unvaccinated and for those who were already immunized after the booster dose, and was associated with quicker recovery, yet not in subjects with three vaccination doses.ConclusionDespite being milder, Omicron's higher transmissibility and vaccine resistance should not lead to underrating its damage potential, especially with regard to hospital and health service saturation.
| S-EPMC10910966 | biostudies-literature
Project description:Predicting epidemic evolution is essential for making informed decisions and guiding the implementation of necessary countermeasures. Computational models are vital tools that provide insights into illness progression and enable early detection, proactive intervention, and targeted preventive measures. This paper introduces Sybil, a framework that integrates machine learning and variant-aware compartmental models, leveraging a fusion of data-centric and analytic methodologies. To validate and evaluate Sybil's forecasts, we employed COVID-19 data from several European and U.S. states. The dataset included the number of new and recovered cases, fatalities, and variant presence over time. We evaluate the forecasting precision of Sybil in periods in which there is a change in the trend of the pandemic evolution or a new variant appears. Results demonstrate that Sybil outperforms conventional data-centric approaches, being able to forecast accurately the changes in the trend, the magnitude of these changes, and the future prevalence of new variants.
| S-EPMC11333698 | biostudies-literature