Related papers: Antigenic waves of virus-immune co-evolution
Several pathogens use evolvability as a survival strategy against acquired immunity of the host. Despite their high variability in time, some of them exhibit quite low variability within the population at any given time, a somehow…
We present a thorough inspection of the dynamical behavior of epidemic phenomena in populations with complex and heterogeneous connectivity patterns. We show that the growth of the epidemic prevalence is virtually instantaneous in all…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
In the studies of dynamics of pathogens and their interactions with a host immune system, an important role is played by the structure of antigenic variants associated with a pathogen. Using the example of a model of antigenic variation in…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
We introduce a minimal multiscale framework that links within-host virus dynamics to population-level SIRS epidemiology through explicit, bidirectional coupling. At the microscopic layer, a two variant quasispecies (master and mutant…
Viral kinetics have been extensively studied in the past through the use of spatially homogeneous ordinary differential equations describing the time evolution of the diseased state. However, spatial characteristics such as localized…
In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so…
We propose a physical theory underlying the temporal evolution of competing virus variants that relies on the existence of (quasi) fixed points capturing the large time scale invariance of the dynamics. To motivate our result we first…
Understanding how genetic changes allow emerging virus strains to escape the protection afforded by vaccination is vital for the maintenance of effective vaccines. In the current work, we use structural and phylogenetic differences between…
We introduce and discuss a minimal individual-based model for influenza dynamics. The model takes into account the effects of specific immunization against viral strains, but also infectivity randomness and the presence of a short-lived…
Cellular populations such as avascular tumors and microbial biofilms may "invade" or grow into surrounding populations. The invading population is often comprised of a heterogeneous mixture of cells with varying growth rates. The population…
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…
Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…
Most antigenically novel and evolutionarily successful strains of seasonal influenza A (H3N2) originate in East, South, and Southeast Asia. To understand this pattern, we simulated the ecological and evolutionary dynamics of influenza in a…
In this work we have investigated the evolutionary dynamics of a generalist pathogen, e.g. a virus population, that evolves towards specialisation in an environment with multiple host types. We have particularly explored under which…
The immune system recognizes a myriad of invading pathogens and their toxic products. It does so with a finite repertoire of antibodies and T cell receptors. We here describe theories that quantify the immune system dynamics. We describe…
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the…