Related papers: Multi-lineage evolution in viral populations drive…
Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict…
The dynamics of epidemic spreading is often reduced to the single control parameter $R_0$, whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, $R_0$ may change over…
Many infectious diseases are comprised of multiple strains with examples including Influenza, tuberculosis, and Dengue virus. The time evolution of such systems is linked to a complex landscape shaped by interactions between competing…
Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely neglected by reconstructions of pathogen evolutionary…
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…
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…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Divergence in antigen response of the immune network is discussed, based on shape-space modelling. The present model extends the shape-space model by introducing the evolution of specificity of idiotypes. When the amount of external antigen…
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…
Seasonal influenza kills hundreds of thousands every year, with multiple constantly-changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system,…
We study macroevolutionary dynamics by extending microevolutionary competition models to long time scales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
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…
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…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
Determining phenotype from genetic data is a fundamental challenge. Influenza A viruses undergo rapid antigenic drift and identification of emerging antigenic variants is critical to the vaccine selection process. Using former seasonal…
We investigate a simple quantitative genetics model subjet to a gradual environmental change from the viewpoint of the phylogenies of the living individuals. We aim to understand better how the past traits of their ancestors are shaped by…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
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…