The adoption of containment measures to reduce the amplitude of the epidemic peak is a key aspect in tackling the rapid spread of an epidemic. Classical compartmental models must be modified and studied to correctly describe the effects of forced external actions to reduce the impact of the disease. The importance of social structure, such as the age dependence that proved essential in the recent COVID-19 pandemic, must be considered, and in addition, the available data are often incomplete and heterogeneous, so a high degree of uncertainty must be incorporated into the model from the beginning. In this work we address these aspects, through an optimal control formulation of a socially structured epidemic model in presence of uncertain data. After the introduction of the optimal control problem, we formulate an instantaneous approximation of the control that allows us to derive new feedback controlled compartmental models capable of describing the epidemic peak reduction. The need for long-term interventions shows that alternative actions based on the social structure of the system can be as effective as the more expensive global strategy. The timing and intensity of interventions, however, is particularly relevant in the case of uncertain parameters on the actual number of infected people. Simulations related to data from the first wave of the recent COVID-19 outbreak in Italy are presented and discussed.
In this paper, we show how to modify a compartmental epidemic model, without changing the dimension, such that separable static heterogeneity is taken into account. The derivation is based on the Kermack-McKendrick renewal equation.
Mathematical models are often regarded as recent innovations in the description and analysis of infectious disease outbreaks and epidemics, but simple models have been in use for projection of epidemic trajectories for more than a century. We recently described a single equation model (the incidence decay with exponential adjustment, or IDEA, model) that can be used for short term forecasting. In the mid-19th century, Dr. William Farr developed a single equation approach (Farr's law) for epidemic forecasting. We show here that the two models are in fact identical, and can be expressed in terms…
We consider the edge-based compartmental models for epidemic spread developed in Part I. We show 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, rigo…
In Fall 2020, several European countries reported rapid increases in COVID-19 cases along with growing estimates of the effective reproduction rates. Such an acceleration in epidemic spread is usually attributed to time-dependent effects, e.g. human travel, seasonal behavioral changes, mutations of the pathogen etc. In this case however the acceleration occurred when counter measures such as testing and contact tracing exceeded their capacity limit. Considering Austria as an example, here we show that this dynamics can be captured by a time-independent, i.e. autonomous, compartmental model tha…
This paper presents a novel extension of the edge-based compartmental model for epidemics with arbitrary distributions of transmission and recovery times. Using the message passing approach we also derive a new pairwise-like model for epidemics with Markovian transmission and an arbitrary recovery period. The new pairwise-like model allows one to formally prove that the message passing and edge-based compartmental models are equivalent in the case of Markovian transmission and arbitrary recovery processes. The edge-based and message passing models are conjectured to also be equivalent for arbi…
Compartmental epidemic models have been widely used for predicting the course of epidemics, from estimating the basic reproduction number to guiding intervention policies. Studies commonly acknowledge these models' assumptions but less often justify their validity in the specific context in which they are being used. Our purpose is not to argue for specific alternatives or modifications to compartmental models, but rather to show how assumptions can constrain model outcomes to a narrow portion of the wide landscape of potential epidemic behaviors. This concrete examination of well-known models…
Nowcasting and forecasting of epidemic spreading rely on incidence series of reported cases to derive the fundamental epidemiological parameters for a given pathogen. Two relevant drawbacks for predictions are the unknown fractions of undocumented cases and levels of nonpharmacological interventions, which span highly heterogeneously across different places and times. We describe a simple data-driven approach using a compartmental model including asymptomatic and presymptomatic contagions that allows to estimate both the level of undocumented infections and the value of effective reproductive …
The importance of spatial networks in the spread of an epidemic is an essential aspect in modeling the dynamics of an infectious disease. Additionally, any realistic data-driven model must take into account the large uncertainty in the values reported by official sources, such as the amount of infectious individuals. In this paper we address the above aspects through a hyperbolic compartmental model on networks, in which nodes identify locations of interest, such as cities or regions, and arcs represent the ensemble of main mobility paths. The model describes the spatial movement and interacti…
Modelling SARS-CoV-2 epidemics via compartmental and cellular automaton SEIRS model with temporal immunity and vaccination
Yukhnovskii Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine（乌克兰国家科学院尤赫诺夫斯基凝聚态物理研究所）；Institute of Applied Mathematics and Fundamental Sciences, Lviv Polytechnic National University（利沃夫国立理工大学应用数学与基础科学研究所）
The duration, type and structure of connections between individuals in real-world populations play a crucial role in how diseases invade and spread. Here, we incorporate the aforementioned heterogeneities into a model by considering a dual-layer static-dynamic multiplex network. The static network layer affords tunable clustering and describes an individual's permanent community structure. The dynamic network layer describes the transient connections an individual makes with members of the wider population by imposing constant edge rewiring. We follow the edge-based compartmental modelling app…
IMT School for Advanced Studies Lucca（卢cca高等研究院）；TREE-TOWER S.R.L.（TREE-TOWER有限责任公司）
Computational models for the simulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic evolution would be extremely useful to support authorities in designing healthcare policies and lockdown measures to contain its impact on public health and economy. In Italy, the devised forecasts have been mostly based on a pure data-driven approach, by fitting and extrapolating open data on the epidemic evolution collected by the Italian Civil Protection Center. In this respect, SIR epidemiological models, which start from the description of the nonlinear interactions between…
The paradigm for compartment models in epidemiology assumes exponentially distributed incubation and removal times, which is not realistic in actual populations. Commonly used variations with multiple exponentially distributed variables are more flexible, yet do not allow for arbitrary distributions. We present a new formulation, focussing on the SEIR concept that allows to include general distributions of incubation and removal times. We compare the solution to two types of agent-based model simulations, a spatially homogeneous one where infection occurs by proximity, and a model on a scale-f…
We discuss the failure of monotonicity properties for even simple compartmental epidemic models, for the case where transmission rates are non-constant. We also identify a special case in which monotonicity holds.
Assessing the performance of compartmental and renewal models for learning $R_{t}$ using spatially heterogeneous epidemic simulations on real geographies
In order to model an epidemic, different approaches can be adopted. Mainly, the deterministic approach and the stochastic one. Recently, a large amount of literature has been published using the two approaches. The aim of this paper is to illustrate the usual framework used for commonly adopted compartmental models in epidemiology and introduce variant analytic and numerical tools that interfere on each one of those models, as well as the general related types of existing, ongoing and future possible contributions.
We consider the control of the COVID-19 pandemic through a standard SIR compartmental model. This control is induced by the aggregation of individuals' decisions to limit their social interactions: when the epidemic is ongoing, an individual can diminish his/her contact rate in order to avoid getting infected, but this effort comes at a social cost. If each individual lowers his/her contact rate, the epidemic vanishes faster, but the effort cost may be high. A Mean Field Nash equilibrium at the population level is formed, resulting in a lower effective transmission rate of the virus. We prove …
An analysis of the COVID-19 epidemic is proposed on the basis of the epiMOX dashboard (publicly accessible at https://www.epimox.polimi.it) that deals with data of the epidemic trends and outbreaks in Italy from late February 2020. Our analysis provides an immediate appreciation of the past epidemic development, together with its current trends by fostering a deeper interpretation of available data through several critical epidemic indicators. In addition, we complement the epiMOX dashboard with a predictive tool based on an epidemiological compartmental model, named SUIHTER, for the forecast …
Existing compartmental models in epidemiology are limited in terms of optimizing the resource allocation to control an epidemic outbreak under disease growth uncertainty. In this study, we address this core limitation by presenting a multi-stage stochastic programming compartmental model, which integrates the uncertain disease progression and resource allocation to control an infectious disease outbreak. The proposed multi-stage stochastic program involves various disease growth scenarios and optimizes the distribution of treatment centers and resources while minimizing the total expected numb…
In this paper, we show that many structured epidemic models may be described using a straightforward product structure. Such products, derived from products of directed graphs, may represent useful refinements including geographic and demographic structure, age structure, gender, risk groups, or immunity status. Extension to multi-strain dynamics, i.e. pathogen heterogeneity, is also shown to be feasible in this framework. Systematic use of such products may aid in model development and exploration, can yield insight, and could form the basis of a systematic approach to numerical structural se…
Over a year after the start of the COVID-19 epidemics, we are still facing the virus and it is hard to correctly predict its future spread over weeks to come, as well as the impacts of potential political interventions. Current epidemic models mainly fall in two approaches: compartmental models, divide the population in epidemiological classes and rely on the mathematical resolution of differential equations to give a macroscopic view of the epidemical dynamics, allowing to evaluate its spread a posteriori; agent-based models are computer models that give a microscopic view of the situation, s…
Stochastic compartmental models are important tools for understanding the course of infectious diseases epidemics in populations and in prospective evaluation of intervention policies. However, calculating the likelihood for discretely observed data from even simple models -- such as the ubiquitous susceptible-infectious-removed (SIR) model -- has been considered computationally intractable, since its formulation almost a century ago. Recently researchers have proposed methods to circumvent this limitation through data augmentation or approximation, but these approaches often suffer from high …
The SEIR model is a compartmental model used to simulate the dynamics of an epidemic. In this chapter, we introduce two control functions in the compartmental SEIR model representing vaccination and plasma transfusion. Optimal control problems are proposed to study the effects of these two control measures, on the reduction of infected individuals and increase of recovered ones, with minimal costs. Up to our knowledge, the plasma transfusion treatment has never been considered as a control strategy for epidemics mitigation. The proposed vaccination and treatment strategies may have a real appl…
Compartmental equations are primary tools in disease spreading studies. Their predictions are accurate for large populations but disagree with empirical and simulated data for finite populations, where uncertainties become a relevant factor. Starting from the agent-based approach, we investigate the role of uncertainties and autocorrelation functions in SIS epidemic model, including their relationship with epidemiological variables. We find new differential equations that take uncertainties into account. The findings provide improved predictions to the SIS model and it can offer new insights f…
Deterministic compartmental models have been used extensively in modeling epidemic propagation. These models are required to fit available data and numerical procedures are often implemented to this end. But not every model architecture is able to fit the data because the structure of the model imposes hard constraints on the solutions. We investigate in this work two such situations: first the distribution of transition times from a compartment to another may impose a variable number of intermediary states; secondly, a non-linear relationship between time-dependent measures of compartments si…
The ongoing COVID-19 pandemic calls for a multi-faceted public health response comprising complementary interventions to control the spread of the disease while vaccines and therapies are developed. Many of these interventions need to be informed by epidemic risk predictions given available data, including symptoms, contact patterns, and environmental factors. Here we propose a novel probabilistic formalism based on Individual-Level Models (ILMs) that offers rigorous formulas for the probability of infection of individuals, which can be parameterised via Maximum Likelihood Estimation (MLE) app…
This paper gives an introduction to rule-based modelling applied to topics in infectious diseases. Rule-based models generalise reaction-based models with reagents that have internal state and may be bound together to form complexes, as in chemistry. Rule-based modelling is directly transferable from molecular biology to epidemiology and allows us to express a broad class of models for processes of interest in epidemiology that would not otherwise be feasible in compartmental models. This includes dynamics commonly found in compartmental models such as the spread of a virus from an infectious …
Epidemic spreading can be suppressed by the introduction of containment measures such as social distancing and lock downs. Yet, when such measures are relaxed, new epidemic waves and infection cycles may occur. Here we explore this issue in compartmentalized epidemic models on graphs in presence of a feedback between the infection state of the population and the structure of its social network for the case of discontinuous control. We show that in random graphs the effect of containment measures is simply captured by a renormalization of the effective infection rate that accounts for the chang…
Analysis of non pharmaceutical interventions with SIR epidemic models: decreasing the infection peak vs. minimizing the epidemic size
Instituto Balseiro, Universidad Nacional de Cuyo（巴塞尔罗研究所，门多萨国立大学）；Comisión Nacional de Energía Atómica（国家原子能委员会）；Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)（国家科学研究委员会）；Centro Atómico Bariloche (CNEA)（巴里洛切原子中心）
In this paper we present a model describing Susceptible-Infected-Susceptible (SIS) type epidemics spreading on a dynamic contact network with random link activation and deletion where link ac- tivation can be locally constrained. We use and adapt a improved effective degree compartmental modelling framework recently proposed by Lindquist et al. [J. Lindquist et al., J. Math Biol. 62, 2, 143 (2010)] and Marceau et al. [V. Marceau et al., Phys. Rev. E 82, 036116 (2010)]. The resulting set of ordinary differential equations (ODEs) is solved numerically and results are compared to those obtained u…
In this article, we develop a deterministic compartmental model including the spatio-temporal aspect and the wearing of masks by the general public for the spread of the Covid-19 epidemic. This model is based on the SIR model of Kermack and McKendrick and includes mobility terms that model the movement of individuals wearing masks between Guadeloupe andMartinique. The objective of the model is to analyze the effects of mobility and the wearing of masks by the general public on the spread of the Covid-19 epidemic in these two regions.Numerical simulations of this model show the importance of we…
Increasing the infection risk early in an epidemic is individually and socially optimal under some parameter values. The reason is that the early patients recover or die before the peak of the epidemic, which flattens the peak. This improves welfare if the peak exceeds the capacity of the healthcare system and the social loss rises rapidly enough in the number infected. The individual incentive to get infected early comes from the greater likelihood of receiving treatment than at the peak when the disease has overwhelmed healthcare capacity. Calibration to the Covid-19 pandemic data suggests t…
Contacts between people are the absolute drivers of contagious respiratory infections. For this reason, limiting and tracking contacts is a key strategy for the control of the COVID-19 epidemic. Digital contact tracing has been proposed as an automated solution to scale up traditional contact tracing. However, the required penetration of contact tracing apps within a population to achieve a desired target in the control of the epidemic is currently under discussion within the research community. In order to understand the effects of digital contact tracing, several mathematical models have bee…
