Dynamics and Control of Diseases in Networks with Community Structure

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network. Human contact networks exhibit strong community structure. Understanding how such community structure affects epidemics may provide insights for preventing the spread of disease between communities by changing the structure of the contact network through pharmaceutical or non-pharmaceutical interventions. We use empirical and simulated networks to investigate the spread of disease in networks with community structure. We find that community structure has a major impact on disease dynamics, and we show that in networks with strong community structure, immunization interventions targeted at individuals bridging communities are more effective than those simply targeting highly connected individuals. Because the structure of relevant contact networks is generally not known, and vaccine supply is often limited, there is great need for efficient vaccination algorithms that do not require full knowledge of the network. We developed an algorithm that acts only on locally available network information and is able to quickly identify targets for successful immunization intervention. The algorithm generally outperforms existing algorithms when vaccine supply is limited, particularly in networks with strong community structure. Understanding the spread of infectious diseases and designing optimal control strategies is a major goal of public health. Social networks show marked patterns of community structure, and our results, based on empirical and simulated data, demonstrate that community structure strongly affects disease dynamics. These results have implications for the design of control strategies

Computational Methods for Assessment and Prediction of Viral Evolutionary and Epidemiological Dynamics

The ability to comprehend the dynamics of viruses’ transmission and their evolution, even to a limited extent, can significantly enhance our capacity to predict and control the spread of infectious diseases. An example of such significance is COVID-19 caused by the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). In this dissertation, I am proposing computational models that present more precise and comprehensive approaches in viral outbreak investigations and epidemiology, providing invaluable insights into the transmission dynamics, and potential inter- ventions of infectious diseases by facilitating the timely detection of viral variants. The first model is a mathematical framework based on population dynamics for the calculation of a numerical measure of the fitness of SARS-CoV-2 subtypes. The second model I propose here is a transmissibility estimation method based on a Bayesian approach to calculate the most likely fitness landscape for SARS-CoV-2 using a generalized logistic sub-epidemic model. Using the proposed model I estimate the epistatic interaction networks of spike protein in SARS-CoV-2. Based on the community structure of these epistatic networks, I propose a computational framework that predicts emerging haplotypes of SARS-CoV-2 with altered transmissibility. The last method proposed in this dissertation is a maximum likelihood framework that integrates phylogenetic and random graph models to accurately infer transmission networks without requiring case-specific data

An Agent-Based Modeling Approach to Reducing Pathogenic Transmission in Medical Facilities and Community Populations

The spread of infectious diseases is a significant and ongoing problem in human populations. In hospitals, the cost of patients acquiring infections causes many downstream effects, including longer lengths of stay for patients, higher costs, and unexpected fatalities. Outbreaks in community populations cause more significant problems because they stress the medical facilities that need to accommodate large numbers of infected patients, and they can lead to the closing of schools and businesses. In addition, epidemics often require logistical considerations such as where to locate clinics or how to optimize the distribution of vaccinations and food supplies. Traditionally, mathematical modeling is used to explore transmission dynamics and evaluate potential infection control measures. This methodology, although simple to implement and computationally efficient, has several shortcomings that prevent it from adequately representing some of the most critical aspects of disease transmission. Specifically, mathematical modeling can only represent groups of individuals in a homogenous manner and cannot model how transmission is affected by the behavior of individuals and the structure of their interactions. Agent-based modeling and social network analysis are two increasingly popular methods that are well-suited to modeling the spread of infectious diseases. Together, they can be used to model individuals with unique characteristics, behavior, and levels of interaction with other individuals. These advantages enable a more realistic representation of transmission dynamics and a much greater ability to provide insight to questions of interest for infection control practitioners. This dissertation presents several agent-based models and network models of the transmission of infectious diseases at scales ranging from hospitals to networks of medical facilities and community populations. By employing these methods, we can explore how the behavior of individual healthcare workers and the structure of a network of patients or healthcare facilities can affect the rate and extent of hospital-acquired infections. After the transmission dynamics are properly characterized, we can then attempt to differentiate between different types of transmission and assess the effectiveness of infection control measures

Networks and the epidemiology of infectious disease

The science of networks has revolutionised research into the dynamics of interacting elements. It could be argued that epidemiology in particular has embraced the potential of network theory more than any other discipline. Here we review the growing body of research concerning the spread of infectious diseases on networks, focusing on the interplay between network theory and epidemiology. The review is split into four main sections, which examine: the types of network relevant to epidemiology; the multitude of ways these networks can be characterised; the statistical methods that can be applied to infer the epidemiological parameters on a realised network; and finally simulation and analytical methods to determine epidemic dynamics on a given network. Given the breadth of areas covered and the ever-expanding number of publications, a comprehensive review of all work is impossible. Instead, we provide a personalised overview into the areas of network epidemiology that have seen the greatest progress in recent years or have the greatest potential to provide novel insights. As such, considerable importance is placed on analytical approaches and statistical methods which are both rapidly expanding fields. Throughout this review we restrict our attention to epidemiological issues

Controlling nosocomial infection based on structure of hospital social networks

Nosocomial infection raises a serious public health problem, as implied by the existence of pathogens characteristic to healthcare and hospital-mediated outbreaks of influenza and SARS. We simulate stochastic SIR dynamics on social networks, which are based on observations in a hospital in Tokyo, to explore effective containment strategies against nosocomial infection. The observed networks have hierarchical and modular structure. We show that healthcare workers, particularly medical doctors, are main vectors of diseases on these networks. Intervention methods that restrict interaction between medical doctors and their visits to different wards shrink the final epidemic size more than intervention methods that directly protect patients, such as isolating patients in single rooms. By the same token, vaccinating doctors with priority rather than patients or nurses is more effective. Finally, vaccinating individuals with large betweenness centrality is superior to vaccinating ones with large connectedness to others or randomly chosen individuals, as suggested by previous model studies. [The abstract of the manuscript has more information.]Comment: 12 figures, 2 table

Disease-induced resource constraints can trigger explosive epidemics

Advances in mathematical epidemiology have led to a better understanding of the risks posed by epidemic spreading and informed strategies to contain disease spread. However, a challenge that has been overlooked is that, as a disease becomes more prevalent, it can limit the availability of the capital needed to effectively treat those who have fallen ill. Here we use a simple mathematical model to gain insight into the dynamics of an epidemic when the recovery of sick individuals depends on the availability of healing resources that are generated by the healthy population. We find that epidemics spiral out of control into "explosive" spread if the cost of recovery is above a critical cost. This can occur even when the disease would die out without the resource constraint. The onset of explosive epidemics is very sudden, exhibiting a discontinuous transition under very general assumptions. We find analytical expressions for the critical cost and the size of the explosive jump in infection levels in terms of the parameters that characterize the spreading process. Our model and results apply beyond epidemics to contagion dynamics that self-induce constraints on recovery, thereby amplifying the spreading process.Comment: 24 pages, 6 figure