Related papers: On a Neutral Host-Virus Model with Recombination
This paper studies a discrete-time time-varying multi-layer networked SIWS (susceptible-infected-water-susceptible) model with multiple resources under both single-virus and competing multi-virus settings. Besides the human-to-human…
The canonical view of the interactions between viruses and their microbial hosts presumes that changes in host and virus fate require the initiation of infection of a host by a virus. That is, first virus particles diffuse randomly outside…
Epidemiological models for the spread of pathogens in a population are usually only able to describe a single pathogen. This makes their application unrealistic in cases where multiple pathogens with similar symptoms are spreading…
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current global COVID-19 pandemic, in which millions of lives have been lost. Understanding the zoonotic evolution of the coronavirus may provide…
Stochastic processes can model many emerging phenomena on networks, like the spread of computer viruses, rumors, or infectious diseases. Understanding the dynamics of such stochastic spreading processes is therefore of fundamental interest.…
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…
We study an abstract model for the co-evolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant strains. Delocalization or error thresholds exhibit…
Early estimates of the transmission properties of a newly emerged pathogen are critical to an effective public health response, and are often based on limited outbreak data. Here, we use simulations to investigate a potential source of bias…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
The mapping between genotype and phenotype is encoded in the complex web of epistatic interaction between genetic loci. In this rugged fitness landscape, recombination processes, which tend to increase variation in the population, compete…
Reputed intractable, the question of the origin of viruses has long been neglected. In the modern literature 'Virus evolution' has come to refer to study more akin to population genetics, such as the world-wide scrutiny on new polymorphisms…
RNA viruses exist as genetically diverse populations displaying different phenotypes, including diverse degrees of virulence. The evolution of virulence in viral populations is, however, poorly understood. Based on the experimental…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
We study the early stages of viral infection, and the distribution of times to obtain a persistent infection. The virus population proliferates by entering and reproducing inside a target cell until a sufficient number of new virus…
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…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
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,…
We study how the spread of computer viruses, worms, and other self-replicating malware is affected by the logical topology of the network over which they propagate. We consider a model in which each host can be in one of 3 possible states -…