Epidemic outbreaks of new pathogens, or known pathogens in new populations, cause a great deal of fear because they are hard to predict. For theoretical models of disease spreading, on the other hand, quantities characterizing the outbreak converge to deterministic functions of time. Our goal in this paper is to shed some light on this apparent discrepancy. We measure the diversity of (and, thus, the predictability of) outbreak sizes and extinction times as functions of time given different scenarios of the amount of information available. Under the assumption of perfect information -- i.e., knowing the state of each individual with respect to the disease -- the predictability decreases exponentially, or faster, with time. The decay is slowest for intermediate values of the per-contact transmission probability. With a weaker assumption on the information available, assuming that we know only the fraction of currently infectious, recovered, or susceptible individuals, the predictability also decreases exponentially most of the time. There are, however, some peculiar regions in this scenario where the predictability decreases. In other words, to predict its final size with a given accuracy, we would need increasingly more information about the outbreak.
To understand the contact patterns of a population -- who is in contact with whom, and when the contacts happen -- is crucial for modeling outbreaks of infectious disease. Traditional theoretical epidemiology assumes that any individual can meet any with equal probability. A more modern approach, network epidemiology, assumes people are connected into a static network over which the disease spreads. Newer yet, temporal network epidemiology, includes the time in the contact representations. In this paper, we investigate the effect of these successive inclusions of more information. Using empiri…
No, they can't. Epidemic spread is characterized by exponentially growing dynamics, which are intrinsically unpredictable. The time at which the growth in the number of infected individuals halts and starts decreasing cannot be calculated with certainty before the turning point is actually attained; neither can the end of the epidemic after the turning point. An SIR model with confinement (SCIR) illustrates how lockdown measures inhibit infection spread only above a threshold that we calculate. The existence of that threshold has major effects in predictability: A Bayesian fit to the COVID-19 …
Predictability of undesired events is a question of great interest in many scientific disciplines including seismology, economy, and epidemiology. Here, we focus on the predictability of invasion of a broad class of epidemics caused by diseases that lead to permanent immunity of infected hosts after recovery or death. We approach the problem from the perspective of the science of complexity by proposing and testing several strategies for the estimation of important characteristics of epidemics, such as the probability of invasion. Our results suggest that parsimonious approximate methodologies…
Predicting adaptive evolutionary trajectories is a primary goal of evolutionary biology. One can differentiate between forward and backward predictability, where forward predictability measures the likelihood of the same adaptive trajectory occurring in independent evolutions and backward predictability measures the likelihood of a particular adaptive path given the knowledge of starting and final states. Recent studies have attempted to measure both forward and backward predictability using experimental evolution in asexual haploid microorganisms. Similar experiments in diploid organisms have…
The long-term evolution of epidemic processes depends crucially on the structure of contact networks. As empirical evidence indicates that human populations exhibit strong community organization, we investigate here how such mesoscopic configurations affect the likelihood of epidemic recurrence. Through numerical simulations on real social networks and theoretical arguments using spectral methods, we demonstrate that highly contagious diseases that would have otherwise died out rapidly can persist indefinitely for an optimal range of modularity in contact networks.
Genotype networks drive oscillating endemicity and epidemic trajectories in viral evolution
University of Zaragoza（萨拉戈萨大学）；Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza（萨拉戈萨大学复杂系统生物计算与物理研究所 (BIFI)）；Universitat Rovira i Virgili（罗维拉-伊-维尔吉利大学）；Pacific Northwest National Laboratory（太平洋西北国家实验室）；University of Kobe（神户大学）
Background: Zipf's law and Heaps' law are two representatives of the scaling concepts, which play a significant role in the study of complexity science. The coexistence of the Zipf's law and the Heaps' law motivates different understandings on the dependence between these two scalings, which is still hardly been clarified. Methodology/Principal Findings: In this article, we observe an evolution process of the scalings: the Zipf's law and the Heaps' law are naturally shaped to coexist at the initial time, while the crossover comes with the emergence of their inconsistency at the larger time bef…
We portray the evolution of the Covid-19 epidemic during the crisis of March-April 2020 in the Paris area, by analyzing the medical emergency calls received by the EMS of the four central departments of this area (Centre 15 of SAMU 75, 92, 93 and 94). Our study reveals strong dissimilarities between these departments. We show that the logarithm of each epidemic observable can be approximated by a piecewise linear function of time. This allows us to distinguish the different phases of the epidemic, and to identify the delay between sanitary measures and their influence on the load of EMS. This …
Population inhomogeneity, in the variation of the individual social contact networks and the individual infectious-recovery rates, renders the dynamics of infectious disease spreading uncertain. As a consequence the overlaying economical production network with its proper collaboration components is to extent impacted unpredictably. Our model proposes a `vector logistic' dynamical approach to SIS dynamics in a social contact network interacting with its economic capacity network. The probabilistic interpretation of the graph state in the vector logistic description provides a method to assess …
The dynamics of epidemic spreading is often reduced to the single control parameter $R_0$, whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, $R_0$ may change over time, potentially leading to a mutation-driven spread, in which an initially sub-pandemic pathogen undergoes a breakthrough mutation. To predict the boundaries of this pandemic phase, we introduce here a modeling framework to couple the network spreading patterns with the intra-host evolutionary dynamics. For many pathogens these two processes, intra- and inter-…
Investigating the effect of adaptive optimal control function in epidemic dynamics: predictions and strategy evolution based on SIR/V game theoretic framework
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…
To model the evolution of diseases with extended latency periods and the presence of asymptomatic patients like COVID-19, we define a simple discrete time stochastic SIR-type epidemic model. We include both latent periods as well as the presence of quarantine areas, to capture the evolutionary dynamics of such diseases.
A system of 4 nonlinearly-coupled Ordinary Differential Equations has been recently introduced to investigate the evolution of human respiratory virus epidemics. In this paper we point out that some explicit solutions of that system can be obtained by algebraic operations, provided the parameters of the model satisfy certain constraints.
Understanding the impact of collective social phenomena in epidemic dynamics is a crucial task to effectively contain the disease spread. In this work we build a mathematical description for assessing the interplay between opinion polarization and the evolution of a disease. The proposed kinetic approach describes the evolution of aggregate quantities characterizing the agents belonging to epidemiologically relevant states, and will show that the spread of the disease is closely related to consensus dynamics distribution in which opinion polarization may emerge. In the present modelling framew…
A pandemic caused by a new coronavirus has spread worldwide, affecting Argentina. We implement an SEIR model to analyze the disease evolution in Buenos Aires and neighbouring cities. The model parameters are calibrated using the number of casualties officially reported. Since infinite solutions honour the data, we show different cases. In all of them the reproduction ratio $R_0$ decreases after early lockdown, but then raises, probably due to an increase in contagion in highly populated slums. Therefore it is mandatory to reverse this growing trend in $R_0$ by applying control strategies to av…
The estimate of the remaining time of an ongoing wave of epidemic spreading is a critical issue. Due to the variations of a wide range of parameters in an epidemic, for simple models such as Susceptible-Infected-Removed (SIR) model, it is difficult to estimate such a time scale. On the other hand, multidimensional data with a large set attributes are precisely what one can use in statistical learning algorithms to make predictions. Here we show, how the predictability of the SIR model changes with various parameters using a supervised learning algorithm. We then estimate the condition in which…
A pandemic caused by a new coronavirus (COVID-19) has spread worldwide, inducing an epidemic still active in Argentina. In this chapter, we present a case study using an SEIR (Susceptible-Exposed-Infected-Recovered) diffusion model of fractional order in time to analyze the evolution of the epidemic in Buenos Aires and neighboring areas (Región Metropolitana de Buenos Aires, (RMBA)) comprising about 15 million inhabitants. In the SEIR model, individuals are divided into four classes, namely, susceptible (S), exposed (E), infected (I) and recovered (R). The SEIR model of fractional order allows…
Interplay between evolutionary and epidemic time scales challenges the outcome of control policies
University of Zaragoza（萨拉戈萨大学）；Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza（萨拉戈萨大学复杂系统生物计算与物理研究所）；Universitat Rovira i Virgili（罗维拉-依维尔吉里大学）；Pacific Northwest National Laboratory（太平洋西北国家实验室）；Complexity Science Hub Vienna（维也纳复杂性科学中心）；ComSCIAM, Universitat Rovira i Virgili（罗维拉-依维尔吉里大学计算科学与数学中心）；Center for Computational Social Science, University of Kobe（神户大学计算社会科学中心）
The process of evolutionary diversification unfolds in a vast genotypic space of potential outcomes. During the past century there have been remarkable advances in the development of theory for this diversification, and the theory's success rests, in part, on the scope of its applicability. A great deal of this theory focuses on a relatively small subset of the space of potential genotypes, chosen largely based on historical or contemporary patterns, and then predicts the evolutionary dynamics within this pre-defined set. To what extent can such an approach be pushed to a broader perspective t…
In the present work, a non-linear stochastic model is presented to study the effect of time variation of transmission rates on the co-evolution of epidemics and its corresponding awareness over a two layered multiplex network. In this model, the infection transmission rate of a given node in the epidemic layer depends upon its awareness probability in the awareness layer. Similarly, the infection information transmission rate of a node in the awareness layer depends upon its infection probability in the epidemic layer. The spread of disease resulting from physical contacts is described in term…
In the present article we introduce an epidemiological model for the investigation of the spread of epidemics caused by viruses. The model is applied specifically to COVID-19, the disease caused by the SARS-Cov-2 virus (aka "novel coronavirus"). The SIR (Susceptible - Infectious - Recovered) model is used as a basis for studying the evolution of the epidemic. Nevertheless, we have modified some of the model hypotheses in order to obtain an estimate of the contamination free of overestimated predictions. This extended model is then applied to the case of the recent advance of the epidemic in Br…
To forecast the time dynamics of an epidemic, we propose a discrete stochastic model that unifies and generalizes previous approaches to the subject. Viewing a given population of individuals or groups of individuals with given health state attributes as living in and moving between the nodes of a graph, we use Monte-Carlo Markov Chain techniques to simulate the movements and health state changes of the individuals according to given probabilities of stay that have been preassigned to each of the nodes. We utilize this model to either capture and predict the future geographic evolution of an e…
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evo…
At the moment of writing (12 February, 2020), the future evolution of the 2019-nCoV virus is unclear. Predictions of the further course of the epidemic are decisive to deploy targeted disease control measures. We consider a network-based model to describe the 2019-nCoV epidemic in the Hubei province. The network is composed of the cities in Hubei and their interactions (e.g., traffic flow). However, the precise interactions between cities is unknown and must be inferred from observing the epidemic. We propose a network-based method to predict the future prevalence of the 2019-nCoV virus in eve…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains of nucleotides that can mutate inside the host. Under the hypothesis of neutral evolution we compute analytically the average pairwise genetic distance between all infecting viruses over time. We also derive a mean-field version of this equation tha…
A recent work (DOI 10.1101/2020.05.06.20093310) indicated that temporarily splitting larger populations into smaller groups can efficiently mitigate the spread of SARS-CoV-2 virus. The fact that, soon afterwards, on May 15, 2020, the two million people Slovenia was the first European country proclaiming the end of COVID-19 epidemic within national borders may be relevant from this perspective. Motivated by this evolution, in this paper we investigate the time dynamics of coronavirus cases in Slovenia with emphasis on how efficient various containment measures act to diminish the number of COVI…
Due to modern transportation networks (airplanes, cruise ships, etc.) an epidemic in a given country or city may be triggered by the arrival of external infected agents. Posterior government quarantine policies are usually taken in order to control the epidemic growth. We formulate a minimal epidemic evolution model that takes into account these components. The previous and posterior evolutions to the quarantine policy are modeled in a separate way by considering different complexities parameters in each stage. Application of this model to COVID-19 data in different countries is implemented. E…
Voluntary vaccination is effective to prevent infectious diseases from spreading. Both vaccination behavior and cognition of the vaccination risk play important roles in individual vaccination decision making. However, it is not clear how the co-evolution of the two shapes the population-wide vaccination behavior. We establish a coupled dynamics of epidemic, vaccination behavior and perceived vaccination risk with three different time scales. We assume that the increase of vaccination level inhibits the rise of perceived vaccination risk, and the increase of perceived vaccination risk inhibits…
Epidemic models with inhomogeneous populations have been used to study major outbreaks and recently Britton and Lindenstrand \cite{BL} described the case when latency and infectivity have independent gamma distributions. They found that variability in these random variables had opposite effects on the epidemic growth rate. That rate increased with greater variability in latency but decreased with greater variability in infectivity. Here we extend their result by using the McKay bivariate gamma distribution for the joint distribution of latency and infectivity, recovering the above effects of v…
Background: The analysis of the Sars-CoV-2 epidemic is of paramount importance to understand the dynamics of the coronavirus spread. This can help health and government authorities take the appropriate measures and implement suitable politics aimed at fighting and preventing it. Methods: A time-dependent dynamic SEIR model inspired in a model previously used during the MERS outbreak in South Korea was used to analyse the time trajectories of active and hospitalized cases in Portugal. Results: The time evolution of the virus spread in the country was adequately modelled. The model has changeabl…
We present an algorithm which explores permutation symmetries to describe the time evolution of agent-based epidemic models. The main idea to improve computation times relies on restricting the stochastic process to one sector of the vector space, labeled by a single permutation eigenvalue. In this scheme, the transition matrix reduces to block diagonal form, enhancing computational performance.
The evolution of epidemiological parameters, such as instantaneous reproduction number Rt, is important for understanding the transmission dynamics of infectious diseases. Current estimates of time-varying epidemiological parameters often face problems such as lagging observations, averaging inference, and improper quantification of uncertainties. To address these problems, we propose a Bayesian data assimilation framework for time-varying parameter estimation. Specifically, this framework is applied to Rt estimation, resulting in the state-of-the-art DARt system. With DARt, time misalignment …
We introduce a theoretical framework that highlights the impact of physical distancing variables such as human mobility and physical proximity on the evolution of epidemics and, crucially, on the reproduction number. In particular, in response to the coronavirus disease (CoViD-19) pandemic, countries have introduced various levels of 'lockdown' to reduce the number of new infections. Specifically we use a collisional approach to an infection-age structured model described by a renewal equation for the time homogeneous evolution of epidemics. As a result, we show how various contributions of th…
We propose a generative model and an inference scheme for epidemic processes on dynamic, adaptive contact networks. Network evolution is formulated as a link-Markovian process, which is then coupled to an individual-level stochastic SIR model, in order to describe the interplay between epidemic dynamics on a network and network link changes. A Markov chain Monte Carlo framework is developed for likelihood-based inference from partial epidemic observations, with a novel data augmentation algorithm specifically designed to deal with missing individual recovery times under the dynamic network set…
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…
The 2014 epidemic of the Ebola virus is governed by a genetically diverse viral population. In the early Sierra Leone outbreak, a recent study has identified new mutations that generate genetically distinct sequence clades. Here we find evidence that major Sierra Leone clades have systematic differences in growth rate and reproduction number. If this growth heterogeneity remains stable, it will generate major shifts in clade frequencies and influence the overall epidemic dynamics on time scales within the current outbreak. Our method is based on simple summary statistics of clade growth, which…
The Susceptible-Infected-Recovered (SIR) epidemic model is extensively used for the study of the spread of infectious diseases. Even that the exact solution of the model can be obtained in an exact parametric form, in order to perform the comparison with the epidemiological data a simple but highly accurate representation of the time evolution of the SIR compartments would be very useful. In the present paper we obtain a series representation of the solution of the SIR model by using the Laplace-Adomian Decomposition Method to solve the basic evolution equation of the model. The solutions are …
In this article, we develop a data assimilation procedure to predict the evolution of epidemics with data uncertainty, with application to the Covid-19 pandemic. We construct a vademecum of solutions by solving the SIR epidemic model for a set of data neighboring the estimated real (or official) ones. A reduced basis is constructed from this vademecum through Proper Orthogonal Decomposition (POD). The reduced POD base is then applied to assimilate the pandemic data (infected, recovered, deceased) during the period in which data are known, by a least squares procedure. The fitted curves are the…
Characterizing the spatial extent of epidemics at the outbreak stage is key to controlling the evolution of the disease. At the outbreak, the number of infected individuals is typically small, so that fluctuations around their average are important: then, it is commonly assumed that the susceptible-infected-recovered (SIR) mechanism can be described by a stochastic birth-death process of Galton-Watson type. The displacements of the infected individuals can be modelled by resorting to Brownian motion, which is applicable when long-range movements and complex network interactions can be safely n…
The Susceptible-Infected-Recovered (SIR) epidemic model as well as its generalizations are extensively used for the study of the spread of infectious diseases, and for the understanding of the dynamical evolution of epidemics. From SIR type models only the model without vital dynamics has an exact analytic solution, which can be obtained in an exact parametric form. The SIR model with vital dynamics, the simplest extension of the basic SIR model, does not admit a closed form representation of the solution. However, in order to perform the comparison with the epidemiological data accurate repre…
Epidemic forecasting is the key to effective control of epidemic transmission and helps the world mitigate the crisis that threatens public health. To better understand the transmission and evolution of epidemics, we propose EpiGNN, a graph neural network-based model for epidemic forecasting. Specifically, we design a transmission risk encoding module to characterize local and global spatial effects of regions in epidemic processes and incorporate them into the model. Meanwhile, we develop a Region-Aware Graph Learner (RAGL) that takes transmission risk, geographical dependencies, and temporal…
Epidemic spreading of infectious diseases is ubiquitous and has often considerable impact on public health and economic wealth. The large variability in spatio-temporal patterns of epidemics prohibits simple interventions and demands for a detailed analysis of each epidemic with respect to its infectious agent and the corresponding routes of transmission. To facilitate this analysis, a mathematical framework is introduced which links epidemic patterns to the topology and dynamics of the underlying transmission network. The evolution both in disease prevalence and transmission network topology …
We show how the standard field theoretical language based on creation and annihilation operators may be used for a straightforward derivation of an SIR-type stochastic model for COVID-19 epidemic, from which we obtain the time evolution of the mean number of infectious (active cases) and deceased individuals. In order to capture the effects of lockdown and social distancing, we use a time-dependent infection rate. The results are in good agreement with the data for three different waves of epidemic activity in South Korea.
The presence of a large number of infected individuals with few or no symptoms is an important epidemiological difficulty and the main mathematical feature of COVID-19. The A-SIR model, i.e. a SIR (Susceptible-Infected-Removed) model with a compartment for infected individuals with no symptoms or few symptoms was proposed by Giuseppe Gaeta, arXiv:2003.08720 [q-bio.PE] (2020). In this paper we investigate a slightly generalized version of the same model and propose a scheme for fitting the parameters of the model to real data using the time series only of the deceased individuals. The scheme is…
For centuries isolation has been the main control strategy of unforeseen epidemic outbreaks. When implemented in full and without delay, isolation is very effective. However, flawless implementation is seldom feasible in practice. We present an epidemic model called SIQ with an isolation protocol, focusing on the consequences of delays and incomplete identification of infected hosts. The continuum limit of this model is a system of Delay Differential Equations, the analysis of which reveals clearly the dependence of epidemic evolution on model parameters including disease reproductive number, …
