Related papers: On a Neutral Host-Virus Model with Recombination
We present a methodology providing a one-directional link from within-host individual heterogeneity to population-level disease transmission dynamics. The methodology works in several steps. A within-host model is investigated numerically…
The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses…
The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have…
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments.…
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity of recombining segments, several studies examined whether this could lead to the…
Mathematical modeling and analysis can provide insight on the dynamics of ecosystems which maintain biodiversity in the face of competitive and prey-predator interactions. Of primary interests are the underlying structure and features which…
A precise estimate of allele and haplotype polymorphism is of great interest in theoretical population genetics, but also has practical applications, such as bone marrow registries management. Allele polymorphism is driven mainly by point…
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…
We consider a spatially-heterogeneous generalization of a well-established model for the dynamics of the Human Immunodeficiency Virus-type 1 (HIV) within a susceptible host. The model consists of a nonlinear system of three coupled…
Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict…
Viruses are submicroscopic agents that can infect all kinds of lifeforms and use their hosts' living cells to replicate themselves. Despite having some of the simplest genetic structures among all living beings, viruses are highly…
We develop a new structured compartmental model for the coevolutionary dynamics between susceptible and infectious individuals in heterogeneous SI epidemiological systems. In this model, the susceptible compartment is structured by a…
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…
This paper analyzes a simplified model of viral infection and evolution using the 'grand canonical ensemble' and formalisms from statistical mechanics and thermodynamics to enumerate all possible viruses and to derive thermodynamic…
Traditional disease transmission models assume that the infectious period is exponentially distributed with a recovery rate fixed in time and across individuals. This assumption provides analytical and computational advantages, however it…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
The adaptive immune system engages in an arms race with evolving viruses, trying to generate new responses to viral strains that continually move away from the set of variants that have already elicited a functional immune response. In…
This paper studies a networked bivirus model, in which two competing viruses spread across a network of interconnected populations; each node represents a population with a large number of individuals. The viruses may spread through…
We investigate the long-time dynamics of a SIR epidemic model in the case of a population of pathogens infecting a homogeneous host population. The pathogen population is structured by a genotypic variable. When the initial mass of the…
A current challenge for disease modeling and public health is understanding pathogen dynamics across scales since their ecology and evolution ultimately operate on several coupled scales. This is particularly true for vector-borne diseases,…