We study contact epidemic models for the spread of infective diseases in finite populations. The size dependence enters in the infection rate. The dynamics of such models is then analyzed within the deterministic approximation, as well as in terms of a stochastic formulation. At the level of the deterministic equations, we deduce relations between the parameters of the model for the disease to become endemic. Within the stochastic formulation, it is possible to write recursion relations for the probability distribution, that lead to exact expression for some of its moments and check the validity of the stochastic threshold theorems.
The challenges presented by the COVID-19 epidemic have created a renewed interest in the development of new methods to combat infectious diseases. A prominent property of the SARS-CoV-2 transmission is the significant fraction of asymptomatic transmission. This may influence the effectiveness of the standard contact tracing procedure for quarantining potentially infected individuals. However, the effects of asymptomatic transmission on the epidemic threshold of epidemic spreading on networks are largely unknown. Here we study the critical percolation transition in a simple epidemic network mod…
Drug resistance and strong contacts actually play crucial roles in epidemic spread in complex systems. Nevertheless, neither theoretical model or methodology is proposed to address this. We thus consider an edge-based epidemic spread model considering the two key ingredients, in which the contacts are grouped into two classes: strong contacts and normal ones. Next, we present a unified edge-based compartmental approach to the spread dynamics on Erdös-Rényi (ER) networks and validate its results by extensive numerical simulations. In case that epidemic is totally drug-resistant, we both numeric…
Different countries -- and sometimes different regions within the same countries -- have adopted different strategies in trying to contain the ongoing COVID-19 epidemic; these mix in variable parts social confinement, early detection and contact tracing. In this paper we discuss the different effects of these ingredients on the epidemic dynamics; the discussion is conducted with the help of two simple models, i.e. the classical SIR model and the recently introduced variant (A-SIR, arXiv:2003.08720) which takes into account the presence of a large set of asymptomatic infectives.
Tracking dynamics of superspreading through contacts, exposures, and transmissions in edge-based network epidemics
Princeton University（普林斯顿大学）；University of Vermont（佛蒙特大学）；University of Copenhagen（哥本哈根大学）；Roskilde University（罗斯基勒大学）；Emory University（埃默里大学）；Complexity Science Hub（复杂性科学中心）；Santa Fe Institute（圣塔菲研究所）
The outbreak of the novel coronavirus, COVID-19, has been declared a pandemic by the WHO. The structures of social contact critically determine the spread of the infection and, in the absence of vaccines, the control of these structures through large-scale social distancing measures appears to be the most effective means of mitigation. Here we use an age-structured SIR model with social contact matrices obtained from surveys and Bayesian imputation to study the progress of the COVID-19 epidemic in India. The basic reproductive ratio R0 and its time-dependent generalization are computed based o…
Social interactions shape the patterns of spreading processes in a population. Techniques such as diaries or proximity sensors allow to collect data about encounters and to build networks of contacts between individuals. The contact networks obtained from these different techniques are however quantitatively different. Here, we first show how these discrepancies affect the prediction of the epidemic risk when these data are fed to numerical models of epidemic spread: low participation rate, under-reporting of contacts and overestimation of contact durations in contact diaries with respect to s…
A method for including additional socio-demographic factors in social contact matrices for compartment-based epidemic models
School of Mathematics and Statistics, University of Canterbury（坎特伯雷大学数学与统计学院）；Ngāi Tahu Research Center, University of Canterbury（坎特伯雷大学恩盖·塔胡研究中心）；Te Pūnaha Matatini Centre of Research Excellence in Complex Systems（复杂系统卓越研究中心 Te Pūnaha Matatini）
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…
The ability to directly record human face-to-face interactions increasingly enables the development of detailed data-driven models for the spread of directly transmitted infectious diseases at the scale of individuals. Complete coverage of the contacts occurring in a population is however generally unattainable, due for instance to limited participation rates or experimental constraints in spatial coverage. Here, we study the impact of spatially constrained sampling on our ability to estimate the epidemic risk in a population using such detailed data-driven models. The epidemic risk is quantif…
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 …
We study the impact of contact heterogeneity on epidemic dynamics. A system characterized by multiple susceptible populations is considered. The description of the spread of an infectious disease is obtained through the study of a system of Boltzmann-type equations for the number densities of social contacts of the introduced compartments. A macroscopic system of equations characterizing observable effects of the epidemic is then derived to assess the impact of contact heterogeneity.
Given the growth of urbanization and emerging pandemic threats, more sophisticated models are required to understand disease propagation and investigate the impacts of intervention strategies across various city types. We introduce a fully mechanistic, activity-based and highly spatio-temporally resolved epidemiological model which leverages on person-trajectories obtained from integrated mobility demand and supply models in full-scale cities. Simulating COVID-19 evolution in two full-scale cities with representative synthetic populations and mobility patterns, we analyze activity-based contac…
Laboratoire de Physique de l’Ecole Normale Supérieure（巴黎高等师范学院物理实验室）；Université PSL（巴黎文理研究大学）；CNRS（法国国家科学研究中心）；Sorbonne Université（索邦大学）；Université Paris-Diderot（巴黎第七大学）；Sorbonne Paris Cité（索邦巴黎西岱大学）；Politecnico di Torino（都灵理工大学）；Italian Institute for Genomic Medicine（意大利基因组医学研究所）；Collegio Carlo Alberto（卡洛·阿尔贝托学院）；INFN Sezione di Torino（意大利国家核物理研究所都灵分部）；The Abdus Salam International Centre for Theoretical Physics（阿卜杜斯·萨拉姆国际理论物理中心）；École Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）
Contact-tracing is an essential tool in order to mitigate the impact of pandemic such as the COVID-19. In order to achieve efficient and scalable contact-tracing in real time, digital devices can play an important role. While a lot of attention has been paid to analyzing the privacy and ethical risks of the associated mobile applications, so far much less research has been devoted to optimizing their performance and assessing their impact on the mitigation of the epidemic. We develop Bayesian inference methods to estimate the risk that an individual is infected. This inference is based on the …
Epidemic spread: limiting contacts to regular circles is not necessarily the safest option
Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET and Facultad de Ciencias Exactas, Universidad Nacional de La Plata（理论物理化学与应用研究所（INIFTA），CONICET和拉普拉塔国立大学理学院）；CCT CONICET La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas（CONICET拉普拉塔科学研究中心，国家科学研究委员会）
A probabilistic approach to the epidemic evolution on realistic social-contact networks allows for characteristic differences among subjects, including the individual number and structure of social contacts, and the heterogeneity of the infection and recovery rates according to age or medical preconditions. Within our probabilistic Susceptible-Infectious-Removed (SIR) model on social-contact networks, we evaluate the `infection load' or `activation margin' of various control scenarios; by confinement, by vaccination, and by their combination. We compare the epidemic burden for subpopulations w…
The outbreak of an infectious disease in a human population can lead to individuals responding with preventive measures in an attempt to avoid getting infected. This leads to changes in contact patterns. However, as we show in this paper, rational behaviour at the individual level, such as social distancing from infectious contacts, may not always be beneficial for the population as a whole. We use epidemic network models to demonstrate the potential negative consequences at the population level. We take into account the social structure of the population through several network models. As the…
Epidemiological contact network models have emerged as an important tool in understanding and predicting the spread of infectious disease, due to their capacity to engage individual heterogeneity that may underlie essential dynamics of a particular host-pathogen system. Just as fundamental are the changes that real-world contact networks undergo over time, both independently of and in response to pathogen spreading. These dynamics play a central role in determining whether a disease will die out or become an epidemic within a population, known as the epidemic threshold. In this paper, we provi…
We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated defence mechanism was described in Bautista et al (2015) for an archaeal host, while Jackson and Fineran (2019) and Meeske et al (2019) describe a related, CRISPR-Cas induced, dormancy defense of bacterial hosts to curb phage epidemics. We first analyse the effect of the dormancy-related model parameters on the probability and time of invasion of a newly arriv…
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 …
Infectious diseases that incorporate pre-symptomatic transmission are challenging to monitor, model, predict and contain. We address this scenario by studying a variant of a stochastic susceptible-exposed-infected-recovered model on arbitrary network instances using an analytical framework based on the method of dynamic message-passing. This framework provides a good estimate of the probabilistic evolution of the spread on both static and contact networks, offering a significantly improved accuracy with respect to individual-based mean-field approaches while requiring a much lower computationa…
The mobility patterns of individuals in China during the early outbreak of the COVID-19 pandemic exhibit reversible changes -- in many regions, the mobility first decreased significantly and later restored. Based on this observation, here we study the classical SIR model on a particular type of time-varying network where the links undergo a freeze-recovery process. We first focus on an isolated network and find that the recovery mechanism could lead to the resurgence of an epidemic. The influence of link freezing on epidemic dynamics is subtle. In particular, we show that there is an optimal v…
Contacts between individuals play an important role in determining how infectious diseases spread. Various methods to gather data on such contacts co-exist, from surveys to wearable sensors. Comparisons of data obtained by different methods in the same context are however scarce, in particular with respect to their use in data-driven models of spreading processes. Here, we use a combined data set describing contacts registered by sensors and friendship relations in the same population to address this issue in a case study. We investigate if the use of the friendship network is equivalent to a …
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.
A key characteristic of the spread of infectious diseases is their ability to use efficient transmission paths within contact graphs. This enables the pathogen to maximise infection rates and spread within a target population. In this work, we devise techniques to localise infections and decrease infection rates based on a principled analysis of disease transmission paths within human-contact networks (proximity graphs). Experimental results of disease spreading shows that that at low visibility rates contact tracing slows disease spreading. However to stop disease spreading, contact tracing r…
In this paper we consider an SIRS epidemic model under a general assumption of density-dependent mortality. We prove the global stability of the disease-free equilibrium and propose a Lyapunov function that allows to demonstrate the global stability of the (unique) endemic state under broad conditions.
An SEIRS epidemic with disease fatalities is introduced in a growing population (modelled as a super-critical linear birth and death process). The study of the initial phase of the epidemic is stochastic, while the analysis of the major outbreaks is deterministic. Depending on the values of the parameters, the following scenarios are possible. i) The disease dies out quickly, only infecting few; ii) the epidemic takes off, the \textit{number} of infected individuals grows exponentially, but the \textit{fraction} of infected individuals remains negligible; iii) the epidemic takes off, the \text…
