Related papers: Population genomics of intrapatient HIV-1 evolutio…
Population dynamics is constrained by the environment, which needs to obey certain conditions to support population growth. We consider a standard model for the evolution of a single species population density, that includes reproduction,…
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance.…
With the launch of second line anti-retroviral therapy for HIV infected individuals, there has been an increased expectation on surviving period of people with HIV. We consider previously well-known models in HIV epidemiology where the…
The twin processes of viral evolutionary escape and reversion in response to host immune pressure, in particular the cytotoxic T-lymphocyte (CTL) response, shape Human Immunodeficiency Virus-1 sequence evolution in infected host…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
In this paper we consider the evolution of the HIV infection under a highly effective treatment based on a combination of RTI and/or PI drugs. This is usually modelled with a set of ODEs where the drug efficacy is a constant. In this paper…
The process of infection of a host is complex, influenced by factors such as microbial variation within and between hosts as well as differences in dose across hosts. This study uses dose-response and within-host microbial infection models…
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…
Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It…
Motivation: HIV is difficult to treat because its virus mutates at a high rate and mutated viruses easily develop resistance to existing drugs. If the relationships between mutations and drug resistances can be determined from historical…
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
We model and calculate the fraction of infected population necessary to reach herd immunity, taking into account the heterogeneity in infectiousness and susceptibility, as well as the correlation between those two parameters. We show that…
Inspired by DNA data of the human cytomegalovirus we propose a model of a two-type parasite population distributed over its hosts. The parasite is capable to persist in its host till the host dies, and to reinfect other hosts. To maintain…
One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status,…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic…
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.…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…