Related papers: Recombination rate and selection strength in HIV i…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution. We explored experimentally the effect of mutation supply and the strength of selective…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
Men who have sex with men (MSM) remain disproportionately affected by HIV, yet optimizing Pre-exposure Prophylaxis (PrEP) distribution remains a public health challenge. Current guidelines and most modelling studies do not incorporate…
Vector-borne diseases often infect multiple host species, increasing the likelihood of disease persistence due to the presence of multiple reservoirs. Vector biting patterns and feeding preferences can shift in response to selective…
Due to the widespread availability of effective antiretroviral therapy (ART) regimens, average lifespans of persons with HIV (PWH) in the United States have increased significantly in recent decades. In turn, the demographic profile of PWH…
Herd immunity is a critical concept in epidemiology, describing a threshold at which a sufficient proportion of a population is immune, either through infection or vaccination, thereby preventing sustained transmission of a pathogen. In the…
A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses…
Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the…
The precise mechanism that causes HIV infection to progress to AIDS is still unknown. This paper presents a mathematical model which is able to predict the entire trajectory of the HIV/AIDS dynamics, then a possible explanation for this…
We study the role of recombination, as practiced by genetically-competent bacteria, in speeding up Darwinian evolution. This is done by adding a new process to a previously-studied Markov model of evolution on a smooth fitness landscape;…
Like many chronic diseases, human immunodeficiency virus (HIV) is managed over time at regular clinic visits. At each visit, patient features are assessed, treatments are prescribed, and a subsequent visit is scheduled. There is a need for…
We study Eigen's model of quasi-species, characterized by sequences that replicate with a specified fitness and mutate independently at single sites. The evolution of the population vector in time is then closely related to that of quantum…
We study within-host HIV dynamics using a three--component nonlinear ordinary differential equation model for healthy CD4$^{+}$ T cells, infected CD4$^{+}$ T cells, and free virus. In addition to the baseline model without treatment, we…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants.…
We study the stationary state of a population evolving under the action of random genetic drift, selection and recombination in which both deleterious and reverse beneficial mutations can occur. We find that the equilibrium fraction of…
Due to the persistence of latently infected CD4$^+$ T cells, achieving a functional cure for HIV-1 remains a significant challenge since the viruses are able to evade immune clearance, which in turn enables post-treatment viral rebound.…
In this article, we propose a network spread model for HIV epidemics, wherein each individual is represented by a node of the transmission network and the edges are the connections between individuals along which the infection may spread.…
Why sex evolved and it prevails in nature remains one of the great puzzles of evolution. Most biologists would explain that it promotes genetic variability, however this explanation suffers from several difficulties. What advantages might…