Related papers: Multi-lineage evolution in viral populations drive…
Mathematical models of infectious disease transmission typically neglect within-host dynamics. Yet within-host dynamics - including pathogen replication, host immune responses, and interactions with microbiota - are crucial not only for…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
Viral infections trigger complex immune responses with heterogeneous outcomes shaped by nonlinear feedbacks. An ordinary differential equation model is developed to investigate immune response dynamics during viral infection, incorporating…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
The temporal dynamics of social interactions were shown to influence the spread of disease. Here, we model the conditions of progression and competition for several viral strains, exploring various levels of cross-immunity over temporal…
Interactions among multiple infectious agents are increasingly recognized as a fundamental issue in the understanding of key questions in public health, regarding pathogen emergence, maintenance, and evolution. The full description of…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
We study the population dynamics of lytic viruses which replicate slowly in dividing host cells within an organism or cell culture, and find a range of viral replication rates that allows viruses to persist, avoiding extinction of host…
Coevolutionary arms races form between interacting populations that constitute each other's environment and respond to mutual changes. This inherently far-from-equilibrium process finds striking manifestations in the adaptive immune system,…
We consider a stochastic model for a pathogen population in the presence of an immune response, in which pathogen types are partially ordered by ancestry and the immune system must eliminate ancestor types before it can eliminate their…
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…
Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly…
Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and re-infect previously infected individuals. Antigenic properties are largely determined by the surface glycoprotein hemagglutinin (HA) and…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
The evolution of two species with different fitness is investigated on degree-heterogeneous graphs. The population evolves either by one individual dying and being replaced by the offspring of a random neighbor (voter model (VM) dynamics)…
Consider a birth and death chain to model the number of types of a given virus. Each type gives birth to a new type at rate $\lambda$ and dies at rate 1. Each type is also assigned a fitness. When a death occurs either the least fit type…
We consider the dynamics of a virus spreading through a population that produces a mutant strain with the ability to infect individuals that were infected with the established strain. Temporary cross-immunity is included using a time delay,…
Cooperation and competition between pathogens can alter the amount of individuals affected by a co-infection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a co-evolutionary model where the…
This chapter gives a synopsis of recent approaches to model and analyse the evolution of microbial populations under selection. The first part reviews two population genetic models of Lenski's long-term evolution experiment with Escherichia…
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…