Related papers: A Selective Advantage for Conservative Viruses
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by continuous genomic diversification and allows to explain a…
Diseases emerge, persist and vanish in an ongoing battle for available hosts. Hosts, on the other hand, defend themselves by developing immunity that limits the ability of pathogens to reinfect them. We here explore a multi-disease system…
Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…
A central feature of vertebrate immune response is affinity maturation, wherein antibody-producing B cells undergo evolutionary selection in microanatomical structures called germinal centers, which form in secondary lymphoid organs upon…
A simple cellular automata model for a two-group war over the same territory is presented. It is shown that a qualitative advantage is not enough for a minority to win. A spatial organization as well a definite degree of aggressiveness are…
This paper studies a preference evolution model in which a population of agents are matched to play a sequential prisoner's dilemma in an incomplete information environment. An institution can design an incentive-compatible screening…
Survival regression is widely used to model time-to-events data, to explore how covariates may influence the occurrence of events. Modern datasets often encompass a vast number of covariates across many subjects, with only a subset of the…
The immune system is a real-time example of an evolving system that navigates the essentially infinite complexity of protein sequence space. How this system responds to disease and vaccination is discussed. Of particular focus is the case…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Broadly neutralizing antibodies are promising candidates for treatment and prevention of HIV-1 infections. Such antibodies can temporarily suppress viral load in infected individuals; however, the virus often rebounds by escape mutants that…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in 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…
Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
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,…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
A stochastic model for the growth of a virus in a cell population is introduced. The virus has two ways of spreading: either by allowing its host cell to live on and duplicate, or else by multiplying in large numbers within the host cell…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
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,…