Related papers: Population genomics of intrapatient HIV-1 evolutio…
We consider the standard three-component differential equation model for the growth of an HIV virion population in an infected host in the absence of drug therapy. The dynamical properties of the model are determined by the set of values of…
HIV-1 infection currently cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). To characterize establishment, turnover, and evolution of viral…
Understanding historical trends in the epidemic of HIV is important for assessing current and projecting future trends in prevalence, incidence and mortality and for evaluating the impact and cost-effectiveness of control measures. In…
During an infection, HIV experiences strong selection by immune system T cells. Recent experimental work has shown that MHC escape mutations form an important pathway for HIV to avoid such selection. In this paper, we study a model of MHC…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
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…
We propose a population model for HIV-TB co-infection dynamics by considering treatments for HIV infection, active tuberculosis and co-infection. The HIV only and TB only models are analyzed separately, as well as full model. The basic…
Human immunodeficiency virus (HIV-1 or simply HIV) induces a persistent infection, which in the absence of treatment leads to AIDS and death in almost all infected individuals. HIV infection elicits a vigorous immune response starting about…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
A central challenge in Human Immunodeficiency Virus (HIV) public health policy lies in determining whether to universally expand treatment access, despite the risk of sub-optimal adherence and consequent drug resistance, or to adopt a more…
Key populations at high risk of HIV infection are critical for understanding and monitoring HIV epidemics, but global estimation is hampered by sparse, uneven data. We analyze data from 199 countries for female sex workers (FSW), men who…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
Extreme enrichment of the human immunodeficiency virus (HIV-1) RNA genome for the purine A parallels the mild purine-loading of the RNAs of most organisms. This should militate against loop-loop "kissing" interactions between the structured…
Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…
RNA viruses provide prominent examples of measurably evolving populations. In HIV infection, the development of drug resistance is of particular interest, because precise predictions of the outcome of this evolutionary process are a…
We consider a simple deterministic model which describes an asymmetric competition between an immune system with a specific and powerful response, and a virus with a broad toxicity and fast mutations. Interest in this model relies on the…
One way in which the human immunodeficiency virus (HIV-1) replicates within a host is by infecting activated CD4+ T-cells, which then produce additional copies of the virus. Even with the introduction of antiretroviral drug therapy, which…