Related papers: Evolutionary stability of antigenically escaping v…
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…
When an infectious disease propagates throughout society, the incidence function may rise at first due to an increase in pathogenicity and then decrease due to inhibitory effects until it reaches saturation. Effective vaccination and…
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…
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish…
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 types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to…
We propose a system theoretic approach to select and stabilize the endemic equilibrium of an SIRS epidemic model in which the decisions of a population of strategically interacting agents determine the transmission rate. Specifically, the…
In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and…
The increase in the connectivity between hosts in recent times has facilitated the emergence of more aggressive mutant viral strains, making their containment and eradication significantly more challenging compared to the original variants.…
RNA virus (e.g., SARS-CoV-2) evolves in a complex manner. Studying RNA virus evolution is vital for understanding molecular evolution and medicine development. Scientists lack, however, general frameworks to characterize the dynamics of RNA…
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…
The extinction and persistence of infective individuals are closely related to the random change of the environment. In this paper, via the random/stochastic SIRS models, we analyze qualitatively and quantitatively the impact caused by the…
Intrapatient HIV-1 evolution is dominated by selection on the protein level in the arms race with the adaptive immune system. When cytotoxic CD8+ T-cells or neutralizing antibodies target a new epitope, the virus often escapes via…
We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…
We formulate a compartmental model for the propagation of a respiratory disease in a patchy environment. The patches are connected through the mobility of individuals, and we assume that disease transmission and recovery are possible during…
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…
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely determined by the network topology and…
We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a real-valued…
We consider the class of SIS epidemic models in which a large population of individuals chooses whether to adopt protection or to remain unprotected as the epidemic evolves. For a susceptible individual, adopting protection reduces the…
Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier…