Infectious diseases are a significant threat to human society which was over sighted before the incidence of COVID-19, although according to the report of the World Health Organisation (WHO) about 4.2 million people die annually due to infectious disease. Due to recent COVID-19 pandemic, more than 2 million people died during 2020 and 96.2 million people got affected by this devastating disease. Recent research shows that applying individual interactions and movements data could help managing the pandemic though modelling the spread of infectious diseases on social contact networks. Infectious disease spreading can be explained with the theories and methods of diffusion processes where a dynamic phenomena evolves on networked systems. In the modelling of diffusion process, it is assumed that contagious items spread out in the networked system through the inter-node interactions. This resembles spreading of infectious virus, e.g. spread of COVID-19, within a population through individual social interactions. The evolution behaviours of the diffusion process are strongly influenced by the characteristics of the underlying system and the mechanism of the diffusion process itself. Thus, spreading of infectious disease can be explained how people interact with each other and by the characteristics of the disease itself. This paper presenters the relevant theories and methodologies of diffusion process that can be used to model the spread of infectious diseases.
Interaction patterns among individuals play vital roles in spreading infectious diseases. Understanding these patterns and integrating their impact in modeling diffusion dynamics of infectious diseases are important for epidemiological studies. Current network-based diffusion models assume that diseases transmit through interactions where both infected and susceptible individuals are co-located at the same time. However, there are several infectious diseases that can transmit when a susceptible individual visits a location after an infected individual has left. Recently, we introduced a diffus…
The transmission dynamics of some infectious diseases is related to the contact structure between individuals in a network. We used five algorithms to generate contact networks with different topological structure but with the same scale-free degree distribution. We simulated the spread of acute and chronic infectious diseases on these networks, using SI (Susceptible - Infected) and SIS (Susceptible - Infected - Susceptible) epidemic models. In the simulations, our objective was to observe the effects of the topological structure of the networks on the dynamics and prevalence of the simulated …
We introduce a Python package for modeling and studying the spread of infectious diseases using an agent-based SEIR style epidemiological model with a focus on university campuses. This document explains the epidemiological model used in the package and gives examples highlighting the ways that the package can be used.
The annual occurrence of many infectious diseases remains a constant burden to public health systems. The seasonal patterns in respiratory disease incidence observed in temperate regions have been attributed to the impact of environmental conditions on pathogen survival. A model describing the transmission of an infectious disease by means of a pathogenic state capable of surviving in an environmental reservoir outside of its host organism is presented in this paper. The ratio of pathogen lifespan to the duration of the infectious disease state is found to be a critical parameter in determinin…
There are often multiple diseases with cross immunity competing for vaccination resources. Here we investigate the optimal vaccination program in a two-layer Susceptible-Infected-Removed (SIR) model, where two diseases with cross immunity spread in the same population, and vaccines for both diseases are available. We identify three scenarios of the optimal vaccination program, which prevents the outbreaks of both diseases at the minimum cost. We analytically derive a criterion to specify the optimal program based on the costs for different vaccines.
Urban areas with larger and more connected populations offer an auspicious environment for contagion processes such as the spread of pathogens. Empirical evidence reveals a systematic increase in the rates of certain sexually transmitted diseases (STDs) with larger urban population size. However, the main drivers of these systemic infection patterns are still not well understood, and rampant urbanization rates worldwide makes it critical to advance our understanding on this front. Using confirmed-cases data for three STDs in US metropolitan areas, we investigate the scaling patterns of infecti…
Infectious diseases spread through human networks. Susceptible-Infected-Removed (SIR) model is one of the epidemic models to describe infection dynamics on a complex network connecting individuals. In the metapopulation SIR model, each node represents a population (group) which has many individuals. In this paper, we propose a modified metapopulation SIR model in which a latent period is taken into account. We call it SIIR model. We divide the infection period into two stages: an infected stage, which is the same as the previous model, and a seriously ill stage, in which individuals are infect…
Spatial big data have the "velocity," "volume," and "variety" of big data sources and additional geographic information about the record. Digital data sources, such as medical claims, mobile phone call data records, and geo-tagged tweets, have entered infectious disease epidemiology as novel sources of data to complement traditional infectious disease surveillance. In this work, we provide examples of how spatial big data have been used thus far in epidemiological analyses and describe opportunities for these sources to improve public health coordination and disease mitigation strategies. In a…
In this study, we develop the mathematical model to understand the coupling between the spreading dynamics of infectious diseases and the mobility dynamics through urban transportation systems. We first describe the mobility dynamics of the urban population as the process of leaving from home, traveling to and from the activity locations, and engaging in activities. We then embed the susceptible-exposed-infectious-recovered (SEIR) process over the mobility dynamics and develops the spatial SEIR model with travel contagion (Trans-SEIR), which explicitly accounts for contagions both during trave…
We propose a risk measure and construct an infectious diseases hazard map for India. Given an outbreak location, a hazard index is assigned to each city using an effective distance that depends on inter-city mobilities instead of geographical distance. We demonstrate its utility using an SIR model augmented with air, rail, and road data between top 446 cities. Simulations show that the effective distance from outbreak location reliably predicts the time of arrival of infection in other cities. The hazard index predictions compare well with the observed spread of SARS-CoV-2. The hazard map can …
Infectious disease models can be of great use for understanding the underlying mechanisms that influence the spread of diseases and predicting future disease progression. Modeling has been increasingly used to evaluate the potential impact of different control measures and to guide public health policy decisions. In recent years, there has been rapid progress in developing spatio-temporal modeling of infectious diseases and an example of such recent developments is the discrete time individual-level models (ILMs). These models are well developed and provide a common framework for modeling many…
Infectious disease outbreaks recapitulate biology: they emerge from the multi-level interaction of hosts, pathogens, and their shared environment. As a result, predicting when, where, and how far diseases will spread requires a complex systems approach to modeling. Recent studies have demonstrated that predicting different components of outbreaks--e.g., the expected number of cases, pace and tempo of cases needing treatment, demand for prophylactic equipment, importation probability etc.--is feasible. Therefore, advancing both the science and practice of disease forecasting now requires testin…
Disease outbreaks, such as those of Severe Acute Respiratory Syndrome in 2003 and the 2009 pandemic A(H1N1) influenza, have highlighted the potential for airborne transmission in indoor environments. Respirable pathogen-carrying droplets provide a vector for the spatial spread of infection with droplet transport determined by diffusive and convective processes. An epidemiological model describing the spatial dynamics of disease transmission is presented. The effects of an ambient airflow, as an infection control, are incorporated leading to a delay equation, with droplet density dependent on t…
In a metapopulation network, infectious diseases spread widely because of the travel of individuals. In the present study, we consider a modified metapopulation Susceptible-Infected-Removed (SIR) model with a latent period, which we call the SHIR model. In the SHIR model, an infectious period is divided into two stages. In the first stage, which corresponds to the latent period, infectious individuals can travel. However, in the second stage, the same individuals cannot travel since they are seriously ill. Final size distributions of the metapopulation SIR and SHIR models are simulated with tw…
The symptoms of many infectious diseases influence their host to withdraw from social activity limiting their own potential to spread. Successful transmission therefore requires the onset of infectiousness to coincide with a time when its host is socially active. Since social activity and infectiousness are both temporal phenomena, we hypothesize that diseases are most pervasive when these two processes are synchronized. We consider disease dynamics that incorporate a behavioral response that effectively shortens the infectious period of the disease. We apply this model to data collected from …
Routine public health surveillance of notifiable infectious diseases gives rise to weekly counts of reported cases -- possibly stratified by region and/or age group. We investigate how an age-structured social contact matrix can be incorporated into a spatio-temporal endemic-epidemic model for infectious disease counts. To illustrate the approach, we analyze the spread of norovirus gastroenteritis over 6 age groups within the 12 districts of Berlin, 2011-2015, using contact data from the POLYMOD study. The proposed age-structured model outperforms alternative scenarios with homogeneous or no m…
During an infectious disease outbreak, biases in the data and complexities of the underlying dynamics pose significant challenges in mathematically modelling the outbreak and designing policy. Motivated by the ongoing response to COVID-19, we provide a toolkit of statistical and mathematical models beyond the simple SIR-type differential equation models for analysing the early stages of an outbreak and assessing interventions. In particular, we focus on parameter estimation in the presence of known biases in the data, and the effect of non-pharmaceutical interventions in enclosed subpopulation…
The dynamics of economies and infectious disease are inexorably linked: economic well-being influences health (sanitation, nutrition, treatment capacity, etc.) and health influences economic well-being (labor productivity lost to sickness and disease). Often societies are locked into "poverty traps" of poor health and poor economy. Here, using a simplified coupled disease-economic model with endogenous capital growth we demonstrate the formation of poverty traps, as well as ways to escape them. We suggest two possible mechanisms of escape both motivated by empirical data: one, through an influ…
Epidemic modeling in complex networks has become one of the latest topics in recent times. The Susceptible-Infectious-Recovered (SIR) model and its variants are often used for epidemic modeling. One important issue in epidemic modeling is the determination of the spreading ability of the nodes in the network. Thus, for example, can be detected in the early stages. In this study, we developed a centrality measure called Lexical Sorting Centrality (LSC) that distinguishes the spreading ability of the nodes. Using other centrality measures calculated for the nodes, LSC sorts the nodes in a way si…
Human mobility, contact patterns, and their interplay are key aspects of our social behavior that shape the spread of infectious diseases across different regions. In the light of new evidence and data sets about these two elements, epidemic models should be refined to incorporate both the heterogeneity of human contacts and the complexity of mobility patterns. Here, we propose a theoretical framework that allows accommodating these two aspects in the form of a set of Markovian equations. We validate these equations with extensive mechanistic simulations and derive analytically the epidemic th…
There has been much recent interest in screening populations for an infectious disease. Here, we present a stochastic-control model, wherein the optimum screening policy is provably difficult to find, but wherein Thompson sampling has provably optimal performance guarantees in the form of Bayesian regret. Thompson sampling seems applicable especially to diseases, for which we do not understand the dynamics well, such as to the super-spreading COVID-19.
In the study of infectious diseases on networks, researchers calculate epidemic thresholds to help forecast whether a disease will eventually infect a large fraction of a population. Because network structure typically changes in time, which fundamentally influences the dynamics of spreading processes on them and in turn affects epidemic thresholds for disease propagation, it is important to examine epidemic thresholds in temporal networks. Most existing studies of epidemic thresholds in temporal networks have focused on models in discrete time, but most real-world networked systems evolve con…
The COVID-19 pandemic has led to significant changes in how people are currently living their lives. To determine how to best reduce the effects of the pandemic and start reopening societies, governments have drawn insights from mathematical models of the spread of infectious diseases. In this article, we give an introduction to a family of mathematical models (called "compartmental models") and discuss how the results of analyzing these models influence government policies and human behavior, such as encouraging mask wearing and physical distancing to help slow the spread of the disease.
In this article, we discuss an age-structured SIR model in which disease not only spread through direct person to person contacts for e.g. infection due to surface contamination but it can also spread through indirect contacts. It is evident that age also plays a crucial role in SARS virus infection including COVID-19 infection. We formulate our model as an abstract semilinear Cauchy problem in an appropriate Banach space to show the existence of solution and also show the existence of steady states. It is assumed in this work that the population is in a demographic stationary state and show t…
A novel predictive modeling framework for the spread of infectious diseases using high dimensional partial differential equations is developed and implemented. A scalar function representing the infected population is defined on a high-dimensional space and its evolution over all directions is described by a population balance equation (PBE). New infections are introduced among the susceptible population from non-quarantined infected population based on their interaction, adherence to distancing norms, hygiene levels and any other societal interventions. Moreover, recovery, death, immunity and…
When an infectious disease strikes a population, the number of newly reported cases is often the only available information that one can obtain during early stages of the outbreak. An important goal of early outbreak analysis is to obtain a reliable estimate for the basic reproduction number, $R_{0}$, from the limited information available. We present a novel method that enables us to make a reliable real-time estimate of the reproduction number at a much earlier stage compared to other available methods. Our method takes into account the possibility that a disease has a wide distribution of i…
We develop a mathematical framework to study the economic impact of infectious diseases by integrating epidemiological dynamics with a kinetic model of wealth exchange. The multi-agent description leads to study the evolution over time of a system of kinetic equations for the wealth densities of susceptible, infectious and recovered individuals, whose proportions are driven by a classical compartmental model in epidemiology. Explicit calculations show that the spread of the disease seriously affects the distribution of wealth, which, unlike the situation in the absence of epidemics, can conver…
The emergence due to the outbreak of the COVID-19 disease, caused by the SARS-CoV-2 virus, suddenly erupted at the beginning of 2020 in China and soon spread worldwide. This has caused an outstanding increase on research about the virus itself and, more in general, epidemics in many scientific fields. In this work we focus on the dynamics of the epidemic spreading and how it can be affected by the individual variability in compliance with social norms, i.e., in the adoption of health and hygienic social norms by population's members.
A well-known characteristic of pandemics such as COVID-19 is the high level of transmission heterogeneity in the infection spread: not all infected individuals spread the disease at the same rate and some individuals (superspreaders) are responsible for most of the infections. To quantify this phenomenon requires the analysis of the effect of the variance and higher moments of the infection distribution. Working in the framework of stochastic branching processes, we derive an approximate analytical formula for the probability of an outbreak in the high variance regime of the infection distribu…
With the exponential growth in the world population and the constant increase in human mobility, the danger of outbreaks of epidemics is rising. Especially in high density urban areas such as public transport and transfer points, where people come in close proximity of each other, we observe a dramatic increase in the transmission of airborne viruses and related pathogens. It is essential to have a good understanding of the `transmission highways' in such areas, in order to prevent or to predict the spreading of infectious diseases. The approach we take is to combine as much information as is …
The most frequent infectious diseases in humans - and those with the highest potential for rapid pandemic spread - are usually transmitted via droplets during close proximity interactions (CPIs). Despite the importance of this transmission route, very little is known about the dynamic patterns of CPIs. Using wireless sensor network technology, we obtained high-resolution data of CPIs during a typical day at an American high school, permitting the reconstruction of the social network relevant for infectious disease transmission. At a 94% coverage, we collected 762,868 CPIs at a maximal distance…
In regard to infectious diseases socioeconomic determinants are strongly associated with differential exposure and susceptibility however they are seldom accounted for by standard compartmental infectious disease models. These associations are explored here with a novel compartmental infectious disease model which, stratified by deprivation and age, accounts for population-level behaviour including social mixing patterns. As an exemplar using a fully Bayesian approach our model is fitted, in real-time if required, to the UKHSA COVID-19 community testing case data from England. Metrics includin…
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；University of Science and Technology of China（中国科学技术大学）
Infectious diseases usually originate from a specific location within a city. Due to the heterogenous distribution of population and public facilities, and the structural heterogeneity of human mobility network embedded in space, infectious diseases break out at different locations would cause different transmission risk and control difficulty. This study aims to investigate the impact of initial outbreak locations on the risk of spatiotemporal transmission and reveal the driving force behind high-risk outbreak locations. First, integrating mobile phone location data, we built a SLIR (suscepti…
