Related papers: Population genomics of intrapatient HIV-1 evolutio…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Metapopulation models are commonly used in ecology, evolution, and epidemiology. These models usually entail homogeneity assumptions within patches and study networks of migration between patches to generate insights into conservation of…
The contact structure of a population plays an important role in transmission of infection. Many ``structured models'' capture aspects of the contact structure through an underlying network or a mixing matrix. An important observation in…
During infectious disease epidemics, pathogen transmission occurs in host populations made up of interacting subpopulations. Using stochastic simulation and analytical approximations, we examine how outbreak sizes in networked populations…
Multipartite viruses replicate through a puzzling evolutionary strategy. Their genome is segmented into two or more parts, and encapsidated in separate particles that appear to propagate independently. Completing the replication cycle,…
Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy is unlikely to evolve. In this letter, we study an…
Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population…
The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the…
In the first part of this paper, we review old and new results about the influence of host population heterogeneity on (various characteristics of) epidemic outbreaks. In the second part we highlight a modelling issue that so far has…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local…
We have analyzed the relations between the mutational pressure, recombination and selection pressure in the bit-string model with sexual reproduction. For specific sets of these parameters we have found three phase transitions with one…
We updated the agent based Monte Carlo code HERITAGE that simulates human evolution within restrictive environments such as interstellar, sub-light speed spacecraft in order to include the effects of population genetics. We incorporated a…
Despite being similar in structure, functioning, and size viral pathogens enjoy very different mostly well-defined ways of life. They occupy their hosts for a few days (influenza), for a few weeks (measles), or even lifelong (HCV), which…
The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the…
Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune…
We study minimal mean-field models of viral drug resistance development in which the efficacy of a therapy is described by a one-dimensional stochastic resetting process with mixed reflecting-absorbing boundary conditions. We derive…
We study the evolutionary dynamics of a maladapted population of self-replicating sequences on strongly correlated fitness landscapes. Each sequence is assumed to be composed of blocks of equal length and its fitness is given by a linear…
Human behavior plays a critical role in shaping epidemic trajectories. During health crises, people respond in diverse ways in terms of self-protection and adherence to recommended measures, largely reflecting differences in how individuals…
The spread of certain diseases can be promoted, in some cases substantially, by prior infection with another disease. One example is that of HIV, whose immunosuppressant effects significantly increase the chances of infection with other…