Related papers: From viral evolution to spatial contagion: a biolo…

Metapopulation models are commonly used in ecology, evolution, and epidemiology. These models usually entail homogeneity assumptions within patches and study networks of migration between patches to generate insights into conservation of…

We use a multitype continuous time Markov branching process model to describe the dynamics of the spread of parasites of two types that can mutate into each other in a common host population. Instead of using a single virulence…

We study how the interplay between the memory immune response and pathogen mutation affects epidemic dynamics in two related models. The first explicitly models pathogen mutation and individual memory immune responses, with contacted…

The contagion dynamics can emerge in social networks when repeated activation is allowed. An interesting example of this phenomenon is retweet cascades where users allow to re-share content posted by other people with public accounts. To…

The movie Ben-Hur highlights the dynamics of contagion associated with leprosy, a pattern of forced aggregation driven by the emergence of symptoms and the fear of contagion. The 2014 Ebola outbreaks reaffirmed the dynamics of…

Viruses constantly undergo mutations with genomic changes. The propagation of variants of viruses is an interesting problem. We perform numerical simulations of the microscopic epidemic model based on network theory for the spread of…

Human mobility plays a crucial role in the spread of human diseases, but is rarely quantified in plant disease epidemics. To address this gap, we integrate a unique, high-resolution network of human movements in New Zealand with a…

A model of an Ebola epidemic is developed with infected individuals structured according to disease age. The transmission of the infection is tracked by disease age through an initial incubation (exposed) phase, followed by an infectious…

Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…

The dynamics of contact networks and epidemics of infectious diseases often occur on comparable time scales. Ignoring one of these time scales may provide an incomplete understanding of the population dynamics of the infection process. We…

We consider a spatially-heterogeneous generalization of a well-established model for the dynamics of the Human Immunodeficiency Virus-type 1 (HIV) within a susceptible host. The model consists of a nonlinear system of three coupled…

The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…

When an infection spreads in a community, an individual's probability of becoming infected depends on both her susceptibility and exposure to the contagion through contact with others. While one often has knowledge regarding an individual's…

Divergence time estimation is crucial to provide temporal signals for dating biologically important events, from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian…

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…

We use a multivariate formulation of sequential Monte Carlo filter that utilizes mechanistic models for Ebola virus propagation and available incidence data to simultaneously estimate the disease progression states and the model parameters.…

Many pathogens spread primarily via direct contact between infected and susceptible hosts. Thus, the patterns of contacts or contact network of a population fundamentally shapes the course of epidemics. While there is a robust and growing…

This work is motivated by an original dataset of reported mumps cases across nine regions of England, and focuses on the modeling of temporal dynamics and time-varying dependency patterns between the observed time series. The goal is to…

Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…

Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…