Related papers: Multiscale feedback drives viral evolution and epi…
We present a novel model that describes the within-host evolutionary dynamics of parasites undergoing antigenic variation. The approach uses a multi-type branching process with two types of entities defined according to their relationship…
We propose a dynamical model for describing the spread of epidemics. This model is an extension of the SIQR (susceptible-infected-quarantined-recovered) and SIRP (susceptible-infected-recovered-pathogen) models used earlier to describe…
We consider a model for an epidemic in a population that occupies geographically distinct locations. The disease is spread within subpopulations by contacts between infective and susceptible individuals, and is spread between subpopulations…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Spatially explicit models have been widely used in today's mathematical ecology and epidemiology to study persistence and extinction of populations as well as their spatial patterns. Here we extend the earlier work--static dispersal between…
In light of the continuing emergence of new SARS-CoV-2 variants and vaccines, we create a simulation framework for exploring possible infection trajectories under various scenarios. The situations of primary interest involve the interaction…
In this work, we derive a system of Boltzmann-type equations to describe the spread of SARS-CoV-2 virus at the microscopic scale, that is by modeling the human-to-human mechanisms of transmission. To this end, we consider two populations,…
We propose a network behavioral-feedback Susceptible-Infected-Recovered (SIR) epidemic model in which the interaction matrix describing the infection rates across subpopulations depends in feedback on the current epidemic state. This model…
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…
How will the novel coronavirus evolve? I study a simple epidemiological model, in which mutations may change the properties of the virus and its associated disease stochastically and antigenic drifts allow new variants to partially evade…
We study the non-equilibrium phase transition in a model for epidemic spreading on scale-free networks. The model consists of two particle species $A$ and $B$, and the coupling between them is taken to be asymmetric; $A$ induces $B$ while…
It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts. Although community ecology approaches have been applied to determine pathogen interactions at the…
Risk-driven behavior provides a feedback mechanism through which individuals both shape and are collectively affected by an epidemic. We introduce a general and flexible compartmental model to study the effect of heterogeneity in the…
In this paper we consider a model for the spread of a stochastic SIR (Susceptible $\to$ Infectious $\to$ Recovered) epidemic on a network of individuals described by a random intersection graph. Individuals belong to a random number of…
Time varying susceptibility of host at individual level due to waning and boosting immunity is known to induce rich long-term behavior of disease transmission dynamics. Meanwhile, the impact of the time varying heterogeneity of host…
We propose a generative model and an inference scheme for epidemic processes on dynamic, adaptive contact networks. Network evolution is formulated as a link-Markovian process, which is then coupled to an individual-level stochastic SIR…
Epidemiological forecasting from surveillance data is a hard problem and hybridizing mechanistic compartmental models with neural models is a natural direction. The mechanistic structure helps keep trajectories epidemiologically plausible,…
The acute phase of the Covid-19 pandemic has made apparent the need for decision support based upon accurate epidemic modeling. This process is substantially hampered by under-reporting of cases and related data incompleteness issues. In…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Several systems can be modeled as sets of interdependent networks where each network contains distinct nodes. Diffusion processes like the spreading of a disease or the propagation of information constitute fundamental phenomena occurring…