A two-valued fitness landscape is introduced for the classical Eigen's quasispecies model. This fitness landscape can be considered as a direct generalization of the so-called single- or sharply peaked landscape. A general, non-permutation invariant quasispecies model is studied, and therefore the dimension of the problem is [Formula: see text], where N is the sequence length. It is shown that if the fitness function is equal to [Formula: see text] on a G-orbit A and is equal to w elsewhere, then the mean population fitness can be found as the largest root of an algebraic equation of degree at most [Formula: see text]. Here G is an arbitrary isometry group acting on the metric space of sequences of zeroes and ones of the length N with the Hamming distance. An explicit form of this exact algebraic equation is given in terms of the spherical growth function of the G-orbit A. Motivated by the analysis of the two-valued fitness landscapes, an abstract generalization of Eigen's model is introduced such that the sequences are identified with the points of a finite metric space X together with a group of isometries acting transitively on X. In particular, a simplicial analog of the original quasispecies model is discussed, which can be considered as a mathematical model of the switching of the antigenic variants for some bacteria.

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11538-016-0172-2DOI Listing

Publication Analysis

Top Keywords

quasispecies model
16
two-valued fitness
12
[formula text]
12
eigen's quasispecies
8
fitness landscapes
8
finite metric
8
fitness landscape
8
algebraic equation
8
metric space
8
model
6

Similar Publications

The impact of immune cell interactions on virus quasi-species formation.

Math Biosci Eng

November 2024

Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, Villeurbanne 69622, France.

The process of viral infection spreading in tissues was influenced by various factors, including virus replication within host cells, transportation, and the immune response. Reaction-diffusion systems provided a suitable framework for examining this process. In this work, we studied a nonlocal reaction-diffusion system of equations that modeled the distribution of viruses based on their genotypes and their interaction with the immune response.

View Article and Find Full Text PDF

Models for viral populations with high replication error rates (such as RNA viruses) rely on the quasispecies concept, in which mutational pressure beyond the so-called "error threshold" leads to a loss of essential genetic information and population collapse, an effect known as the "error catastrophe." We explain how crossing this threshold, as a result of increasing mutation rates, can be understood as a second-order phase transition, even in the presence of lethal mutations. In particular, we show that, in fitness landscapes with a single peak, this collapse is equivalent to a ferroparamagnetic transition, where the back-mutation rate plays the role of the external magnetic field.

View Article and Find Full Text PDF

Viroids occur in plants as swarms of sequence variants clustered around a dominant variant, leading to adoption of the term 'quasispecies' to describe the viroid population in an individual host. The composition of the quasispecies can potentially change according to the age of the infection, the position of the leaf or branch in the canopy, and the host species. The primary aim of this study was to investigate the quasispecies concept for citrus viroid VII (CVd-VII), a recently discovered member of the family Pospiviroidae.

View Article and Find Full Text PDF

Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous since it is obtained from noisy read coverages. Typical generalizations of the MFD problem to handle errors are based on least-squares formulations or modelling the erroneous flow values as ranges.

View Article and Find Full Text PDF

Unlabelled: Human parainfluenza virus (HPIV) causes respiratory infections, which are exacerbated in children and older people. Correct evaluation of viral characteristics is essential for the study of countermeasures. However, adaptation of viruses to cultured cells during isolation or propagation might select laboratory passage-associated mutations that modify the characteristics of the virus.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!