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Rapidly mutating pathogens may be able to persist in the population and reach an endemic equilibrium by escaping hosts' acquired immunity. For such diseases, multiple biological, environmental and population-level mechanisms determine the…

Changing environmental conditions can significantly affect the dynamics of disease spread. These changes may arise naturally or result from human interventions; in the latter case, lockdown measures that lead to abrupt but temporary…

We present a modelling framework for the spreading of epidemics on temporal networks from which both the individual-based and pair-based models can be recovered. The proposed temporal pair-based model that is systematically derived from…

We study epidemic arrival times in meta-population disease models through the lens of front propagation into unstable states. We demonstrate that several features of invasion fronts in the PDE context are also relevant to the network case.…

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…

The paper presents an algorithm for syndromic surveillance of an epidemic outbreak formulated in the context of stochastic nonlinear filtering. The dynamics of the epidemic is modeled using a generalized compartmental epidemiological model…

We consider the class of SIS epidemic models in which a large population of individuals chooses whether to adopt protection or to remain unprotected as the epidemic evolves. For a susceptible individual, adopting protection reduces the…

Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…

The emergence and spread of deadly pandemics has repeatedly occurred throughout history, causing widespread infections and loss of life. The rapid spread of pandemics have made governments across the world adopt a range of actions,…

Testing is a crucial control mechanism in the beginning phase of an epidemic when the vaccines are not yet available. It enables the public health authority to detect and isolate the infected cases from the population, thereby limiting the…

Consider stochastic models for the spread of an infection in a structured community, where this structured community is itself described by a random network model. Some common network models and transmission models are defined and large…

Data describing human interactions often suffer from incomplete sampling of the underlying population. As a consequence, the study of contagion processes using data-driven models can lead to a severe underestimation of the epidemic risk.…

We consider a spatial model related to bond percolation for the spread of a disease that includes variation in the susceptibility to infection. We work on a lattice with random bond strengths and show that with strong disorder, i.e. a wide…

Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent parameters, such as effective population size, offer limited…

Epidemics are emergent phenomena depending on the epidemiological characteristics of pathogens and the interaction and movement of people. Public transit systems have provided much important information about the movement of people, but…

The evolution of network structure and the spreading of epidemic are common coexistent dynamical processes. In most cases, network structure is treated either static or time-varying, supposing the whole network is observed in a same time…

The viral load is known to be a chief predictor of the risk of transmission of infectious diseases. In this work, we investigate the role of the individuals' viral load in the disease transmission by proposing a new…

These notes describe stochastic epidemics in a homogenous community. Our main concern is stochastic compartmental models (i.e. models where each individual belongs to a compartment, which stands for its status regarding the epidemic under…

Standard epidemic models exhibit one continuous, second order phase transition to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally alter epidemic dynamics. Here we reveal how such interventions modify the…

In this paper we study a discrete-time SIS (susceptible-infected-susceptible) model, where the infection and healing parameters and the underlying network may change over time. We provide conditions for the model to be well-defined and…